Datasets

What are Datasets?

Datasets are defined file collections, whose access is governed by a Data Access Committee (DAC).

Total number of Datasets: 3898
Displaying 1 - 3898

Dataset Accessionsort descending Description Technology Samples File Types
EGAD00000000001 WTCCC1 project samples from 1958 British Birth Cohort Affymetrix 500K 1,504
EGAD00000000002 WTCCC1 project samples from UK National Blood Service Affymetrix 500K 1,500
EGAD00000000003 WTCCC1 project Bipolar Disorder (BD) samples Affymetrix 500K 1,998
EGAD00000000004 WTCCC1 project Coronary Artery Disease (CAD) samples Affymetrix 500K 1,998
EGAD00000000005 WTCCC1 project Inflammatory Bowel Disease (IBD) samples Affymetrix 500K 2,005
EGAD00000000006 WTCCC1 project Hypertension (HT) samples Affymetrix 500K 2,001
EGAD00000000007 WTCCC1 project Rheumatooid arthritis (RA) samples Affymetrix 500K 1,999
EGAD00000000008 WTCCC1 project Type 1 Diabetes (T1D) samples Affymetrix 500K 2,000
EGAD00000000009 WTCCC1 project Type 2 Diabetes (T2D) samples Affymetrix 500K 1,999
EGAD00000000010 WTCCC1 project Ankylosing Spondylitis (AS) samples Illumina 15K 957
EGAD00000000011 WTCCC1 project Autoimmune Thyroid Disease (ATD) samples Illumina 15K 900
EGAD00000000012 WTCCC1 project Multiple Sclerosis (MS) samples Illumina 15K 975
EGAD00000000013 WTCCC1 project Breast cancer (BC) samples Illumina 15K 1,004
EGAD00000000014 WTCCC1 project samples from 1958 British Birth Cohort Illumina 15K 1,504
EGAD00000000015 WTCCC project African control samples Affymetrix 500K 1,496
EGAD00000000016 WTCCC project Tuberculosis (TB) samples Affymetrix 500K 1,498
EGAD00000000017 Cord blood control samples from Gambia 0
EGAD00000000018 Severe malaria cases from Gambia 0
EGAD00000000019 840 families where both parents have been genotyped together with the child with severe malaria 0
EGAD00000000020 685 families where both parents have been genotyped together with the child with severe malaria 0
EGAD00000000021 WTCCC2 project samples from 1958 British Birth Cohort Affymetrix 6.0 3,000
EGAD00000000022 WTCCC2 project samples from 1958 British Birth Cohort Illumina 1.2M 3,000
EGAD00000000023 WTCCC2 project samples from National Blood Donors (NBS) Cohort 1
EGAD00000000024 WTCCC2 project samples from National Blood Donors (NBS) Cohort 1
EGAD00000000025 WTCCC2 project Ulcerative Colitis (UC) samples Affymetrix 6.0 2,869
EGAD00000000026 Randomly-selected, unrelated individuals Illumina 610-Quad 518
EGAD00000000027 eQTL data for European newborns Ilumina HumanHap550-2v3_B-Beadstudio 176
EGAD00000000028 Aggregate results from a GWAS study on 3352 cases abd 3145 controls iSelect Beadchip 6,497
EGAD00000000029 Aggregate results from a case-control study on stroke and ischemic stroke. 19,602
EGAD00000000030 T1DGC project 1958 British Birth Cohort samples Illumina HumanHap 550 2,604
EGAD00000000031 HLA genotyping of 1958 British Birth Cohort samples unknown 1
EGAD00000000032 NcOEDG Helsinki 1 samples Illumina HumanHap 300 19
EGAD00000000033 NcOEDG Helsinki 2 samples Illumina HumanHap 300 180
EGAD00000000034 NcOEDG Helsinki 3 samples Illumina HumanHap 300 20
EGAD00000000035 NcOEDG Helsinki 4 samples Illumina CNV370 693
EGAD00000000036 NcOEDG Stockholm 1 samples Affymetrix 500K 484
EGAD00000000037 NcOEDG Stockholm 2 samples Affymetrix 5.0 514
EGAD00000000038 NcOEDG Stockholm 3 samples Illumina HumanHap 550 761
EGAD00000000039 NcOEDG Malmo - Lund samples Affymetrix 500K 1,374
EGAD00000000040 GenomEUtwin Danish (DK) samples Illumina HumanHap 300 162
EGAD00000000041 GenomEUtwin Swedish (SWE) samples Illumina HumanHap 300 302
EGAD00000000042 GenomEUtwin Finnish (FIN) samples Illumina HumanHap 300 153
EGAD00000000043 GenomeEUtwin control samples Illumina HumanHap300-Duo, Illumina HumanHap 550K 2,099
EGAD00000000044 Northern Finland Birth Cohort 1966 samples Illumina HumanHap370 5,844
EGAD00000000045 Genomic sequencing and transcriptome shotgun sequencing of a metastatic tumour and its recurrence after drug therapy in a single patient Illumina Genome Analyzer II 1
EGAD00000000046 RNA-SEQ data from 3 recurrent and 1 ovarian primary Granulosa Cell Tumour samples Illumina Genome Analyzer II 4
EGAD00000000047 Signal data for from 3 recurrent and 1 ovarian primary Granulosa Cell Tumour samples Affymetrix 6.0 4
EGAD00000000048 Sequencing data from oestrogen-receptor-alpha-positive metastatic lobular breast cancer sample Illumina Genome Analyzer II 1
EGAD00000000049 RNA-SEQ data from oestrogen-receptor-alpha-positive metastatic lobular breast cancer sample Illumina Genome Analyzer II 1
EGAD00000000051 Sequencing data from matching Renal Carcinoma samples Illumina Genome Analyzer II 25
EGAD00000000052 Sequencing data from natching Pancreatic Carcinoma samples Illumina Genome Analyzer II 25
EGAD00000000053 Sequencing data from Breast Cancer samples Illumina Genome Analyzer II 1
EGAD00000000054 NCI-H209 is an immortal cell line derived from a bone marrow metastasis of a patient with small cell lung cancer, taken before chemotherapy. The specimen showed histologically typical small cells with classic neuroendocrine features. NCI-BL209 is an EBV-transformed B-cell line derived from the same patient as the small cell lung cancer cell line, NCI-H209 Life Tech - Solid 1
EGAD00000000055 COLO-829 is a publicly available immortal cancer cell line and COLO-829BL is a lymphoblastoid cell line derived from the same patient Illumina Genome Analyzer II 2
EGAD00000000056 WTCCC project samples from the primary biliary cirrhosis cohort Illumina 610K Quad 1,705
EGAD00000000057 WTCCC project samples from the Parkinson's disase cohort Illumina 610K Quad 1,705
EGAD00000000058 Aggregate results from 22 Carbamazepine-induced hypersensitivity syndrome patients and 2691 UK National Blood Service (NBS) control samples Illumina Infinium 1.2M 2,713
EGAD00000000059 Aggregate results from 43 Carbamazepine-induced hypersensitivity syndrome patients and 1296 1958 British Birth Cohort control samples Affymetrix 500K, Illumina 610K Quad 1,339
EGAD00000000060 Samples from the UK Glomerulonephritis DNA bank Illumina 610K Quad, Illumina Hap300 1,705
EGAD00000000073 Gabriel samples from the 1958 British Birth Cohort unknown 1
EGAD00000000074 Gabriel samples from the Swedish BAMSE Cohort unknown 1
EGAD00000000075 Gabriel samples from the Swedish BAMSE Cohort unknown 1
EGAD00000000076 Gabriel samples from the Australian Bussleton Cohort unknown 1
EGAD00000000077 Gabriel samples from the Australian Bussleton Cohort unknown 1
EGAD00000000082 Gabriel samples from the French EGEA Cohort unknown 1
EGAD00000000083 Gabriel samples from the French EGEA Cohort unknown 1
EGAD00000000084 Gabriel samples from the German Gabriel Advanced Survey unknown 1
EGAD00000000085 Gabriel samples from the German Gabriel Advanced Survey unknown 1
EGAD00000000086 Gabriel samples from the multicenter GAIN cohort unknown 1
EGAD00000000087 Gabriel samples from the multicenter GAIN cohort unknown 1
EGAD00000000088 Gabriel samples from the Karelia Allergy Study unknown 1
EGAD00000000089 Gabriel samples from the Karelia Allergy Study unknown 1
EGAD00000000090 Gabriel samples from the Russian KMSU cohort unknown 1
EGAD00000000091 Gabriel samples from the Russian KMSU cohort unknown 1
EGAD00000000092 Gabriel samples from the German MAGIS cohort unknown 1
EGAD00000000093 Gabriel samples from the German MAGIS cohort unknown 1
EGAD00000000094 Gabriel samples from the UK MRCA cohort unknown 1
EGAD00000000095 Gabriel samples from the Dutch PIAMA cohort unknown 1
EGAD00000000096 Gabriel samples from the Dutch PIAMA cohort unknown 1
EGAD00000000097 Gabriel samples from the Swiss SALPADIA cohort unknown 1
EGAD00000000098 Gabriel samples from the Swiss SALPADIA cohort unknown 1
EGAD00000000101 Gabriel samples from the Russian TOMSK cohort unknown 1
EGAD00000000102 Gabriel samples from the Russian TOMSK cohort unknown 1
EGAD00000000103 Gabriel samples from the Russian UFA cohort unknown 1
EGAD00000000104 Gabriel samples from the Russian UFA cohort unknown 1
EGAD00000000105 Gabriel samples from the multicenter occupational cohort unknown 1
EGAD00000000106 Gabriel samples from the multicenter occupational cohort unknown 1
EGAD00000000107 Gabriel samples from the multicenter occupational cohort unknown 1
EGAD00000000108 Gabriel samples from the UK AUGOSA cohort unknown 1
EGAD00000000109 Gabriel samples from the UK SEVERE cohort unknown 1
EGAD00000000114 Whole transcriptome sequence data from 18 ovarian clear-cell carcinoma samples and one TOV21G ovarian clear-cell carcinoma cell line Illumina Genome Analyzer II 1
EGAD00000000115 Summary data from GWAS analysis on 856 cases and 2836 control Illumina CytoSNP-12 3,719
EGAD00000000119 Genotypes from cell lines derived from breast carcinoma tissue Affymetrix 6.0 51
EGAD00000000120 WTCCC2 project Multiple Sclerosis (MS) samples Human670-QuadCustom v1 11,375
EGAD00000000121 Genotypes at MITF E318K variant Taqman and sequencing 2,488
EGAD00000000122 Genotypes at MITF E318K variant Illumina HumanHap 300 v2 Duo, Illumina HumanCNV370, Illumina Human660W-Quad 1,925
EGAD00001000001 Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma 18 srf
EGAD00001000002 Massive genomic rearrangement acquired in a single catastrophic event during cancer development 11 srf
EGAD00001000003 Gencode Exome Pilot Illumina Genome Analyzer II 7 srf
EGAD00001000004 CLL cancer Sample Sequencing Illumina Genome Analyzer II, Illumina Genome Analyzer 5 srf
EGAD00001000005 Various Cancer Fusion Gene Sequencing Illumina Genome Analyzer II;, Illumina Genome Analyzer II 14 bam,srf
EGAD00001000007 Osteosarcoma Sequencing Illumina Genome Analyzer II;, Illumina Genome Analyzer II 43 bam,srf
EGAD00001000013 CLL Cancer Whole Genome Sequencing Illumina Genome Analyzer II 19 srf
EGAD00001000014 Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 25 renal cancers and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 50 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Illumina Genome Analyzer II;, Illumina Genome Analyzer II 54 bam,srf
EGAD00001000015 Exome sequencing of hyperplastic polyposis patients. Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 84 bam,srf
EGAD00001000016 Familial Melanoma Sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 89 bam,srf
EGAD00001000017 PAS Pedigrees: Identification of novel genetic variants contributing to cardiovascular disease in pedigrees with premature atherosclerosis. Illumina HiSeq 2000, Illumina Genome Analyzer II 18 bam,srf
EGAD00001000018 Identifying causative mutations for Thrombocytopenia with Absent Radii Illumina Genome Analyzer II 5 bam
EGAD00001000019 Lethal malformation syndrome Illumina Genome Analyzer II 6 srf
EGAD00001000021 Paroxysmal neurological disorders Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 97 bam,srf
EGAD00001000022 Exome sequencing in patients with cardiac arrhythmias Illumina Genome Analyzer II 20 srf
EGAD00001000023 Recurrent Somatic Mutations in CLL Illumina Genome Analyzer IIx 11 fastq
EGAD00001000024 Whole Exome Sequencing for Characterization of Disease Causing Mutations in two Pakistani Families Suffering from Autosomal Recessive Ocular Disorders. Illumina Genome Analyzer II 4 srf
EGAD00001000025 Determination of the molecular nature of the Vel blood group by exome sequencing Illumina Genome Analyzer II 4 srf
EGAD00001000026 Investigation of the genetic basis of the rare syndrome Post-Transfusion Purpura (PTP) Illumina Genome Analyzer II 5 bam,srf
EGAD00001000027 ICGC Germany PedBrain Medulloblastoma Pilot_2_LM Illumina HiSeq 2000, Illumina Genome Analyzer IIx 8 bam
EGAD00001000029 Grey Platelet Syndrome (GPS) Illumina Genome Analyzer II 5 srf
EGAD00001000030 Analysis of genomic integrity of disease-corrected human induced pluripotent stem cells by exome sequencing Illumina HiSeq 2000 4 bam
EGAD00001000031 Human Colorectal Cancer Exome Sequencing Illumina Genome Analyzer II 16 srf
EGAD00001000032 Hepatitis C IL28B pooled resequencing study with 100 responders and 100 non-responders Illumina Genome Analyzer IIx 4 Illumina_native
EGAD00001000033 "SNV detection from formalin fixed paraffin embedded (FFPE) samples" Illumina Genome Analyzer II 6 bam
EGAD00001000034 "Usage of small amounts of DNA for Illumina sequencing" Illumina Genome Analyzer II 3 bam
EGAD00001000035 "Single nucleotide variant detection in multiple foci of three prostate cancer tumors" Illumina Genome Analyzer II 9 bam
EGAD00001000036 "Copy number variant detection in multiple foci of three prostate cancer tumors" Illumina Genome Analyzer II 9 bam
EGAD00001000037 An evaluation of different strategies for large-scale pooled sequencing study design. Illumina Genome Analyzer II 7 bam,srf
EGAD00001000038 Hyperfibrinolysis Illumina Genome Analyzer II 5 bam
EGAD00001000039 Platelet collagen defect Illumina HiSeq 2000, Illumina Genome Analyzer II 11 bam
EGAD00001000040 Bleeding Illumina Genome Analyzer II 6 bam
EGAD00001000041 Various Platelet Disorders Illumina Genome Analyzer II 7 bam
EGAD00001000042 Whole-Exome-Seq-Dataset Illumina Genome Analyzer IIx 30 bam
EGAD00001000043 RNA-Seq-Dataset Illumina Genome Analyzer IIx 16 bam
EGAD00001000044 Recurrent Somatic Mutations in CLL Illumina Genome Analyzer IIx 212 fastq
EGAD00001000045 Somatic mutation of SF3B1 in myelodysplasia with ring sideroblasts and other cancers Illumina Genome Analyzer II, Illumina HiSeq 2000; 33 bam,cram,srf
EGAD00001000046 Gastric Cancer Exome Sequencing Illumina HiSeq 2000, Illumina Genome Analyzer IIx 43 fastq
EGAD00001000047 exome sequence data for 49 HIV elite long term non-progressors and rapid progressors. Partial dataset (overlap with EGAD00001000087) of raw BAMs mapped to GRCh37_53. Illumina HiSeq 2000, Illumina HiSeq 2000; 49 bam,cram
EGAD00001000048 monozygotic twin discordant for schizophrenia CompleteGenomics build 1.4.2.8 - CG Build 1.4.2.8 2 CompleteGenomics_native
EGAD00001000049 Pancreatic adenocarcinoma QCMG 20110901 AB SOLiD System 3.0, AB SOLiD 4 System 26 bam,fastq
EGAD00001000050 Tandem duplication of chromosomal segments is common in ovarian and breast cancer genomes Illumina Genome Analyzer II 13 bam
EGAD00001000052 UK10K_NEURO_MUIR REL-2011-01-28 Illumina Genome Analyzer II; 104 vcf,bam,bam
EGAD00001000053 Exome sequencing in patients with Calcific Aortic Valve Stenosis Illumina HiSeq 2000 20 bam
EGAD00001000054 Mutational Screening of Human Acute Myleloid Leukaemia Samples Illumina HiSeq 2000 10 bam
EGAD00001000057 RNA-Seq analysis Illumina Genome Analyzer II 15 Illumina_native_qseq
EGAD00001000058 Exome Sequencing analysis Illumina Genome Analyzer II 21 Illumina_native_qseq
EGAD00001000059 Screening for human epigenetic variation at CpG islands Illumina Genome Analyzer II 116 bam
EGAD00001000060 Acral melanoma study whole genomes Complete Genomics 3 CompleteGenomics_native
EGAD00001000061 Acral melanoma study whole exomes Illumina Genome Analyzer IIx 3 fastq
EGAD00001000062 ADCC Rearrangement Screen Illumina HiSeq 2000, Illumina Genome Analyzer II 14 bam,srf
EGAD00001000063 Triple Negative Breast Cancer sequencing Illumina Genome Analyzer II 6 bam
EGAD00001000064 Cell Line Sub Clone Rearrangement Screen Illumina Genome Analyzer II 6 bam
EGAD00001000065 Mixed Leukemia Rearrangement Screen Illumina Genome Analyzer II 5 bam
EGAD00001000066 Breast Cancer Follow Up Series Illumina Genome Analyzer II 288 bam
EGAD00001000067 Cancer Single Cell Sequencing Illumina HiSeq 2000, Illumina HiSeq 2000; 16 bam,srf
EGAD00001000068 Multifocal Breast Project Illumina Genome Analyzer II, Illumina HiSeq 2000; 22 bam,srf
EGAD00001000069 Lung Rearrangement Study Illumina HiSeq 2000 48 bam
EGAD00001000070 TMD_AMLK Exome Study Illumina HiSeq 2000, Illumina HiSeq 2000; 50 bam,cram
EGAD00001000071 Kaposi sarcoma exome Illumina HiSeq 2000 20 bam
EGAD00001000072 Fanconi Anemia transformation to AML Illumina HiSeq 2000 6 bam
EGAD00001000073 MDSMPN Rearrangement Screen Illumina HiSeq 2000, Illumina HiSeq 2000; 11 bam
EGAD00001000074 Integrative Oncogenomics of Multiple Myeloma Illumina HiSeq 2000, Illumina Genome Analyzer II 174 bam,srf
EGAD00001000075 Gastric and Esophageal tumour rearrangement screen Illumina HiSeq 2000 32 bam
EGAD00001000076 CRLF2 sequencing project Illumina HiSeq 2000 13 bam
EGAD00001000077 CRLF2 sequencing project Exomes Illumina HiSeq 2000 26 bam
EGAD00001000078 ALK inhibitors in the context of ALK-dependent cancer cell lines Illumina HiSeq 2000, Illumina HiSeq 2000; 16 bam,cram
EGAD00001000079 PREDICT Illumina HiSeq 2000, Illumina HiSeq 2000; 186 bam,cram
EGAD00001000080 Genomics of Colorectal Cancer Metastases - Massively Parallel Sequencing of Matched Primary and Metastatic tumours to Identify a Metastatic Signature of Somatic Mutations (MOSAIC) Illumina HiSeq 2000, Illumina HiSeq 2000; 351 bam,cram
EGAD00001000081 Splenic Marginal Zone Lymphoma with villous lymphocytes exome sequencing Illumina HiSeq 2000 1 bam
EGAD00001000082 20 Matched Pair Breast Cancer Genomes Illumina HiSeq 2000;ILLUMINA, Illumina Genome Analyzer II;ILLUMINA 42 bam
EGAD00001000083 Recurrent Somatic Mutations in CLL Illumina Genome Analyzer II;, Illumina Genome Analyzer IIx 61 fastq
EGAD00001000084 Matched Ovarian Cancer Sequencing Illumina Genome Analyzer II 23 bam
EGAD00001000085 Somatic Histone H3 mutations Illumina HiSeq 2000 14
EGAD00001000086 Analysis of genomic integrity of disease-corrected human induced pluripotent stem cells by exome sequencing Illumina HiSeq 2000 16 bam
EGAD00001000087 exome sequence data for 25 HIV elite long term non-progressors and rapid progressors. Partial dataset (overlap with EGAD00001000047) of raw BAMs mapped to GRCh37_53. Illumina HiSeq 2000 25 bam
EGAD00001000088 ER-, HER2-, PR- breast Cancer genome sequencing Illumina Genome Analyzer II 6 bam
EGAD00001000089 Acute Lymphoblastic Leukemia Exome sequencing Illumina Genome Analyzer II 20 bam
EGAD00001000090 Glioma cell lines rearrangement screen Illumina Genome Analyzer II 3 bam
EGAD00001000091 Non Tumour Renal Cell Line Sequencing Illumina Genome Analyzer II 1 bam
EGAD00001000092 Cancer Exome Resequencing Illumina Genome Analyzer II 58 bam
EGAD00001000093 Breast Cancer Exome Resequencing Illumina Genome Analyzer II 21 bam
EGAD00001000094 Cancer Genome Libraries Tests Illumina Genome Analyzer II 16 bam
EGAD00001000095 Acute Myeloid Leukemia Sequencing Illumina Genome Analyzer II 9 bam
EGAD00001000096 Pancreatic adenocarcinoma QCMG 20120201 AB SOLiD 4 System 166 bam
EGAD00001000097 Matched breast cancer fusion gene study Illumina Genome Analyzer II 46 bam,srf
EGAD00001000098 FRCC Exome sequencing Illumina Genome Analyzer II 16 bam
EGAD00001000099 Meningioma Exome Illumina Genome Analyzer II 26 bam
EGAD00001000100 Renal Matched Pair Cell Line Exome Sequencing Illumina Genome Analyzer II 10 bam
EGAD00001000101 ADCC Exome Sequencing Illumina Genome Analyzer II, Illumina HiSeq 2000; 125 bam
EGAD00001000102 Myeloproliferative Disorder Sequencing Illumina Genome Analyzer II 6 bam
EGAD00001000103 Myeloproliferative Disorder Sequencing Illumina Genome Analyzer II 4 bam
EGAD00001000104 Acute Lymphoblastic Leukemia Exome sequencing 2 Illumina Genome Analyzer II 97 bam
EGAD00001000105 MuTHER adipose tissue small RNA expression Illumina Genome Analyzer II 130 bam
EGAD00001000106 Primary Myelofibrosis Myeloproliferative Disease exome sequencing Illumina Genome Analyzer II, Illumina HiSeq 2000; 67 bam
EGAD00001000107 SCAT osteosarcoma sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II 114 bam
EGAD00001000108 Paroxysmal neurological disorders Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 327 bam,srf
EGAD00001000109 Unraveling the genetic basis of a collagen migration defect in patients with a combined platelet dysfunction and reduced bone density Illumina HiSeq 2000 29 bam
EGAD00001000110 Breast Cancer Exome Sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II 179 bam
EGAD00001000111 CML Discovery Project Illumina Genome Analyzer II 6 bam
EGAD00001000112 Identifying Novel Fusion Genes in Myeloma Illumina Genome Analyzer II 6 bam
EGAD00001000113 Mutational landscapes of primary triple negative breast cancers - Exomes Illumina Genome Analyzer IIx, Illumina Genome Analyzer IIx; 108 bam
EGAD00001000115 Mutational landscapes of primary triple negative breast cancers - WGS ABI_SOLID 32 bam
EGAD00001000116 Acute Lymphoblastic Leukemia Sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 61 bam,srf
EGAD00001000117 Myelodysplastic Syndrome Exome Sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 152 bam,srf
EGAD00001000118 Osteosarcoma Exome Sequencing Illumina Genome Analyzer II, Illumina HiSeq 2000; 102 bam
EGAD00001000119 Chordoma Exome Sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 50 bam
EGAD00001000121 Breast Cancer Whole Genome Sequencing Illumina HiSeq 2000 6 bam
EGAD00001000122 DATA_SET_ICGC_PedBrainTumor_Medulloblastoma Illumina HiSeq 2000, Illumina Genome Analyzer IIx 206 bam
EGAD00001000123 Polycythemia Vera Myeloproliferative Disease exome sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 119 bam,srf
EGAD00001000124 Sequencing Acute Myeloid Leukaemia Illumina HiSeq 2000, Illumina HiSeq 2000; 4 bam
EGAD00001000125 Chondrosarcoma Exome Illumina HiSeq 2000, Illumina HiSeq 2000; 104 bam
EGAD00001000126 HER2 positive Breast Cancer Illumina HiSeq 2000 101 bam,cram
EGAD00001000127 Burden of Disease in Sarcoma Illumina HiSeq 2000, Illumina HiSeq 2000; 220 bam,cram
EGAD00001000128 Familial Thrombocytosis germline exome sequencing Illumina HiSeq 2000, Illumina HiSeq 2000; 4 bam
EGAD00001000129 Essential Thrombocythemia Myeloproliferative Disease exome sequencing Illumina HiSeq 2000, Illumina HiSeq 2000; 189 bam
EGAD00001000130 Breast Cancer Matched Pair Cell Line Whole Genomes Illumina HiSeq 2000, Illumina HiSeq 2000; 22 bam
EGAD00001000131 Genetic landscape of hepatocellular carcinoma Illumina HiSeq 2000 48 bam
EGAD00001000132 Mutational landscapes of primary triple negative breast cancers - RNA seq Illumina Genome Analyzer IIx, Illumina Genome Analyzer IIx; 80 bam
EGAD00001000133 The landscape of cancer genes and mutational processes in breast cancer Illumina HiSeq 2000, Illumina Genome Analyzer II 199 bam
EGAD00001000134 Sequence reads for pediatric GBM samples for manuscript: Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma Illumina HiSeq 2000, Illumina HiSeq 2500; 54 fastq
EGAD00001000135 Neuroblastoma whole genome sequencing Illumina HiSeq 2000 80 bam
EGAD00001000136 CML blast phase rearrangement screen Illumina HiSeq 2000 6 bam
EGAD00001000138 The expression data for this study can be found here: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1088/ and its SNP6 data can be found here: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1087/ Illumina HiSeq 2000, Illumina Genome Analyzer II 58 bam,srf
EGAD00001000139 Tumor sample of a serious ovarian carcinoma Complete Genomics 1 CompleteGenomics_native
EGAD00001000140 Blood sample of serious ovarian carcinoma patient Complete Genomics 1 CompleteGenomics_native
EGAD00001000141 Triple Negative Breast Cancer Whole Genomes Illumina Genome Analyzer II;, Illumina HiSeq 2000; 243
EGAD00001000142 Renal Follow Up Series Illumina HiSeq 2000, Illumina HiSeq 2000; 637 bam
EGAD00001000143 Xenograft Seqeuncing Illumina HiSeq 2000, Illumina HiSeq 2000; 16 bam
EGAD00001000144 Lung Cancer Whole Genomes Illumina HiSeq 2000, Illumina HiSeq 2000; 18 bam
EGAD00001000145 Matched Pair Cancer Cell line Whole Genomes Illumina HiSeq 2000, Illumina HiSeq 2000; 58 bam
EGAD00001000147 Osteosarcoma Whole Genome Illumina HiSeq 2000, Illumina HiSeq 2000; 108 bam,cram
EGAD00001000149 A Comprehensive Catalogue of Somatic Mutations from a Human Cancer Genome Illumina HiSeq 2000 2 srf
EGAD00001000150 Targeted re-sequencing of 97 genes in T-ALL 454 GS FLX Titanium 33 sff
EGAD00001000151 UK10K OBESITY REL-2011-07-14 Illumina HiSeq 2000; 88 vcf
EGAD00001000152 UK10K_RARE_THYROID REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 27 vcf
EGAD00001000153 UK10K_RARE_SIR REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 38 vcf
EGAD00001000154 Single-cell genome sequencing reveals DNA-mutation per cell cycle Illumina HiSeq 2000, Illumina Genome Analyzer II 12 bam,srf
EGAD00001000158 Subgroup-specific structural variation across 1,000 medulloblastoma genomes 23 bam
EGAD00001000159 DATA FILES FOR SJOS Illumina HiSeq 2000 37 bam
EGAD00001000160 DATA FILES FOR SJACT Illumina HiSeq 2000 16 bam
EGAD00001000161 DATA FILES FOR SJLGG Illumina HiSeq 2000 33 bam
EGAD00001000162 DATA FILES FOR SJEPD Illumina HiSeq 2000 44 bam
EGAD00001000163 DATA FILES FOR SJPHALL Illumina HiSeq 2000 18 bam
EGAD00001000164 DATA FILES FOR SJRHB Illumina HiSeq 2000, Illumina HiSeq 2000; 29 bam
EGAD00001000165 DATA FILES FOR SJINF Illumina HiSeq 2000 46 bam
EGAD00001000167 UK10K_RARE_HYPERCHOL REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 48 vcf
EGAD00001000168 UK10K_RARE_CILIOPATHIES REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 50 vcf
EGAD00001000170 UK10K_NEURO_MUIR REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 167 vcf
EGAD00001000171 UK10K_RARE_FIND REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 44 vcf
EGAD00001000173 UK10K_NEURO_ASD_FI REL-2012-01-13 Illumina HiSeq 2000; 85 vcf
EGAD00001000174 DATA_SET_Coverage_bias_sensitivity_of_variant_calling_for_4_WG_seq_tech Complete Genomics;, unspecified; 4 bam
EGAD00001000175 Identification of SPEN as a novel cancer gene and FGFR2 as a potential therapeutic target in adenoid cystic carcinoma Illumina Genome Analyzer II; 48 bam
EGAD00001000176 DATA_SET_Comparing_sequencing_four_proto-typical_Burkitt_lymphomas_BL_IG-MYC_translocation Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 8 bam
EGAD00001000177 Whole Genome Methylation in CLL Illumina Genome Analyzer IIx; 6 fastq
EGAD00001000178 UK10K_RARE_CHD REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 46 vcf
EGAD00001000179 UK10K_RARE_COLOBOMA REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 75 vcf
EGAD00001000180 UK10K_RARE_NEUROMUSCULAR REL-2012-01-13 Illumina HiSeq 2000; 47 vcf
EGAD00001000181 UK10K_OBESITY_SCOOP REL-2012-01-13 Illumina HiSeq 2000; 212 vcf
EGAD00001000182 UK10K_NEURO_UKSCZ REL-2012-01-13 Illumina HiSeq 2000; 95 vcf
EGAD00001000183 UK10K_NEURO_FSZNK REL-2012-01-13 Illumina HiSeq 2000; 273 vcf
EGAD00001000184 UK10K_NEURO_FSZ_REL_2012_01_13 Illumina HiSeq 2000; 120 vcf
EGAD00001000185 UK10K_RARE_COLOBOMA REL-2012-02-22 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 98 vcf
EGAD00001000186 UK10K_RARE_HYPERCHOL REL-2012-02-22 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 71 vcf
EGAD00001000187 UK10K_RARE_THYROID REL-2012-02-22 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 65 vcf
EGAD00001000188 UK10K_RARE_SIR REL-2012-02-22 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 63 vcf
EGAD00001000189 UK10K_RARE_NEUROMUSCULAR REL-2012-02-22 Illumina HiSeq 2000; 86 vcf
EGAD00001000190 UK10K_RARE_FIND REL-2012-02-22 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 90 vcf
EGAD00001000191 UK10K_RARE_CILIOPATHIES REL-2012-02-22 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 128 vcf
EGAD00001000192 UK10K_RARE_CHD REL-2012-02-22 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 46 vcf
EGAD00001000193 UK10K_OBESITY_SCOOP REL-2012-02-22 Illumina HiSeq 2000; 573 vcf
EGAD00001000194 UK10K_COHORT_TWINS REL-2011-12-01 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 1,713 vcf
EGAD00001000195 For information about this sample set, please contact the sample custodian Nic Timpson: N.J.Timpson@bristol.ac.uk Illumina HiSeq 2000; 740
EGAD00001000196 Neuroblastoma samples Complete Genomics; 203 CompleteGenomics_native
EGAD00001000197 Progressive Hearing Loss Illumina Genome Analyzer II; 8 bam
EGAD00001000198 Gene Discovery in Age-Related Hearing Loss Illumina Genome Analyzer II;, Illumina HiSeq 2000; 20 bam
EGAD00001000199 ORCADES_WGA Illumina HiSeq 2000; 400 bam
EGAD00001000200 Dilgom Exome Illumina HiSeq 2000; 130 bam
EGAD00001000201 MDACC-endo AB SOLiD System 3.0; 28 bam
EGAD00001000202 Neuroblastoma samples (Analyses_vcf files) 204 vcf
EGAD00001000203 Otosclerosis gene discovery Illumina HiSeq 2000; 10 bam
EGAD00001000204 Hearing loss in adults from South Carolina Illumina HiSeq 2000; 10 bam
EGAD00001000205 BRAF and MEK resistant cell line clones Illumina HiSeq 2000; 3
EGAD00001000206 UK10K_RARE_COLOBOMA REL-2012-07-05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 123 vcf
EGAD00001000207 UK10K_RARE_HYPERCHOL REL-2012-07-05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 88 vcf
EGAD00001000208 UK10K_RARE_THYROID REL-2012-07-05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 65 vcf
EGAD00001000209 UK10K_RARE_FIND REL-2012-07-05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 121 vcf
EGAD00001000210 UK10K_RARE_CHD REL-2012-07-05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 124 vcf
EGAD00001000212 Functional characterisation of CpG islands in human tissues Illumina Genome Analyzer II; 26 bam
EGAD00001000213 Screening for abnormal CGI methylation in primary colorectal tumours Illumina Genome Analyzer II; 21 bam
EGAD00001000214 Whole genome sequencing of colon samples Illumina HiSeq 2000; 11 fastq
EGAD00001000215 RNA sequencing of colon tumor/normal sample pairs Illumina HiSeq 2000; 139 fastq
EGAD00001000216 Exome capture sequencing of colon tumor/normal pairs Illumina HiSeq 2000; 144 fastq
EGAD00001000217 UK10K_RARE_CILIOPATHIES REL-2012-07-05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 150 vcf
EGAD00001000218 UK10K_RARE_SIR REL-2012-07-05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 81 vcf
EGAD00001000219 UK10K_RARE_NEUROMUSCULAR REL-2012-07-05 Illumina HiSeq 2000; 117 vcf
EGAD00001000220 Deep sequencing of CTCs 454 GS FLX Titanium;, Illumina MiSeq; 3 bam
EGAD00001000221 Whole genome sequencing of SCLC tumor/normal samples Illumina HiSeq 2000; 4 fastq
EGAD00001000222 Exome capture sequencing of SCLC tumor/normal pairs and cell lines Illumina HiSeq 2000; 103 fastq
EGAD00001000223 RNA sequencing of SCLC tumor/normal sample pairs and cell lines Illumina HiSeq 2000; 79 fastq
EGAD00001000224 Enrichment of CRC 454 GS FLX Titanium; 2 bam
EGAD00001000225 Deep sequencing of KRAS 454 GS FLX Titanium; 8 fastq
EGAD00001000226 Chordoma is a rare malignant bone tumor that expresses the transcription factor T. We conducted an association study of 40 patients with chordoma and 358 ancestry-matched, unaffected individuals with replication in an independent cohort. Whole-exome and Sanger sequencing of T exons reveals a strong risk association ( allelic odds ratio (OR) = 4.9, P = 3.3x10-11, CI= 2.9-8.1) with the common (minor allelic frequency >5%) non-synonymous SNP rs2305089 in chordoma, which is exceptional in cancer genetics. Illumina Genome Analyzer II;, Illumina HiSeq 2000; 18 bam
EGAD00001000227 EGAD00001000227_UK10K_NEURO_ABERDEEN_REL_2012_07_05 Illumina HiSeq 2000; 347 vcf
EGAD00001000228 EGAD00001000228_UK10K_NEURO_ASD_BIONED_REL_2012_07_05 Illumina HiSeq 2000; 59 vcf
EGAD00001000229 EGAD00001000229_UK10K_NEURO_ASD_FI_REL_2012_07_05 Illumina HiSeq 2000; 85 vcf
EGAD00001000230 EGAD00001000230_UK10K_NEURO_ASD_GALLAGHER_REL_2012_07_05 Illumina HiSeq 2000; 72 vcf
EGAD00001000231 EGAD00001000231_UK10K_NEURO_ASD_SKUSE_REL_2012_07_05 Illumina HiSeq 2000; 320 vcf
EGAD00001000232 EGAD00001000232_UK10K_NEURO_ASD_TAMPERE_REL_2012_07_05 Illumina HiSeq 2000; 54 vcf
EGAD00001000233 EGAD00001000233_UK10K_NEURO_EDINBURGH_REL_2012_07_05 Illumina HiSeq 2000; 219 vcf
EGAD00001000234 EGAD00001000234_UK10K_NEURO_FSZNK_REL_2012_07_05 Illumina HiSeq 2000; 281 vcf
EGAD00001000235 EGAD00001000235_UK10K_NEURO_IOP_COLLIER_REL_2012_07_05 Illumina HiSeq 2000; 170 vcf
EGAD00001000236 EGAD00001000236_UK10K_NEURO_MUIR_REL_2012_07_05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 167 vcf
EGAD00001000237 EGAD00001000237_UK10K_NEURO_GURLING_REL_2012_07_05 Illumina HiSeq 2000; 43 vcf
EGAD00001000239 EGAD00001000239_UK10K_NEURO_IMGSAC_REL_2012_07_05 Illumina HiSeq 2000; 114 vcf
EGAD00001000240 UK10K_NEURO_FSZ_REL_2012_07_05 Illumina HiSeq 2000; 120 vcf
EGAD00001000241 EGAD00001000241_UK10K_OBESITY_SCOOP_REL_2012_07_05 Illumina HiSeq 2000; 674 vcf
EGAD00001000242 EGAD00001000242_UK10K_NEURO_ASD_MGAS_REL_2012_07_05 Illumina HiSeq 2000; 60 vcf
EGAD00001000243 Melanoma-TIL Study Exomes Illumina HiSeq 2000; 43 bam,cram
EGAD00001000245 Pulldown cytosine deaminases Illumina HiSeq 2000; 20 bam
EGAD00001000246 Integrative Oncogenomics of multiple myeloma Illumina HiSeq 2000; 106 bam
EGAD00001000247 Integrative Oncogenomics of multiple myeloma Illumina HiSeq 2000; 51 bam
EGAD00001000248 RNAseq Pulldown Illumina HiSeq 2000; 6 bam
EGAD00001000249 This is the bam file generated after alignment using BWA program for the SAIF genome Illumina HiSeq 2000; 1 bam
EGAD00001000251 De novo mutations in schizophrenia Illumina HiSeq 2000; 611 bam
EGAD00001000252 Evaluation of PCR library method on whole genome samples Illumina HiSeq 2000; 12 bam
EGAD00001000253 AML targeted resequencing study Illumina HiSeq 2000; 1,972 bam
EGAD00001000254 This dataset contain the raw files generated for SAIF genome project Illumina HiSeq 2000; 1 fastq
EGAD00001000255 Testing the feasibility of genome scale sequencing in routinely collected FFPE cancer specimens versus matched fresh frozen samples Illumina HiSeq 2000; 32 bam
EGAD00001000256 UK10K_NEURO_UKSCZ REL-2012-07-05 Illumina HiSeq 2000; 595 vcf
EGAD00001000258 Deep RNA sequencing in CLL Illumina Genome Analyzer II; 107 fastq
EGAD00001000259 DATA FILES FOR SJAMLM7 Illumina HiSeq 2000; 8 bam
EGAD00001000260 Hypodiploid acute lymphoblastic leukemia whole genome sequencing Illumina HiSeq 2000; 40 bam
EGAD00001000261 Retinoblastoma whole genome sequencing Illumina HiSeq 2000; 8 bam
EGAD00001000262 OICR PANCREATIC CANCER DATASET 4 bam
EGAD00001000263 We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331 Illumina HiSeq 2000; 18 bam
EGAD00001000264 Resistance towards chemotherapy is one of the main causes of treatment failure and death among breast cancer patients.The main objective of this project is to identify genetic mechanisms causing some breast cancer patients not to respond to a particluar type of chemotherapy (epirubicin) while other patients respond very well to the same treatment. In the project we will perform genome / exome sequencing of a selection of breast cancer patients (n=30). These patients are drawn from a cohort where all patients have recieved treatment with epirubicin monotherapy before surgical removal of a locally advanced breast tumour, and where all patients have been subjected to objective evaluation of the response to the therapy. Subsequent to sequencing, we will analyse the data and compare with the clinical data for each patient (object response to therapy). The main aim being to identify mutations that are associated with resistance to epirubicin. Identification of mutations with strong predictive value, may have a direct impact on cancer treatment since it opens the possibility for genetic testing of a tumour, and desicion on which drug is likely to work best, prior to treatment start. Illumina HiSeq 2000; 29 bam
EGAD00001000265 This Study uses a focused bespoke bait pull down library method to target findings of Chondrosarcoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples. Illumina HiSeq 2000;ILLUMINA 190
EGAD00001000266 This Study uses a focused bespoke bait pull down library method to target findings of Osteosarcoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples. Illumina HiSeq 2000; 110 bam
EGAD00001000267 This Study uses a focused bespoke bait pull down library method to target findings of Chordoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples. Illumina HiSeq 2000; 46 bam
EGAD00001000268 DATA FILES FOR SJCBF Illumina HiSeq 2000; 34 bam
EGAD00001000269 OLD DATA FILES FOR SJMB - Superseded by EGAD00001001864 Illumina HiSeq 2000; 68 bam
EGAD00001000270 DATA_SET_EOP-PCA-LargeAndSmallTumors1 Illumina HiSeq 2000; 18 bam
EGAD00001000271 Pilot study Pilocytic Astrocytoma ICGC PedBrain, whole genome sequencing of 5 tumors and matched blood Illumina HiSeq 2000; 10 bam
EGAD00001000272 Genomic Alterations in Gingivo-buccal Cancer: ICGC-India Project_YR01 454 GS FLX Titanium;, Illumina HiSeq 2000; 200 bam
EGAD00001000273 This Study uses a focused bespoke bait pull down library method to target findings of Meningioma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples. Illumina HiSeq 2000; 147 bam
EGAD00001000274 DATA_SET_TRANSCIPTOME_Comparing_sequencing_four_proto-typical_Burkitt_lymphomas_BL_IG-MYC_translocation Illumina HiSeq 2000; 4 bam
EGAD00001000275 Data set for Whole-genome-Sequencing of adult medulloblastoma Illumina HiSeq 2000; 10 bam
EGAD00001000276 OICR PANCREATIC CANCER DATASET 2 10 bam
EGAD00001000277 High Quality Variant Call files, generated by bioscope, converted to vcf format. Complete dataset for all 300 samples. 300 vcf
EGAD00001000278 ICGC MMML-seq Data Freeze November 2012 whole genome sequencing Illumina HiSeq 2000; 12 bam
EGAD00001000279 ICGC MMML-seq Data Freeze November 2012 whole exome sequencing Illumina Genome Analyzer IIx; 4 bam
EGAD00001000280 This experiment is to validate putative somatic substitutions and indels identified in an exome screen of ~50 osteosarcoma tumour/normal pairs. It is the first stage in our ICGC commitment to study osteosarcoma. The validation process is an important component of our analysis to clarify the data prior to looking for evidence of new cancer genes, or subverted pathways important in the development of cancer. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 112 bam
EGAD00001000281 ICGC MMML-seq Data Freeze November 2012 transcriptome sequencing Illumina HiSeq 2000; 6 bam
EGAD00001000282 Neuroblastomas are tumors of peripheral sympathetic neurons and are the most common solid tumor in children. To determine the genetic basis for neuroblastoma we performed whole-genome sequencing (6 cases), exome sequencing (16 cases), genome-wide rearrangement analyses (32 cases), and targeted analyses of specific genomic loci (40 cases) using massively parallel sequencing. On average each tumor had 19 somatic alterations in coding genes (range, 3-70). Among genes not previously known to be involved in neuroblastoma, chromosomal deletions and sequence alterations of chromatin remodeling genes, ARID1A and ARID1B, were identified in 8 of 71 tumors (11%) and were associated with early treatment failure and decreased survival. Using tumor-specific structural alterations, we developed an approach to identify rearranged DNA fragments in sera, providing personalized biomarkers for minimal residual disease detection and monitoring. These results highlight dysregulation of chromatin remodeling in pediatric tumorigenesis and provide new approaches for the management of neuroblastoma patients. Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 114 fastq
EGAD00001000283 Agilent whole exome hybridisation capture was performed on genomic DNA derived from MDS and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to discover the prevalence of our findings using bespoke pulldown methods and sequencing the products from a larger set of patient DNA. Illumina HiSeq 2000; 764 bam
EGAD00001000284 Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing Illumina Genome Analyzer IIx; 1
EGAD00001000285 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina Genome Analyzer II;, Illumina HiSeq 2000; 55 bam
EGAD00001000286 Whole-exome study of congenital macrothrombocytopenia Illumina HiSeq 2000; 21 fastq
EGAD00001000287 Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 25 renal cancers and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 50 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Illumina Genome Analyzer II; 54 bam,srf
EGAD00001000288 Invasive lobular carcinoma (ILC) is the second most common histological subtype of breast cancer accounting for 10-15% of cases. ILC differs from invasive ductal carcinoma (IDC)with respect to epidemiology, histology, and clinical presentation. Moreover, ILC is less sensitive to chemotherapy, more frequently bilateral, and more prone to form gastrointestinal, peritoneal, and ovarian metastases than IDCs. In contrast to IDC, the prognostic value of histological grade (HG) in ILC is controversial. One of the three major components of histological grading (tubule formation) is missing in ILC which hinders the process of grading in this histological subtype and results in the classification of approximately two thirds of ILC as HG 2. Over the last decade, a number of gene expression signatures have shed light onto breast cancer classification, allowing breast cancer care to become more personalized. With respect to the management of estrogen receptor (ER)-positive breast cancer, several gene expression signatures provide prognostic and/or predictive information beyond what is possible with current classical clinico-pathological parameters alone. Nevertheless, most studies using gene expression signature have not considered different histologic subtypes separately. Recently, a comprehensive research program has elucidated some of the biological underpinnings of invasive lobular carcinoma. Genetic material extracted from 200 ILC tumor samples were studied using gene expression profiling and identified ILC molecular subtypes. These proliferation-driven gene signatures of ILC appear to have prognostic significance. In particular, the Genomic Grade (GG) gene signature improved upon HG in ILC and added prognostic value to classic clinico-pathologic factors. In addition this study demonstrated that most ILC are molecularly characterized as luminal-A (~75%)followed by luminal-B (~20%) and HER2-positve tumors (~5%). Moreover, we investigated the prognostic value of known gene signatures/ gene modules in the same cohort of ILC. As a second step within the scope of this project, we aim to investigate the interactions between somatic ILC tumor mutations to observed transcriptome findings. To this end, we aim to perform somatic mutation analysis for the ILC tumors for which Affymetrix gene expression profiling is available. To this end, we will use a gene screen assay, which specifically interrogates the mutational status of a few hundreds of cancer genes. We believe that this pioneering effort will be fundamental for a tailored treatment of ILC with improvement in patients' outcome. Illumina HiSeq 2000; 1,130 bam,cram
EGAD00001000289 Agilent whole exome hybridisation capture was performed on genomic DNA derived from cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products. Illumina HiSeq 2000; 12 bam
EGAD00001000290 Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing Illumina Genome Analyzer IIx; 1
EGAD00001000291 Exome sequencing identifies mutation of the ribosome in T-cell acute lymphoblastic leukemia Illumina HiSeq 2000; 128 bam
EGAD00001000292 Whole genome sequencing analysis was performed on 6 patients within matched germline, follicular lymphoma and transformed follicular lymphoma. Illumina HiSeq 2000; 20 bam
EGAD00001000293 Sequencing data for Australian Ovarian Cancer study submitted 20121116 AB SOLiD 4 System; 72 bam
EGAD00001000294 UK10K_RARE_CHD REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 124 vcf
EGAD00001000295 UK10K_RARE_HYPERCHOL REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 120 vcf
EGAD00001000296 UK10K_RARE_CILIOPATHIES REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 108 vcf
EGAD00001000297 UK10K_RARE_FIND REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 124 vcf
EGAD00001000298 UK10K_RARE_NEUROMUSCULAR REL-2012-11-27 Illumina HiSeq 2000; 130 vcf
EGAD00001000299 Whole exome sequencing of samples selected from the Finrisk sample collection. The samples sequenced in this study have all been collected in Kuusamo, Finland. Illumina HiSeq 2000; 24 bam
EGAD00001000300 UK10K_OBESITY_GS_REL_2012_07_05 Illumina HiSeq 2000; 430 bam
EGAD00001000301 A couple of previously characterized and sequenced libraries will be repeated using a couple of differing size selection criteria and skim sequenced using an Illumina HiSeq. The resulting sequence will be analyzed to determine the optimal DNA library size for our specific downstream analysis. Illumina HiSeq 2000; 1 bam
EGAD00001000302 This experiment is looking at the mutational signatures generated by engineered HRAS mutations by using whole genome sequence generated on massively parallel next generation sequencers. Illumina HiSeq 2000; 6 bam
EGAD00001000303 ICGC prostate cancer whole genome mate-pair sequencing Illumina Genome Analyzer IIx; 22 bam
EGAD00001000304 ICGC prostate cancer miRNA sequencing Illumina HiSeq 2000; 8 fastq
EGAD00001000305 ICGC prostate cancer RNA sequencing Illumina HiSeq 2000; 12 fastq
EGAD00001000306 ICGC prostate cancer whole genome sequencing Illumina HiSeq 2000; 22 bam
EGAD00001000307 UK10K_RARE_COLOBOMA REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 117 vcf
EGAD00001000308 Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing 1 bam
EGAD00001000309 UK10K_OBESITY_GS REL-2012-11-27 Illumina HiSeq 2000; 424 vcf
EGAD00001000310 UK10K_NEURO_ASD_BIONED REL-2012-11-27 Illumina HiSeq 2000; 76 vcf,bam
EGAD00001000311 UK10K_NEURO_ASD_FI REL-2012-11-27 Illumina HiSeq 2000; 84 vcf
EGAD00001000312 UK10K_NEURO_ASD_MGAS REL-2012-11-27 Illumina HiSeq 2000; 96 vcf
EGAD00001000313 UK10K_NEURO_ASD_SKUSE REL-2012-11-27 Illumina HiSeq 2000; 305 vcf
EGAD00001000314 UK10K_NEURO_ASD_TAMPERE REL-2012-11-27 Illumina HiSeq 2000; 48 vcf
EGAD00001000315 UK10K_NEURO_ABERDEEN REL-2012-11-27 Illumina HiSeq 2000; 313 vcf
EGAD00001000316 UK10K_NEURO_ASD_GALLAGHER REL-2012-11-27 Illumina HiSeq 2000; 75 vcf
EGAD00001000317 UK10K_NEURO_EDINBURGH REL-2012-11-27 Illumina HiSeq 2000; 214 vcf
EGAD00001000318 UK10K_NEURO_FSZ REL-2012-11-27 Illumina HiSeq 2000; 119 vcf
EGAD00001000319 UK10K_NEURO_GURLING REL-2012-11-27 Illumina HiSeq 2000; 48 vcf
EGAD00001000320 UK10K_NEURO_IMGSAC REL-2012-11-27 Illumina HiSeq 2000; 111 vcf
EGAD00001000321 UK10K_NEURO_IOP_COLLIER REL-2012-11-27 Illumina HiSeq 2000; 158 vcf
EGAD00001000322 UK10K_NEURO_MUIR REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 166 vcf
EGAD00001000323 Sequencing data for Australian Pancreatic Cancer study submitted 20130102 AB SOLiD 4 System;, Illumina HiSeq 2000; 200 bam
EGAD00001000324 We will sequence the RNA of lymphoblast samples, transformed with EBV, which have poikiloderma syndrome with mutations in c16orf57. The aim of the experiment is to characterise RNA structural effects in this disease. Illumina HiSeq 2000; 4 bam
EGAD00001000325 In this study, mutations present in a series of human melanomas (stage IV disease) will be determined, using autologous blood cells to obtain a reference genome. From each of the samples that are analyzed, tumour-infiltrating T lymphocytes have also been isolated. This offers a unique opportunity to determine which (fraction of) mutations in human cancer leads to epitopes that are recognized by T cells. The resulting information is likely to be of value to understand how T cell activating drugs exert their action. Illumina HiSeq 2000; 22 bam
EGAD00001000327 release_2: ICGC PedBrain: whole genome mate-pair sequencing Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 70 bam,fastq
EGAD00001000328 ICGC PedBrain: RNA sequencing Illumina HiSeq 2000; 28 fastq
EGAD00001000329 UK10K_RARE_THYROID REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 113 vcf
EGAD00001000332 UK10K_NEURO_FSZNK REL-2012-11-27 Illumina HiSeq 2000; 258 vcf
EGAD00001000333 Cancer is driven by mutations in the genome. We will uncover the mutations that give rise to Ewing's sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewing,s sarcoma tumours. Illumina HiSeq 2000; 58
EGAD00001000334 UK10K_RARE_SIR REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 111 vcf
EGAD00001000335 UK10K_NEURO_UKSCZ REL-2012-11-27 Illumina HiSeq 2000; 527 vcf
EGAD00001000336 UK10K_OBESITY_SCOOP REL-2012-11-27 Illumina HiSeq 2000; 784 vcf
EGAD00001000337 Illumina RNA-Seq will be performed on four Ewing's sarcoma cell lines and two control cell lines. RNA was extracted from all the lines using a basic Trizol extraction protocol. Illumina HiSeq 2000; 12 bam
EGAD00001000338 We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000; 3 bam
EGAD00001000339 Multiple myeloma is an incurable plasma cell malignancy whose molecular pathogenesis is incompletely understood. We used whole exome sequencing, copy number profiling and cytogenetic to analyses 84 samples from 67 patients with myeloma. In addition to known myeloma genes, we identify new candidate genes, including truncations of SP140, ROBO1 and FAT3 and clustered missense mutations in EGR1. We find oncogenic mutations in cancer genes not previously implicated in myeloma, including SF3B1, PI3KCA and PTEN. We define diverse processes contributing to the mutational repertoire, including kataegis and somatic hypermutation. Most cases have at least one cluster of subclonal variants, including subclonal driver mutations, implying on-going tumor evolution. Serial samples revealed diverse patterns of clonal evolution, including linear evolution, differential clonal response and branching evolution. Our findings reveal the myeloma genome to be heterogeneous across patients and, within individual patients, to exhibit diversity in clonal admixture and dynamics in response to therapy. Illumina Genome Analyzer II;, Illumina HiSeq 2000; 154 bam,srf
EGAD00001000340 The objective of this study is to resequence of targeted intervals containing autosomal recessive variants causing neurological disorders in consanguineous pedigrees. Using homozygosity mapping, three intervals of very different sizes have previously been unambiguously mapped for three different neurological diseases: 2.4Mb, 8Mb and 14.3Mb in size, for Microlissencephaly, Severe Mental Retardation and Complicated hereditary spastic paraplegia respectively. This study is a pilot to assess how well custom targeted resequencing performs across a broad size range of intervals. The study design is to use a different custom capture probe set for each interval, pulldown from a single patient from each family, and sequence 1 lane using Illumina paired-reads for each sample. Candidate variants will be followed up in the families themselves, and in patients with similar phenotypes from outbred populations Illumina Genome Analyzer II; 3 bam
EGAD00001000341 This pilot study aims to generate pilot data to inform future study designs in consanguineous families or inbred populations by resequencing the exome of six individuals from five families with neurodevelopmental diseases. For all of these families a single mapping interval containing the causal variant has previously been identified. Illumina HiSeq 2000; 6 bam
EGAD00001000342 This project aims to find causal variants in 50 patients diagnosed with Microcephalic Osteodysplastic Primordial Dwarfism (MOPD), of presumed recessive inheritance performing whole exome sequencing to ~50x mean depth. This is a collaboration with Prof A. Jackson, MRC Human Genetics Unit, Edinburgh Illumina Genome Analyzer II;, Illumina HiSeq 2000; 66 bam
EGAD00001000343 This project aims to identify highly penetrant coding variants increasing the risk of Congenital Heart Disease (CHD) performing whole exome sequencing on DNA samples from 23 affected individuals, selected from 10 families with presumed Autosomal Recessive Inheritance. This is a collaboration with Prof. Eamonn Maher and Dr. Chirag Patel from the Department of Medical and Molecular Genetics, University of Birmingham plans to sequence 23 indexed Agilent whole exome pulldown libraries on 75Bp PE HiSeq (Illumina) Illumina HiSeq 2000; 24 bam
EGAD00001000344 Exome sequencing of 30 parent-offspring trios to >50X mean depth, where the offspring has sporadic TOF, to identify potential causal de novo mutations. We will use the exome plus design for pulldown that incorporates ~6.8Mb of additional regulatory sequences in addition to the ~50Mb GENCODE exome. Illumina HiSeq 2000; 90 bam
EGAD00001000345 Exome sequencing of 12 DNA samples obtained from patients with structural brain malformations. Illumina HiSeq 2000; 9 bam
EGAD00001000346 Exome sequencing of patients and their families with diverse rare neurological disorders. Some families have prior linkage data identifying a specific chromosomal interval or interest, other families do not have linkage data available. Many of these families come from special populations whose demography or preference for consanguineous marriages make them particularly tractable for genetic studies. Illumina HiSeq 2000; 30 bam
EGAD00001000347 These samples include exome sequences of family members with dyslipidemias from Finnish origin. Illumina HiSeq 2000; 95 bam
EGAD00001000348 Exome sequencing of Bilateral Anophthalmia cases- Pilot Study Illumina Genome Analyzer II; 16 bam
EGAD00001000349 These samples are from locally advanced breast cancers that have been treated with epirubicin monotherapy before surgery. We will sequence some samples from patients with good response to the therapy and some with poor response to the therapy. Illumina HiSeq 2000; 33 bam
EGAD00001000350 We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. Illumina HiSeq 2000; 17 bam
EGAD00001000351 This pilot study aims to generate pilot data to inform future study designs by resequencing the whole exomes of 10 unrelated individuals diagnosed with Congenital Heart Disease (CHD). Illumina Genome Analyzer II; 16 bam
EGAD00001000352 DATA FILES FOR SJLGG Illumina HiSeq 2000; 7 bam
EGAD00001000353 DATA FILES FOR SJLGG Illumina HiSeq 2000; 45 bam
EGAD00001000354 Testing the feasibility of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing. Illumina HiSeq 2000; 81 bam
EGAD00001000355 ICGC MMML-seq Data Freeze March 2013 whole genome sequencing Illumina HiSeq 2000; 46 bam
EGAD00001000356 ICGC MMML-seq Data Freeze March 2013 transcriptome sequencing Illumina HiSeq 2000; 23 bam
EGAD00001000357 PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced by MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 4 bam
EGAD00001000358 Chondrosarcoma (CHS) is a heterogeneous collection of malignant bone tumours and is the second most common primary malignancy of bone after osteosarcoma. Recent work has identified frequent, recurrent mutations in IDH1/2 in nearly half of central CHS. However, there has been little systematic genomic analysis of this tumour type and thus the contribution of other genes is unclear. Here we report comprehensive genomic analyses of 49 cases of CHS. We identified hypermutability of the major cartilage collagen COL2A1 with insertions, deletions and rearrangements identified in 37% of cases. The patterns of mutation were consistent with selection for variants likely to impair normal collagen biosynthesis. In addition we identified mutations in IDH1/2 (59%), TP53 (20%), the RB1 pathway (27%) and hedgehog signaling (22%). Illumina HiSeq 2000; 17 bam
EGAD00001000359 In this study we will sequence the transcriptome of Verified Cancer Cell lines. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found. Illumina HiSeq 2000; 2 bam
EGAD00001000360 The genome-wide landscape of somatically acquired mutations in mesothelioma has not been deeply characterised to date, but advances in DNA sequencing technology now allow this to be addressed comprehensively. Harnessing massively parallel DNA sequencing platforms, we will identify somatically acquired point mutations in all coding regions of the genome from patients with mesothelioma. In addition, using paired-end sequencing, we will map copy number changes and genomic rearrangements from the same patients. Illumina HiSeq 2000; 232 bam,cram
EGAD00001000361 This is a small pilot data set to test the feasibility of cDNA exomes across 1200 cancer cell line panel. cDNA exomes or Fus-seq is further explained in this studies Abstract. Illumina HiSeq 2000; 3 bam
EGAD00001000362 Human induced pluripotent stem (hiPS) cells hold great promise for regenerative medicine. Safety issues of use of hiPS cells however remain to be addressed. One of such issues is mutations derived from somatic donor cells and introduced during genome manipulation. We sequence whole genomes of hiPS cells and analyzed mutations. Our study brings hiPS cell technology one step closer to application to regenerative medicine. Illumina HiSeq 2000; 7 bam
EGAD00001000363 Common variable immunodeficiency (CVID) is the most common form of primary immunodeficiency with an estimated incidence of 1:10,000. It has been apparent for many years that CVID has a genetic component, occurs frequently in families and can have both a recessive or dominant mode of inheritance. In recent years, 4 genes underlying CVID have been identified; however, mutations within in them are estimated to account for no more than 10% of all cases of CVID. We have identified a multi-generational family with autosomal dominant CVID. Genome-wide linkage analysis has mapped the locus underlying CVID in this family to an approximately 9.2 Mb interval on chromosome 3q27.3-q29, between the markers D3S3570 and D3S1265. This locus is distinct from any of the previously mapped susceptibility loci suggesting a novel genetic variant is responsible for disease in this family. The aim of this study is to use exome sequencing of affected (n = 4) and unaffected (n = 4) individuals, in tandem with the available genetic mapping data, to identify the causal variant underlying CVID in this family. Illumina HiSeq 2000; 8 bam
EGAD00001000364 We performed low coverage whole genome sequencing of plasma DNA from prostate cancer patients to establish copy number profiles on both a genome-wide and a gene-specific level. The data include plasma samples from prostate cacner patients (n=13), non-malignant controls (males, n=10 and females, n=9), plasma samples from pregnancies with aneuploid and euploid fetuses (n=4). Furthermore, we sequenced different tumor samples (n=6) of one patients and a serial dilution of HT29 in a background of normal DNA (n=9). Illumina MiSeq; 50 fastq
EGAD00001000365 In this study we analysed patients with metastatic prostate cancer to scan their tumor genomes noninvasively in plasma DNA. We enriched 1.3 Mbp of seven plasma DNAs (4 CRPC cases: CRPC1-3 and CRPC5; 3 CSPC cases: CSPC1-2 and CSPC4) including exonic sequences of 55 cancer genes and 38 introns of 18 genes, where fusion breakpoints have been described using Sure Select Custom DNA Kit. Illumina MiSeq; 7 fastq
EGAD00001000366 WGBS data of whole blood samples from smoking and non-smoking mothers and their children at gestation/birth and follow-up years. Illumina HiSeq 2000; 52 bam
EGAD00001000367 Genomic libraries (500 bps) will be generated from total genomic DNA derived from lung cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions. Illumina HiSeq 2000; 5 bam
EGAD00001000368 Genomic libraries (500 bps) will be generated from total genomic DNA derived from Osteosarcoma cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions. Illumina HiSeq 2000; 3 bam
EGAD00001000369 We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. Illumina HiSeq 2000; 3 bam
EGAD00001000370 This dataset is compromised of 5 sequencing experiments from a single patient with sporadic and recurring parathyroid carcinoma. The samples include whole genome sequence of the primary tumor, the first recurrent tumor and peripheral blood. Whole transcriptome sequence of the first and second recurrent tumors are also included. Illumina HiSeq 2000; 5 bam
EGAD00001000371 Sequencing data for PDAC cell lines generated by QCMG Illumina HiSeq 2000;, Illumina HiSeq 2500; 54 bam
EGAD00001000372 We conducted whole genome sequencing and DNA SNP array of 12 uveal melanoma genomes and their matched DNA from blood. We also conducted RNA-seq of the 12 tumour samples. Illumina HiSeq 2000; 24 bam
EGAD00001000380 Illumina paired-end sequencing of whole- exome pulldown DNA from Severe Insulin Resistant patients. Illumina Genome Analyzer II;, Illumina HiSeq 2000; 64 bam
EGAD00001000381 Illumina paired-end sequencing of whole- exome pulldown DNA from Severe Insulin Resistant patients. Illumina HiSeq 2000; 3 bam
EGAD00001000382 Whole Exome Sequencing of Permanent Neonatal Diabetes Patients Illumina HiSeq 2000; 25 bam
EGAD00001000383 In collaboration with Dr Robert Semple we have identified a family harbouring an autosomal dominant variant, which leads to severe insulin resistance (SIR), short stature and facial dysmorphism. This family is unique within the SIR cohort in having normal lipid profiles, preserved adiponectin and normal INSR expression and phosphorylation. DNA is available for 7 affected and 7 unaffected family members across 3 generations. All 14 samples have been genotyped using microsatellites and the Affymetrix 6.0 SNP chip. Linkage analysis identified an 18.8Mb haplotype on chromosome 19 as a possible location of the causative variant. However, Exome sequencing of 3 affected and 1 unaffected family members has not identified the causative variant suggesting the possibility of an intronic or intergenic variant in this region or elsewhere in the genome. We propose to conduct whole genome sequencing of 5 members of the pedigree at a depth of 20X. The chosen samples are two sets of parents plus one member of an unaffected branch of the pedigree who shares the risk haplotype on chromosome 19. Sequencing of the two sets of parents will be used along with the genome-wide SNP data to impute 4 affected children giving an effect sample size of 6 affected individuals. Illumina HiSeq 2000; 7 bam
EGAD00001000384 In order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs but it is unlcear whether some cell types carry through fewer mutations through reprogramming (either due to mutations present in the primary cells, or mutations accumulated during reprogramming). Through in depth analysis of hiPSCs generated from different somatic cells, it will be possible to assess the variation in genetic stability of different cell types. Illumina HiSeq 2000; 35 bam
EGAD00001000385 Wholegenome libraries will be prepared from at least two serial samples reflecting different stages of disease progression and matched constitutional DNA for 30 Myeloproliferative Disease samples. Five lanes of Illumina HiSeq sequencing will be performed on each of the tumour samples and four lanes for each of the constitutional DNA. Sequencing data will mapped to build 37 of the human reference genome and analysis will be performed to characterize the spectrum of somatic variation present in these samples including single base pair mutations, insertions, deletions as well as larger structural variants and genomic rearrangements. Illumina HiSeq 2000; 108 bam,cram
EGAD00001000386 Wholegenome libraries will be prepared from at least two serial samples reflecting different stages of disease progression and matched constitutional DNA for 30 Myelodysplastic syndrome patient samples. Five lanes of Illumina HiSeq sequencing will be performed on each of the tumour samples and four lanes for each of the constitutional DNA. Sequencing data will mapped to build 37 of the human reference genome and analysis will be performed to characterize the spectrum of somatic variation present in these samples including single base pair mutations, insertions, deletions as well as larger structural variants and genomic rearrangements. Illumina HiSeq 2000; 83 bam,cram
EGAD00001000387 This study aims to whole genome sequence DNA derived from breast cancer patients who received neo-adjuvany chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved. Illumina HiSeq 2000; 35 bam
EGAD00001000388 Genomic libraries (500 bps) will be generated from total genomic DNA derived from lung cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions. Illumina HiSeq 2000; 15 bam
EGAD00001000389 Cancer is driven by mutations in the genome. We will uncover the mutations that give rise to Ewing's sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewing's sarcoma tumours. Illumina HiSeq 2000; 20 bam
EGAD00001000390 We propose to definitively characterise the somatic genetics of triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000; 101 bam,cram
EGAD00001000392 Agilent whole exome hybridisation capture was performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products. Illumina MiSeq; 60 bam
EGAD00001000393 Illumina HiSeq 2000; 30 vcf
EGAD00001000394 DNA methylation has been shown to play a major role in determining cellular phenotype by regulating gene expression. Moreover, dysregulation of differentially methylated genes has been implicated in disease pathogenesis of various conditions including cancer development as well as autoimmune diseases such as systemic Lupus erythematosus and rheumatoid arthritis. Evidence is rapidly accumulating for a role of DNA methylation in regulating immune responses in health and disease. However, the exact mechanisms remain unknown. The overall aim of the project is to investigate the role of epigenetic mechanisms in regulating immunity and their impact on autoimmune disease pathogenesis. The aim of this pilot study is to perform whole genome methylation analysis in peripheral blood mononuclear cells (PBMCs) and cell subsets (CD4, CD8, CD14, CD19, CD16 and whole PBMCs) obtained from 6 healthy volunteers. Whole genome methylation analysis will be performed using two methodological approaches, the Infinium Methylation Bead Array K450 (Illumina) and MeDIP-seq. mRNA expression arrays will also be performed in order to correlate DNA methylation with gene expression as well as genotyping on the Illumina OmniExpress chip Illumina Genome Analyzer II; 6 bam
EGAD00001000395 Noninvasive Prenatal Molecular Karyotyping from Maternal Plasma 1 bam
EGAD00001000396 We performed serial plasma-Seq analyses on a male who progressed from castration-sensitive to castration-resistant prostate cancer within 10 months following treatment with androgen-deprivation therapy. Illumina MiSeq; 2 fastq
EGAD00001000397 The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts. Illumina HiSeq 2000; 47 bam
EGAD00001000398 The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts. Illumina Genome Analyzer II; 8 bam
EGAD00001000399 In 2009 we identified a four-generation family with over 700 members and 41 affected with Crohn's disease (CD). At the time we sequenced the exome of 6 affected individuals but did not identify any coding variants which appear to explain the high prevalence of disease. Since then we have collected DNA from a large number of additional family members, genotyped linkage arrays on the entire family to refine genomic regions shared by identity by descent and genotyped affected and unaffected members at known CD risk loci identified by Genome Wide Association Studies (GWAS). These analyses have confirmed that a significant unexplained excess of disease remains after accounting for all known genetic factors, and that several regions of the genome are shared by a large fraction of affected individuals. We therefore perform whole genomes sequencing from 8 individuals which will allow us to impute the complete sequence of nearly all the members of the two largest and most severely affected branches of the family. Illumina HiSeq 2000; 8 bam
EGAD00001000400 The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts. Illumina HiSeq 2000; 12 bam
EGAD00001000401 Population based sequencing of whole genomes of Crohn's disease patients. Illumina HiSeq 2000 (ILLUMINA) 2,926
EGAD00001000402 The study will analyse by exome sequencing 42 Greek patients with premature MI and no vessel disease to identify genetic factors underlying this condition. Illumina HiSeq 2000; 46 bam
EGAD00001000403 The ENGAGE project is a FP7 funded EU project aiming to combine genetic and phenotype information from European population based cohorts. In this sub-project we aim to do whole exome sequencing of individuals selected from Health 2000 and FINRISK cohorts. Individuals have been selected based on their metabolic trait phenotypes Illumina HiSeq 2000; 394 bam
EGAD00001000404 Acute myeloid leukaemia (AML) is an aggressive and molecularly diverse disease with a poor overall survival of 20-25%. With an annual incidence of 2.9 per 100,000, AML is currently the commonest myeloid malignancy in Europe, yet the two main therapeutic options for this disease, anthracyclines and purine analogues, have remained unchanged for over 20 years. Currently patients are stratified at diagnosis according to a series of clinicopathological parameters (e.g. age, white cell count and presence/absence of previous clonal haematological disease) and molecular markers (e.g. chromosomal translocations/deletions, aneuploidy and mutations in genes such as FLT3 and NPM1). Patients with adverse prognostic features, whose prognosis is particularly poor (e.g. <15% long-term survival) are offered treatment with allogeneic bone marrow transplantation (allo-BMT) if a sibling or unrelated donor is available. This can significantly improve survival (e.g. up to 40% long-term survival in some contexts), albeit at the expense of significant toxicity and transplant-related mortality (TRM). Allo-BMT is thought to work in part by allowing the delivery of large doses of chemotherapy followed by haemopoietic "rescue" with donor haemopoietic stem cells (haemopoietic failure would otherwise ensue). However, potentially the most potent effect of allo-BMT is the cytotoxic effect of donor lymphocytes against AML blasts, a phenomenon known as graft-vs-leukaemia (GVL) effect. Increasingly, transplants using reduced chemotherapy intensity (mini-allografts) are being used that partially circumvent the toxicity from chemotherapy and rely on GVL to effect cure. Nevertheless, AML relapse after allo-BMT still occurs at a significant rate of up to 80% depending on the type of transplant. There is accumulating evidence that genetic events in residual leukaemic cells enable them to evade immunodetection and therefore survive the GVL effect and expand to cause relapse. The most striking example of this is the loss of HLA antigens after transplants in which donor and recipient are not fully HLA-matched. In these cases, the leukaemia "deletes" the genomic region containing the disparate HLA antigen which was preferentially targeted as "foreign" by the GVL effect. However, the genetic basis of immune evasion in the majority of transplants, which are fully HLA matched, is not known. One possibility is that loss of genes coding for antigens outside the HLA locus but which are also targets of GVL may operate, alternatively genetic events that affect processes downstream of immunological cytotoxicity may be responsible. The identification of genetic events that mediate immune evasion would not only facilitate the understanding of this process but can help plan therapeutic interventions that improve the outcomes of allogeneic transplantation for AML and other disorders. We intend to study this by conducting exome sequencing on 6 cases of AMLs from patients that attend my clinic at Addenbrooke's hospital and have relapsed after allogeneic transplantation. Samples from AML diagnosis, remission/normal and AML relapse (total n=18) will be studied to identify somatic mutations in the primary AML and those acquired by the relapsed clone. The 18 samples will also be studied by array CGH to detect regions of genomic amplification or deletion. Illumina HiSeq 2000; 25 bam
EGAD00001000405 In this project we will sequence the exomes of 250 patients with Parkinson's disease Illumina HiSeq 2000; 247 bam
EGAD00001000406 Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and aggressive haematological malignancy derived from precursors of plasmacytoid dendritic cells. Due to the rarity of BPDCNs our knowledge of their molecular pathogenesis was until recently confined to observations describing reccurent chromosomal deletions involving chromosomes 5q, 12p, 13q, 6q, 15q and 9. A recent publication went on to delineate the common deleted regions using aCGH and demonstrated that these centred around known tumour suppressor genes including CDKN2A/B (9p21.3), RB1 (12p13.2-14.3), CDKN1B (13q11-q12) and IKZF1 (7p12.2). These mutations are found recurrently in several different cancers and in most cases are thought to be involved in tumour progression rather than initiation. However, the well-defined nature and cellular ontogeny of these neoplasms suggests strongly that they share one or a few characteristic mutations as has been demonstrated for other uncommon but well-defined neoplasms such as Hairy Cell Leukemia (BRAF) and ovarian Granulosa Cell tumours (FOXL2). Illumina HiSeq 2000; 14 bam
EGAD00001000407 We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of the International Headache Genetics consortium and EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls. Illumina HiSeq 2000; 327 bam
EGAD00001000408 We aim to whole-exome sequence DNA samples from 75 individuals with severe forms of Inflammatory Bowel Disease and related autoimmune diseases to identify the rare, highly penetrant, variants that we believe underlie these phenotypes. Case samples will be obtained from both new and existing (UK IBD Genetics Consortium) collaborators to ensure only the most extreme cases are sequenced. Illumina HiSeq 2000; 4 bam
EGAD00001000409 2000 ulcerative colitis cases drawn from the UKIBD Genetics Consortium cohort and whole-genome sequenced at 2X depth. A case control association study using control samples whole-genome sequenced by UK10K will be undertaken to identify common, low-frequency and rare variants associated with ulcerative colitis. Data will be combined with similar data across 3000 Crohn's disease cases from the same cohort to identify inflammatory bowel disease (IBD) loci and better understand the genetic differences and similarities of the two common forms of IBD. Illumina HiSeq 2000; 1,992 bam
EGAD00001000410 We will perform exome sequencing on selected cases of splenic marginal zone lymphoma (SMZL) and diffuse large B-cell lymphoma (DLBCL) in order to characterise their genetic makeup and identify biomarkers for prognosis and prediction of treatment response. Illumina HiSeq 2000; 78 bam,cram
EGAD00001000411 These samples include exome sequences of family members with dyslipidemias from northern Finnish origin. Illumina HiSeq 2000; 68 bam
EGAD00001000412 We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of the International Headache Genetics consortium and EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls. Illumina HiSeq 2000; 477 bam,cram
EGAD00001000413 UK10K_RARE_CHD REL-2013-04-20 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 125 vcf
EGAD00001000414 UK10K_RARE_CILIOPATHIES REL-2013-04-20 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 122 vcf
EGAD00001000415 UK10K_RARE_COLOBOMA REL-2013-04-20 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 123 vcf
EGAD00001000416 UK10K_RARE_FIND REL-2013-04-20 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 124 vcf
EGAD00001000417 UK10K_RARE_HYPERCHOL REL-2013-04-20 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 125 vcf
EGAD00001000418 UK10K_RARE_NEUROMUSCULAR REL-2013-04-20 Illumina HiSeq 2000; 140 vcf
EGAD00001000419 UK10K_RARE_SIR REL-2013-04-20 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 121 vcf
EGAD00001000420 UK10K_RARE_THYROID REL-2013-04-20 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 124 vcf
EGAD00001000421 The aim of this project is to identify rare variants in the 1q region associated with type 2 diabetes. To this end 651 case samples and 651 control samples from six populations have been pooled (pool sizes range from 27-33 individuals), and are being sequenced. The hybridization solution being used captures the exons and UTRs of genes in the 1q region. Illumina HiSeq 2000; 48 bam
EGAD00001000422 We perform whole exome sequencing on samples from a large IBD pedigree. The selected samples are from more distantly related family members (healthy and with IBD) and a set of matched population (Ashkenazy Jewish ancestry) samples. Illumina HiSeq 2000; 86 bam
EGAD00001000423 The aim is to find rare variants of intermediate penetrance in those at risk of Crohn's disease Illumina Genome Analyzer II; 10 bam
EGAD00001000424 The aim of this project is to identify rare variants in the 1q region associated with type 2 diabetes. To this end 651 case samples and 651 control samples from six populations have been pooled (pool sizes range from 27-33 individuals), and are being sequenced. The hybridization solution being used captures the exons and UTRs of genes in the 1q region. Illumina Genome Analyzer II;, Illumina HiSeq 2000; 23 bam
EGAD00001000425 GENCORD2 RNA-seq BAM files using BWA Illumina Genome Analyzer II;, Illumina HiSeq 2000; 568 bam
EGAD00001000427 Illumina HiSeq 2000; 30 bam
EGAD00001000428 204 individuals were genotyped with the Illumina 2.5M Omni chip. Filtered genotypes were imputed into the 1000 genomes project European panel SNPs. Beagle R2 is indicated in VCF files for further filtering. See Materials and Methods in publication for details. 204 vcf
EGAD00001000429 UK10K_OBESITY_TWINSUK REL-2013-04-20 Illumina HiSeq 2000; 68 vcf
EGAD00001000430 UK10K_NEURO_UKSCZ REL-2013-04-20 Illumina HiSeq 2000; 554 vcf
EGAD00001000431 UK10K_OBESITY_GS REL-2013-04-20 Illumina HiSeq 2000; 428 vcf
EGAD00001000432 UK10K_OBESITY_SCOOP REL-2013-04-20 Illumina HiSeq 2000; 985 vcf
EGAD00001000433 UK10K_NEURO_ABERDEEN REL-2013-04-20 Illumina HiSeq 2000; 392 vcf
EGAD00001000434 UK10K_NEURO_ASD_BIONED REL-2013-04-20 Illumina HiSeq 2000; 77 vcf
EGAD00001000435 UK10K_NEURO_ASD_FI REL-2013-04-20 Illumina HiSeq 2000; 84 vcf
EGAD00001000436 UK10K_NEURO_ASD_GALLAGHER REL-2013-04-20 Illumina HiSeq 2000; 77 vcf
EGAD00001000437 UK10K_NEURO_ASD_TAMPERE REL-2013-04-20 Illumina HiSeq 2000; 55 vcf
EGAD00001000438 UK10K_NEURO_EDINBURGH REL-2013-04-20 Illumina HiSeq 2000; 234 vcf
EGAD00001000439 UK10K_NEURO_FSZNK REL-2013-04-20 Illumina HiSeq 2000; 285 vcf
EGAD00001000440 UK10K_NEURO_GURLING REL-2013-04-20 Illumina HiSeq 2000;ILLUMINA 46 bam,vcf
EGAD00001000441 UK10K_NEURO_IMGSAC REL-2013-04-20 Illumina HiSeq 2000; 113 vcf
EGAD00001000442 UK10K_NEURO_IOP_COLLIER REL-2013-04-20 Illumina HiSeq 2000; 172 vcf
EGAD00001000443 UK10K_NEURO_MUIR REL-2013-04-20 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 175 vcf
EGAD00001000444 Cancer is driven my mutations in the genome. We will uncover the mutations that give rise to Ewing's sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewing's sarcoma tumours. Illumina HiSeq 2000; 3 bam
EGAD00001000445 We recently worked-up a pulldown protocol for studying 21 genes recurrently mutated in AML (Study1770). Our manuscript is currently under revision and to address the reviewers' comments we need to validate some mutations by re-sequencing. In this add-on study we will be using PCR followed by MiSeq for this purpose. Illumina MiSeq; 9 bam
EGAD00001000446 Fastq files of 213 samples of hepatocellular carcinoma (NCCRI) Illumina HiSeq 2000; 213 fastq
EGAD00001000596 This project is to develop and validate a method to detect de novo mutations in a foetal genome through deep sequencing of cell-free DNA from the plasma of pregnant women. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 5 bam
EGAD00001000597 Illumina HiSeq 2000; 212 bam
EGAD00001000598 The Ethiopian area stands among the most ancient ones ever occupied by human populations and their ancestors. Particularly, according to archaeological evidences, it is possible to trace back the presence of Hominids up to at least 3 million years ago. Furthermore, the present day human populations show a great cultural, linguistic and historic diversity which makes them essential candidate to investigate a considerable part of the African variability. Following the typing of 300 Ethiopian samples on Illumina Omni 1M (see Human Variability in Ethiopia project, previously approved by the Genotyping committee) we now have a clearer idea on which populations living in the area include the most of the diversity. This project therefore aims to sequence the whole genome of 300 individuals at low (4-8x) depth belonging to the six most representative populations of the Ethiopian area to produce a unique catalogue of variants peculiar of the North East Africa. Furthermore 6 samples (one from each population) will also be sequenced at high (30x) depth to ensure full coverage of the diversity spectrum. The retrieved variants will be of great help in evaluating the demographic dynamics of those populations as well as shedding light on the migrations out of Africa. Illumina HiSeq 2000; 120 bam
EGAD00001000599 We have collected material from a patient who had BrafV600E mutant melanoma that was treated with PLX4032. We have germline DNA from the patient and DNA and RNA from distinct lesions before and after treatment with PLX4032. We have transcriptome sequenced these samples to obtain a snap shot of the mechanisms of resistance that are operative. Illumina HiSeq 2000; 6 bam
EGAD00001000601 Illumina HiSeq 2000; 1 bam
EGAD00001000602 Illumina HiSeq 2000; 1 bam
EGAD00001000603 We recently used the Agilent SureSelect platform to re-sequence a set of genes known to be mutated in human AML. The results from 10 AML DNA samples were very satisfactory, but the effort required was significant. Thus, we decided to re-sequence the same genes using the Haloplax system for target enrichment in 48 AML samples. We planned to do this using MiSeq and have data from a pilot of 3 samples. The data is promising but coverage appears pathcy so far. However, in order to get a better understanding of the data we will need deeper sequencing. We will need two lanes of HiSeq to get the same degree coverage as Sureselect. his data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 54 bam,cram
EGAD00001000604 In order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs and from studies in the mouse, it appears that an epigenetic memory of the starting cell type is carried over to hiPSCs. However a comprehensive comparative study of the characteristics of these hiPSCs has been missing from the literature. Importantly studies which aimed to address these aspects of hiPSCs have used cells from different patients. In order to avoid this important confounding variable and to keep the genetic background constant, tissue samples were procured from the patients and reprogrammed to iPS cells. The transcriptomes of these iPS cells will be compared. Protocol: primary cultures of cells were reprogrammed to iPS cells. RNA was extracted using a standard column extraction kit. Illumina HiSeq 2000; 47 bam
EGAD00001000605 CR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq;, Illumina HiSeq 2000; 10 bam
EGAD00001000606 Background Massively parallel sequencing technology has transformed cancer genomics. It is now feasible, in a clinically relevant time-frame, for a clinically manageable cost, to screen DNA from patient tumours for mutations essentially genome-wide. The challenge for personalised medicine will be to increase the sample size to thousands or tens of thousands of well-characterised cases in order to attain sufficient statistical power to stratify patients accurately across the complexity and genomic heterogeneity expected for most of the common tumour types. Currently, whole genome sequencing on this scale is not feasible, and targeted sequencing of relevant portions of the genome will be required. Pilot data We have developed protocols for large-scale, multiplexed sequencing of 100-200 genes in thousands of samples. Essentially, using robotic technology, genomic DNA from the cancer specimen is processed into sequencing libraries with unique DNA barcodes, thereby allowing sequencing reads to be attributed to the sample they derive from. Currently, these sequencing libraries can be generated in a 96-well format using fully automated protocols, and we are exploring methods to expand this to a 384-well format. The sequencing libraries are pooled and hybridized to custom sets of RNA baits representing the genomic regions of interest. Sequencing of the pulled-down libraries is done in pools of 48-96 samples per lane of an Illumina Hi-Seq. This protocol is already implemented at the Sanger Institute. We have published proof that somatic mutations in novel cancer genes can be identified from exome-wide sequencing. In unpublished pilot data, we have established the feasibility of robotic library production, custom pull-down, and multiplexed sequencing of barcoded libraries for 100 known myeloid cancer genes across 760 myelodysplasia samples. Highlights of the data thus far analysed reveal that the coverage is remarkably even between samples; when 96 samples are run, average coverage per lane of sequencing is ~250, with 90-95% of targeted exons covered by >25 reads; known mutations can be discovered in the data set; and the protocol is amenable to whole genome amplified DNA. The bioinformatic algorithms for identification of substitutions and indels in pull-down data are well-established; we have pilot data proving that copy number changes, LOH and genomic rearrangements in specific regions of interest can also be identified by tiling of baits across the relevant loci. Proposal We propose to apply this methodology to 10000 samples from patients with AML enrolled in clinical trials over the last 10-20 years. Oncogenic point mutations and potentially genomic rearrangements will be identified, and linked to clinical outcome data, with a view to undertaking the following sorts of analyses: ? Identification of co-occurrence, mutual exclusivity and clusters of driver mutations. ? Correlation of prognosis with driver mutations and potentially gene-gene interactions ? Exploration of genomic markers of drug response Ultimately, we would like to be in a position to release the mutation data together with matched clinical outcome data to genuine medical researchers via a controlled access approach, possibly within the COSMIC framework (www.sanger.ac.uk/genetics/CGP/cosmic/). The vision here is to generate a portal whereby a clinician faced with an AML patient and his / her mutational profile can obtain a ?personalised? prediction of outcome, together with a fair assessment of the uncertainty of the estimate. With a sufficient sample size, there would also be the potential to develop decision support algorithms for therapeutic choices based on such data. Illumina MiSeq; 38 bam
EGAD00001000607 PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 2 bam
EGAD00001000608 PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 60 bam
EGAD00001000609 Whole transcriptome sequencing of 28 untreated prostate cancers, 13 castration resistant prostate cancers, and 12 benign prostatic hyperplasias. Illumina HiSeq 2000; 53
EGAD00001000610 Methylated DNA immunoprecipitation sequencing of 28 untreated prostate cancers, 11 castration resistant prostate cancers, and 12 benign prostatic hyperplasias. Illumina HiSeq 2000; 51
EGAD00001000611 Small RNA sequencing of 28 untreated prostate cancers, 12 castration resistant prostate cancers, and 3 benign prostatic hyperplasias. Illumina HiSeq 2000; 43
EGAD00001000612 Low coverage whole genome sequencing of 27 untreated prostate cancers, 9 castration resistant prostate cancers, and 4 benign prostatic hyperplasias. Illumina HiSeq 2000; 40
EGAD00001000613 UK10K_NEURO_ASD_MGAS REL-2013-04-20 Illumina HiSeq 2000; 97 vcf
EGAD00001000614 UK10K_NEURO_ASD_SKUSE REL-2013-04-20 Illumina HiSeq 2000; 341 vcf
EGAD00001000615 UK10K_NEURO_FSZ REL-2013-04-20 Illumina HiSeq 2000; 128 vcf
EGAD00001000616 Pilocytic Astrocytoma ICGC PedBrain whole genome sequencing Illumina HiSeq 2000; 192 bam
EGAD00001000617 Pilocytic Astrocytoma ICGC PedBrain RNA sequencing Illumina HiSeq 2000; 73 fastq
EGAD00001000618 1204 Sardinian males 1,195 bam
EGAD00001000619 Experiments using targeted pulldown methods will be sequenced to validate findings in the exomes of patients with Myeloproliferative Neoplasms (MPN). Illumina HiSeq 2000; 360 bam
EGAD00001000620 A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients. Illumina HiSeq 2000; 14 bam
EGAD00001000621 We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. This study will aim to validate the findings of the whole genome study by re-sequencing regions of interest using a bespoke pulldown bait. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331 Illumina MiSeq; 18 bam
EGAD00001000623 This VCF contains the full sequence data post QC. This consists of 41,911 individuals. All polymorphic sites are present in this VCF. 41,911 vcf
EGAD00001000624 Multifocality or multicentricity in breast cancer may be defined as the presence of two or more tumor foci within a single quadrant of the breast or within different quadrants of the same breast, respectively. This original classification of the breast cancer as multicentric or multifocal was based on the assumption that cancers arising in the same quadrant were more likely to arise from the same ductal structures than those occurring in separate areas of the breast. The problem with these definitions is that the ?quadrants? of the breast are arbitrary external designations, as no internal boundaries do exist. This project will therefore focus both on synchronous multifocal and multicentric tumors. The incidence of multifocal and multicentric breast cancers was reported to be between 13 and 75% depending on the definition used, the extent of the pathologic sampling of the breast and whether in situ disease is considered evidence of multicentricity (1). Although this incidence is variable, those figures show that it is a frequent phenomenon. Multiple (multifocal/multicentric) breast carcinomas, especially when occurring in the same breast, represent a real challenge for both pathologists and clinicians in terms of identifying the cellular origin and the best therapeutic management of the cancer. Multifocality or multicentricity has been associated with a number of more aggressive features including an increased rate of regional lymph node metastases and adverse patient outcome when compared with unifocal tumors (2-3), and a possible increased risk of local recurrence following breast conserving surgery (4). For the moment, the literature is divided on whether there is a corresponding impact on survival outcomes. Today, the current convention to stage and to treat multifocal and multicentric tumors is the classical tumor-node-metastasis (TNM) staging guidelines with which tumor size is assessed by the largest tumor focus without taking other foci of disease into consideration. If some papers, as the recent one from Lynch and colleagues, support the current staging convention (3), others, however, as Boyages et al. suggested that aggregate size and not the size of the largest lesion should be considered in order to refine the prognostic assessment of those tumors (5). On the top of that, the question whether multifocal/multicentric carcinomas are due to the spread of a single carcinoma throughout the breast or is due to multiple carcinomas arising simultaneously has been a matter of debate. Some studies suggested that multifocal breast cancer may result from either intramammary spread from a single primary tumor or multiple synchronous primary tumors; whereas others suggest that multiple breast carcinomas always arise from the same clone (6-8). Recently, Pietri and colleagues analyzed the biological characterization of a series of 113 multifocal/multicentric breast cancers (8) which were diagnosed over a 5-year period. The expression of estrogen (ER) and progesterone (PgR) receptors, Ki-67 proliferative index, expression of HER2 and tumor grading were prospectively determined in each tumor focus, and mismatches among foci were recorded. Mismatches in ER status were present in 5 (4.4%) cases and PgR in 18 (15.9%) cases. Mismatches in tumor grading were present in 21 cases (18.6%), proliferative index (Ki-67) in 17 (15%) cases and HER2 status in 11 (9.7%) cases. Interestingly, this heterogeneity among foci has led to 14 (12.4%) patients receiving different adjuvant treatments compared with what would have been indicated if we had only taken into account the biologic status of the primary tumor. This study therefore showed that differences in biological characteristics of multifocal/multicentric lesions play a crucial role in the adjuvant treatment decision making process. In this study, we will concentrate on a larger series of patients with multifocal invasive ductal breast cancer lesions. We aim at: 1. Evaluating the incidence of multifocality according to the different breast cancer molecular subtypes (ER-/HER2-, HER2+, ER+/HER2-). 2. Evaluating the incidence of multifocality in patients with hereditary breast cancer disease (presence of germline BRCA1 or BRCA2 mutations). Moreover, we would like to investigate if multifocal lesions with BRCA1 or BRCA2 mutations exhibit a characteristic combination of substitution mutation signatures and a distinctive profile of deletions as demonstrated recently by Nik-Zainal and colleagues (9). 3. Correlating multifocality with clinical information in order to define its influence on patients? survival (DFS and OS). 4. Carrying high coverage targeted gene sequencing of driver cancer genes and genes whose mutation is of therapeutic importance in order to compare clinically-relevant genetic differences between several multifocal breast cancer lesions. 5. Evaluating the impact of the distance between the different lesions on the clinical outcome but also on the genetic differences. 6. Comparing gene expression patterns between several multifocal breast cancer lesions and correlate them with the results of the targeted genes screen. 7. Characterizing the genomic and transcriptomic status of cancer related genes in metastatic lesions (local recurrence, positive lymph node or distant metastatic sites) from the same multifocal invasive ductal breast cancer patients in order to evaluate the consequence of genomic and transcriptomic heterogeneity of multifocal lesions on metastatic lesions. Multiple (multifocal/multicentric) breast carcinomas, especially when occurring in the same breast, represent a real challenge for both pathologists and clinicians in terms of identifying the cellular origin and the best therapeutic choice. This project has the potential to identify genetic/transcriptomic differences existing between several lesions constituting multifocal breast cancers, which in the routine clinical practice are usually considered to be homogeneous among them. We foresee validating significant results in a larger series of patients and this, in turn, could have a remarkable impact on the treatment and clinical management of multifocal breast cancers. Indeed, we hope to provide some evidence whether or not each focus matters in multifocal and multicentric breast cancer to define the adequate therapeutic approach, especially in the context of targeted therapies. The work to be done at Sanger will be target gene screen pooling of 1400 samples. Illumina HiSeq 2000; 908 bam,cram
EGAD00001000625 The main objective of this benchmark is the comparison of the full sequencing pipeline of different ICGC partners, including procedures, methods and performance of library preparation and whole-genome deep-sequencing. A secondary objective will be a follow-up comparison of data analysis pipelines for identification of germline and somatic variants subsequent to the results of the ICGC Somatic Variant Calling Pipeline Benchmark. Illumina HiSeq 2000; 2 bam
EGAD00001000626 Exome sequencing data for tumor and matched normal samples of the EGAS00001000495 project. Illumina HiSeq 2000; 114 fastq
EGAD00001000627 Transcriptome sequencing data of tumor and 10 matched normal samples of the EGAS00001000495 project Illumina HiSeq 2000; 68 fastq
EGAD00001000628 Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 66 bam
EGAD00001000630 In this study we will sequence the transcriptome of Verified Matched Pair Cancer Cell line tumour samples. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found. Illumina HiSeq 2000; 7 bam
EGAD00001000631 PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 4 bam
EGAD00001000632 AB SOLiD 4 System; 12 SOLiD_native_csfasta,SOLiD_native_qual,bam
EGAD00001000634 The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL), is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize the critical secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, accounting for at least 43% of genomic rearrangements and characterized by the presence of recombination signal sequence motifs near the breakpoints; incorporation of non-templated sequence at the junction and a ten-fold enrichment at promoters and enhancers of genes actively transcribed in early B-lineage development. Single-cell tracking shows that this mechanism is not restricted to one founder cell but is rather active throughout leukemic evolution. Integration of point mutation and rearrangement data identifies recurrent inactivation of ATF7IP and MGA as two new tumor suppressor genes.Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1 lymphoblasts, striking promoters and enhancers of the genes that normally control B-cell differentiation. Illumina HiSeq 2000; 2 bam
EGAD00001000635 The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL), is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize the critical secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, accounting for at least 43% of genomic rearrangements and characterized by the presence of recombination signal sequence motifs near the breakpoints; incorporation of non-templated sequence at the junction and a ten-fold enrichment at promoters and enhancers of genes actively transcribed in early B-lineage development. Single-cell tracking shows that this mechanism is not restricted to one founder cell but is rather active throughout leukemic evolution. Integration of point mutation and rearrangement data identifies recurrent inactivation of ATF7IP and MGA as two new tumor suppressor genes.Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1 lymphoblasts, striking promoters and enhancers of the genes that normally control B-cell differentiation. Illumina Genome Analyzer II;, Illumina HiSeq 2000; 50 bam,srf
EGAD00001000636 The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL), is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize the critical secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, accounting for at least 43% of genomic rearrangements and characterized by the presence of recombination signal sequence motifs near the breakpoints; incorporation of non-templated sequence at the junction and a ten-fold enrichment at promoters and enhancers of genes actively transcribed in early B-lineage development. Single-cell tracking shows that this mechanism is not restricted to one founder cell but is rather active throughout leukemic evolution. Integration of point mutation and rearrangement data identifies recurrent inactivation of ATF7IP and MGA as two new tumor suppressor genes.Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1 lymphoblasts, striking promoters and enhancers of the genes that normally control B-cell differentiation. Illumina Genome Analyzer II; 117 bam
EGAD00001000637 Insertion of processed pseudogenes is known to occur in the germline but has not previously been observed in somatic cells. Formation of pseudogenes could represent a new class of mutation in cancers and a new source of potential driver events. Illumina Genome Analyzer II;, Illumina HiSeq 2000; 4 bam
EGAD00001000638 Insertion of processed pseudogenes is known to occur in the germline but has not previously been observed in somatic cells. Formation of pseudogenes could represent a new class of mutation in cancers and a new source of potential driver events. Illumina HiSeq 2000; 20 bam
EGAD00001000639 Insertion of processed pseudogenes is known to occur in the germline but has not previously been observed in somatic cells. Formation of pseudogenes could represent a new class of mutation in cancers and a new source of potential driver events. Illumina HiSeq 2000; 3 bam
EGAD00001000640 Transcriptome studies in patients with rare genetic diseases can potentially aid in the interpretation of likely causal genetic variation through identification of altered transcript abundance and/or structure. RNA-Seq is the most sensitive assay for both investigating transcript structure and abundance The primary aim of this pilot project is to investigate to what degree integrating exome-Seq and RNA-Seq data on the same individual can accelerate the identification of causal alleles for rare genetic diseases. There are two main strands to this: (i) identifying which variants discovered in exome-seq appear to be having a functional impact on transcripts, and (ii) identifying transcript outliers, especially among known causal genes, that may not necessarily have a causal variant identified from exome sequencing. The latter may identify the presence of causal variants that lie far from coding regions (e.g. the formation of cryptic splice sites deep within introns, or loss of long range regulatory elements), which can be confirmed with further targeted genetic assays. Just over 50% of all disease-causing variants recorded in the Human Gene Mutation Database (HGMD) affect transcript structure and abundance (e.g. nonsense SNVs, essential splice site SNVs, frameshifting indels, CNVs). This pilot project will study RNA from lymphoblastoid cell-lines from 12 patients with primordial dwarfism syndromes, for 10 of these samples we have previously generate exome data as part of our collaboration with the group of Prof Andrew Jackson. The two remaining samples are positive controls where the causal mutation is known, and is known to affect transcript structure and/or abundance. Primordial dwarfism is a prime candidate for these RNA-seq studies because all known causal mutations to date have key roles in DNA replication and thus, unsurprisingly, the products of the causal genes are typically ubiquitously expressed. Each RNA will be sequenced, with two technical replicates (independent RT-PCR and libraries) per sample, and each replicate run in 1/2 of a HiSeq lane using 100bp paired reads. Samples preparation was as follows :The cells were grown to confluency, then pellets frozen at -80. RNA samples were prepared using the Qiagen RNeasy kit, then nanodropped and analyzed using the bioanalyzer to determine concentration and purity. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 24 bam
EGAD00001000641 DNA replication errors occurring in mismatch repair (MMR) deficient cells persist as mismatch mutations and predispose to a range of tumors. Here, we sequenced the first whole-genomes from MMR-deficient endometrial tumors. Complete Genomics;, Illumina HiSeq 2000; 44 CompleteGenomics_native,bam
EGAD00001000642 Illumina HiScanSQ; 2 bam
EGAD00001000643 Illumina HiScanSQ; 2 bam
EGAD00001000644 ICGC PedBrain DNA Methylation project Illumina HiSeq 2000; 42 fastq
EGAD00001000645 ICGC MMML-seq Data Freeze July 2013 whole genome sequencing 42 bam
EGAD00001000646 A selection of human cancers harbours somatic driver mutations in genes encoding histones, most notably childhood brain tumours with K27M substitutions of the histone 3.3 gene, H3F3A. We performed whole genome sequencing of the benign cartilage tumour, chondroblastoma, and targeted sequencing of histone 3.3 genes, H3F3A and H3F3B, in seven further skeletal tumour types. We identified an exceptionally high prevalence of novel histone 3.3 driver mutations at glycine 34 and at lysine 36. Histone 3.3 gene mutations were found in 91% in giant cell tumours of bone (48/53), mainly H3F3A G34W variants, and in 92% of chondroblastoma (73/79), predominantly K36M mutations in H3F3B. H3F3B is paralogous to the cancer gene H3F3A. However, H3F3B driver variants have not previously been reported in human cancer. Our observation demonstrate remarkable tumour-specificity of mutations, with respect to which histone 3.3 gene and residue is mutated, indicating that the advantage these mutations confer is tumour dependent. Moreover, tumour-specific mutation of H3F3A and H3F3B suggests, that although both genes encode identical proteins, they are likely non-redundant and employed differentially during skeletal development. Illumina HiSeq 2000; 14 bam
EGAD00001000647 We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls. Illumina HiSeq 2000; 110 bam,cram
EGAD00001000648 ICGC MMML-seq Data Freeze July 2013 transcriptome sequencing 31 bam
EGAD00001000650 ICGC MMML-seq Data Freeze July 2013 miRNA sequencing 52 bam
EGAD00001000652 Pulldown experiments will be performed on a number of patients with Myeloproliferative Neoplasms (MPN). The pulldown will be a bespoke design targeting known mutations, this pulldown will be sequenced and analysed to inform prevalence of mutations and to inform to the possibility of use as a diagnostic tool. Illumina HiSeq 2000; 1,036 bam
EGAD00001000653 This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work. Illumina HiSeq 2000; 10 bam,cram
EGAD00001000654 DATA FILES FOR BALL-PAX5 Illumina HiSeq 2000; 153 bam
EGAD00001000655 DATA FILES FOR Histone-NSD2_RNASeq Illumina HiSeq 2000; 8 bam
EGAD00001000656 FACS phenotype of 1629 Sardinian samples 1,629 phenotype_file
EGAD00001000657 DATA FILES FOR Histone Capture bams Illumina HiSeq 2000; 962 bam
EGAD00001000658 Changes in gene dosage are a major driver of cancer1, engineered from a finite, but increasingly well annotated, repertoire of mutational mechanisms2-6. These processes operate over levels ranging from individual exons to whole chromosomes, often generating correlated copy number alterations across hundreds of linked genes. An example of the latter is the 2% of childhood acute lymphoblastic leukemia (ALL) characterized by recurrent intrachromosomal amplification of megabase regions of chromosome 21 (iAMP21)7,8 To dissect the interplay between mutational processes and selection on this scale, we used genomic, cytogenetic and transcriptional analysis, coupled with novel bioinformatic approaches, to reconstruct the evolution of iAMP21 ALL. We find that individuals born with the rare constitutional Robertsonian translocation between chromosomes 15 and 21, rob(15;21)(q10;q10)c, have ~2700-fold increased risk of developing iAMP21 ALL compared to the general population. In such cases, amplification is initiated by chromothripsis involving both sister chromatids of the dicentric Robertsonian chromosome. In contrast, sporadic iAMP21 is typically initiated by breakage-fusion-bridge (BFB) events, often followed by chromothripsis or other rearrangements. In both sporadic and iAMP21 in rob(15;21)c individuals, the final stages of amplification frequently involve large-scale duplications of the abnormal chromosome. The end-product is a derivative chromosome 21 or a derivative originating from the rob(15;21)c chromosome, der(15;21), respectively, with gene dosage optimised for leukemic potential, showing constrained copy number levels over multiple linked genes. In summary, the constitutional translocation, rob(15;21)c, predisposes to leukemia through a novel mechanism, namely a propensity to undergo chromothripsis, likely related to its dicentric nature. More generally, our data illustrate that several cancer-specific mutational processes, applied sequentially, can co-ordinate to fashion copy number profiles over large genomic scales, incrementally refining the fitness benefits of aggregated gene dosage changes. Illumina Genome Analyzer II;, Illumina HiSeq 2000; 9 bam
EGAD00001000659 Illumina HiSeq 2000; 12 bam
EGAD00001000660 Analysis .bam files from HiSeq sequencing of Australian ICGC PDAC study samples, submitted 20130826 353 bam
EGAD00001000661 Bespoke validation experiments will be performed on ER+ Breast Cancer cases to confirm the presence of mutations found in whole genome sequencing. Illumina HiSeq 2000; 46 bam
EGAD00001000662 We propose to definitively characterise the somatic genetics of Triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. This study will use a bespoke bait set to pulldown regions of interest found in whole genome sequencing to validate mutations found. Illumina HiSeq 2000; 46 bam
EGAD00001000663 This study aims to re-sequence findings from whole genome studies using a bespoke pulldown method to validate mutations in those genomes sequenced. Illumina HiSeq 2000; 47 bam
EGAD00001000664 Whole Genome Seq: Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Paired-end RNA sequencing reads were mapped to the hg19 assembly of the human reference genome using BWA. Each ChIP-seq library was sequenced with two complete lanes on the Illumina HiSeq 2500 in the 101-bases paired-end rapid mode and aligned to hg19 using bwa. This resulted in the following coverage values (genome-wide, after deduplication, including all uniquely mapping reads): GBM103 macroH2A1: 17x H3K36me3: 20x MB59 macroH2A1: 11x H3K36me3: 11x 7 bam
EGAD00001000665 Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Sample derived from secondary myelodysplastic syndrome (MDS), arising after treatment for medulloblastoma in an 11-year old female Li-Fraumeni syndrome case (LFS-MB1; Rausch et al., 2012; matching WGS data available under EGAS00001000085). 1 bam
EGAD00001000666 HSC73_clone: Bone marrow mononuclear cells from the healthy 73 years old female were thawed and labeled with Alexa-Fluor 488-conjugated anti-CD34 (581, Biolegend), Alexa-Fluor 700-conjugated anti-CD38 (HIT2, eBioscience), a cocktail of APC-conjugated lineage antibodies consisting of anti-CD4 (RPA-T4), anti-CD8 (RPA-T8), anti-CD11b (ICRF44), anti-CD20 (2H7), anti-CD56 (B159, all BD Biosciences), anti-CD14 (61D3), anti-CD19 (HIB19) and anti-CD235a (HIR2, all eBiocience) and 1 micro-gram/ml propidium iodide (Sigma). Using a BD FACSAria cell sorter, single Lin-CD34+CD38-PI- cells were individually sorted into low-adhesion 96-well tissue culture plates (Corning) containing 100micro-litre of StemSpan Serum-Free Expansion Medium (Stemcell technologies) supplemented with 100ng/ml of human SCF and FLT-3L, 50ng/ml of human TPO, 20ng/ml of human IL-3, IL-6 and G-CSF (all cytokines from Peprotech) and 50U/ml of penicillin and 50μg/ml of streptomycin (Sigma). Cells were incubated at 37 degrees C in a humidified atmosphere with 5% CO2 in air. After 5 days in culture, another 100micro litres of cytokine-containing medium were added. 13 days after seeding, clones B6 and G2 had expanded to approx. 105 cells and were selected for whole genome sequencing (2x101bp, paired-end, Illumina HiSeq2500) after tagmentation-based library preparation (see Extended Experimental Procedures) for clone B6 and standard library preparation for clone G2. For germline-control ~106 unsorted bone marrow mononuclear cells from the same donor were used for sequencing. An average of 30-fold sequence coverage for each the clones and the matching control were obtained. L4clone: A progenitor cell clone was raised from a peripheral blood sample of the 39 year old healthy female. Frozen peripheral blood mononuclear cells (PBMCs) were isolated from 2 ml heparinised peripheral blood via Ficoll Paque density centrifugation. A methylcellulose assay was performed as described earlier (Weisse et al., 2012). In brief, non-adherent mononuclear cells were incubated in the presence of the recombinant human cytokines IL-3, IL-5 and GM-CSF (R&D systems) over 14 days to induce colony formation. Colonies were detected under an inverted light microscope, and plucked by a pipette when colonies had approximately 10,000 cells/CFU. Each colony was washed three times in PBS and finally frozen as a cell pellet in -80 degrees C. Genomic DNA was isolated using the QIAamp DNA micro kit according to the instructions of the manufacturer (Qiagen, Hilden, Germany). Whole genome sequencing (2x101bp, paired-end, Illumina HiSeq2500) was performed for colony 4 after tagmentation-based library preparation and resulted in 15-fold sequence coverage for each the colony and the matching whole blood. 5 bam
EGAD00001000667 Illumina HiSeq 2000; 72 bam
EGAD00001000669 High-grade serous ovarian cancer (HGSC) is characterized by poor outcome, often attributed to the emergence of treatment-resistant subclones. We sought to measure the degree of genomic diversity within primary, untreated HGSCs to examine the natural state of tumour evolution prior to therapy. We performed exome sequencing, copy number analysis, targeted amplicon deep sequencing and gene expression profiling on 31 spatially and temporally separated HGSC tumour specimens (six patients), including ovarian masses, distant metastases and fallopian tube lesions. We found widespread intratumoural variation in mutation, copy number and gene expression profiles, with key driver alterations in genes present in only a subset of samples (eg PIK3CA, CTNNB1, NF1). On average, only 51.5% of mutations were present in every sample of a given case (range 10.2 to 91.4%), with TP53 as the only somatic mutation consistently present in all samples. Complex segmental aneuploidies, such as whole-genome doubling, were present in a subset of samples from the same individual, with divergent copy number changes segregating independently of point mutation acquisition. Reconstruction of evolutionary histories showed one patient with mixed HGSC and endometrioid histology, with common aetiologic origin in the fallopian tube and subsequent selection of different driver mutations in the histologically distinct samples. In this patient, we observed mixed cell populations in the early fallopian tube lesion, indicating that diversity arises at early stages of tumourigenesis. Our results revealed that HGSCs exhibit highly individual evolutionary trajectories and diverse genomic tapestries prior to therapy, exposing an essential biological characteristic to inform future design of personalized therapeutic solutions and investigation of drug-resistance mechanisms Illumina Genome Analyzer; 25 bam
EGAD00001000670 A potential and very serious side effect of treating IBD with antiTNFa therapies (the current gold standard) is the development of systemic lupus erythematosis (SLE). This side effect is rare and unpredictable. Out of several thousand cases having received treatment, the University of Calgary have accumulated 12 individuals with full phenotyping and novel serological antibody discovery panel data. We propose to exome sequence these samples in an effort to identify rare highly-penetrant variants that could be underlying this severe phenotype. Illumina HiSeq 2000; 15 bam
EGAD00001000671 Primary sclerosing chloangitis is a rare autoimmune disease of the liver (prevalence = 10/100,000) with a mean age of onset of 40 years. We are currently undertaking GWAS and immunochip experiments to identify loci underlying PSC susceptibility. Through our collaborators at the University of Calgary we have access to DNA from three parent-offspring trios where the children required liver transplants due to PSC before the age of 9. These are extremely rare cases indeed and we believe that exome-sequencing represents a powerful means of identifying the causal mutation underlying this severe phenotype. Illumina HiSeq 2000; 5 bam
EGAD00001000672 Whole-genome Bisulfite sequencing of two multiple myeloma samples and one pooled sample of plasma cells. Illumina HiSeq 2000; 3 bam
EGAD00001000673 WGBS-seq for monocytes and neutrophils Illumina HiSeq 2000; 12 bam,readme_file
EGAD00001000674 DNaseI-seq for monocytes Illumina HiSeq 2000; 4 fastq
EGAD00001000675 RNA-seq for monocytes and neutrophils Illumina HiSeq 2000; 12 fastq
EGAD00001000676 ChIP-seq for monocytes and neutrophils 14
EGAD00001000677 Genome-wide analysis of H3K27me3 occupancy and DNA methylation in K27M-mutant and H3.3-WT primary pediatric high-grade gliomas (pHGGs) as well as pediatric pHGG cell lines. The study aims to elucidate the connection between K27M-induced H3K27me3 reduction and changes in DNA methylation as well as gene expression. Illumina HiSeq 2000; 19 fastq
EGAD00001000678 FFPE CPA accreditation of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing. Illumina HiSeq 2000; 341 bam,cram
EGAD00001000679 A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients. Illumina HiSeq 2000; 107 bam
EGAD00001000680 Single end short-read (50 bp) SOLiD 4 sequencing data for 300 individuals, constituting 100 patient-parent trios. For more details please read; http://www.nejm.org/doi/full/10.1056/NEJMoa1206524 AB SOLiD 4 System; 300 bam
EGAD00001000688 In this study we performed ultra deep sequencing of genes associated with anti-EGFR resistance, such as KRAS, BRAF, PIK3CA, and EGFR in 17 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy. Illumina MiSeq; 25 bam
EGAD00001000689 Whole genome DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of 3 men. We found that mutations were already present at high levels in morphologically normal tissue distant from the cancer suggesting clonal expansion. A subgroup of these mutations are present in adjacent cancer. A single nodule of cancer may contain multiple, predominantly genetically independent cancer clones each harbouring distinct ERG fusions. Separate lineages of cancer were in some cases connected by common low frequency mutations. Together our observations support the existence of a genetic field-effect underlying carcinogenesis The presence of a field effect, and of multiple cancer lineages within the same prostate pose serious questions regarding the effectiveness of focal therapy in those with a long life expectancy and imply that predicting future behaviour based on genetic analysis of single tumour sample may be unreliable. For each of three different prostates, multiple tumour samples (4, 5, and 3 depending on the case) and one normal tissue sample were whole genome sequenced with a matched blood sample using the Illumiuna HiSeq platform. Tumour samples were sequenced to a target depth of 50X and normals and blood to a target depth of 30X. Illumina HiSeq 2000; 18 bam
EGAD00001000691 Whole genome sequencing data from Illumina platform were generated using 10 human cancer cell lines and 2 primary tumor samples. Nine of these samples contained fragments of human papillomavirus (HPV). 12 bai,bam
EGAD00001000692 Files associated with the dataset: HS1626.bam, HS1484.bam, HS1483.bam, HS1482.bam, HS1481.bam, HS1480.bam, HS1479.bam, HS1478.bam, A13805.bam, A13800.bam, A13799.bam, A05253.bam, A05252.bam, A13806.bam Illumina Genome Analyzer II;, Illumina HiSeq 2000;, Illumina Genome Analyzer; 12 bam
EGAD00001000693 The genetic consequences of cellular transformation by Epstein-Barr-Virus were assessed by comparing whole genome sequences of the original genome (before transformation) and the genome after transformation. 2 bam,vcf
EGAD00001000694 This is an ongoing project and continuation to all the sequencing we have been doing over the last few years. We have some additional families and probands with syndromes of insulin resistance not previously sequenced within uk10k or other core funded projects. We would like to complete the sequencing in all of the good quality families and probands we have, this would require another ~50 samples to be WES sequenced. This cohort has already proven to be a rich source of interesting findings with papers in Science and Nature genetics. Illumina HiSeq 2000; 68 bam,cram
EGAD00001000695 DATA FILES FOR SJLGG Illumina HiSeq 2000; 46 bam
EGAD00001000696 The Ethiopian area stands among the most ancient ones ever occupied by human populations and their ancestors. Particularly, according to archaeological evidences, it is possible to trace back the presence of Hominids up to at least 3 million years ago. Furthermore, the present day human populations show a great cultural, linguistic and historic diversity which makes them essential candidate to investigate a considerable part of the African variability. Following the typing of 300 Ethiopian samples on Illumina Omni 1M (see Human Variability in Ethiopia project, previously approved by the Genotyping committee) we now have a clearer idea on which populations living in the area include the most of the diversity. This project therefore aims to sequence the whole genome of 300 individuals at low (4-8x) depth belonging to the six most representative populations of the Ethiopian area to produce a unique catalogue of variants peculiar of the North East Africa. Furthermore 6 samples (one from each population) will also be sequenced at high (30x) depth to ensure full coverage of the diversity spectrum. The retrieved variants will be of great help in evaluating the demographic dynamics of those populations as well as shedding light on the migrations out of Africa. Illumina HiSeq 2000; 5 bam
EGAD00001000697 Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 90 bam
EGAD00001000698 Illumina HiSeq sequence data (with >80x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. The whole exome sequencing data of 20 SHH medulloblastomas from phs000504.v1.p1 dataset has been used in our study on SHH medulloblastomas: http://www.ncbi.nlm.nih.gov/projects/gap/cgi- bin/study.cgi?study_id=phs000504.v1.p1 4 bam
EGAD00001000699 Illumina HiSeq sequence data (with >80x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Illumina HiSeq 2000; 78 bam
EGAD00001000702 Complete set of bam files associated with study EGAS00001000622 190 bam
EGAD00001000703 SCLC - Whole genome sequencing data Publication Peifer et al., 2012, Nature Genetics Illumina Genome Analyzer IIx; 29 bam
EGAD00001000704 Illumina HiSeq 2000; 44 bam
EGAD00001000705 Whole genome sequencing of 20 tumour and normal pairs of diffuse intrinsic pontine glioma (DIPG) Illumina HiSeq 2000; 40 bam
EGAD00001000706 Whole exome sequencing of 6 tumour and normal pairs of diffuse intrinsic pontine glioma (DIPG) Illumina HiSeq 2000; 12 bam
EGAD00001000707 Discovery of resistance mechanisms to the BRAF inhibitor vemurafenib in metastatic BRAF mutant melanoma by massively-parallel sequencing of tumour samples. Comparison of genomic characteristics of pretreatment 'sensitive' to recurrence 'resistant' tumours to identify the genetics of drug resistance. Illumina HiSeq 2000; 57 cram
EGAD00001000708 AZIN1 amplicon sequencing data of the EGAS00001000495 project. 454 GS FLX Titanium; 69 fastq
EGAD00001000709 Dataset of CageKid Blood DNA samples 95 bam
EGAD00001000710 Whole Genome Bisulfite-seq of four B cell samples Illumina HiSeq 2000; 4 bam
EGAD00001000711 Illumina HiSeq 2000; 42 bam
EGAD00001000712 Illumina HiSeq 2000; 72 bam
EGAD00001000713 Illumina HiSeq 2000; 12 bam
EGAD00001000714 102 bam
EGAD00001000715 Exome sequencing was performed for paired tumor/normal samples from patients with corticotropin-independnet Cushing's syndrome. Tumor DNA was extracted from adrenocortical adenomas and normal DNA was extracted from adjacent adrenal tissues or periphral blood. Illumina HiSeq 2000; 16 bam
EGAD00001000716 RNAseq data, Publication Fernandez-Cuesta et al., 2014, CD74-NRG1 fusions in lung adenocarcinoma Illumina HiSeq 2000; 25 fastq
EGAD00001000717 Dataset of CageKid Tumor DNA samples 95 bam
EGAD00001000718 Dataset of CageKid Tumor RNA samples 91 bam
EGAD00001000719 Dataset of CageKid Normal RNA samples 45 bam
EGAD00001000720 Dataset of CageKid tumor-normal paired RNA samples 90 bam
EGAD00001000721 This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work. Illumina HiSeq 2000; 20 bam,cram
EGAD00001000722 Extension of angiosarcoma whole genome sequencing study Illumina HiSeq 2000; 8 cram
EGAD00001000723 Relative Spatial Homogeneity of Embryonal Brain Tumors of Childhood 42 bam
EGAD00001000724 Illumina HiSeq 2000; 68 bam
EGAD00001000725 This dataset contains RNA sequencing data for 675 cancer cell lines. RNA libraries were made with the TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer protocol. The libraries were sequenced on an Illumnia HiSeq 2000 Illumina HiSeq 2000; 675
EGAD00001000726 In total 30 Acute Myeloid Leukemias with an acquired inv(3)(q21q26) or t(3;3)(q21;q26) have been characterized by whole transcriptome sequencing (RNA-Seq). The 3q-aberration leads to overexpression of the proto-oncogene EVI1, but the mechanism of overexpression has thus far been elusive. The RNA-Seq was integral in determining the precise enhancer inducing the overexpression and led to other key discoveries. Illumina HiSeq 2500; 30 fastq
EGAD00001000727 Targeted resequencing on the specific regions chr3:126036241-130672290 and chr3:157712147-175694147 in hg19 centered on the chromosomal regions 3q21 and 3q26 respectively. The focus lies on the detection of the exact breakpoints in Acute Myeloid Leukemia (AML) patients having acquired a inv(3)(q21q26) or t(3;3)(q21;q26). This dataset contains all information to detect all structural variants contained within these regions, including the 3q-aberrations inducing the overexpression of the proto-oncogene EVI1. Illumina HiSeq 2500; 38 fastq
EGAD00001000728 Low coverage whole genome sequencing of samples from individuals from Friuli Venezia Giulia, an Italian genetic isolate population. Illumina HiSeq 2000; 199 bam
EGAD00001000729 The Val Borbera is a region characterized by low iodine and high prevalence of thyroid disorders, the commonest endocrine disorders in the general population. About 30% of the participants of the Val Borbera Project were affected by such disorders and were characterized by several parameters, TSH level, anti TPO antibodies, echography, family origin. Individuals with extreme phenotypes were identified and could be clustered based on family origin and genotype. We propose to exome sequence 6 of them, affected with true goiter, at high dept (40-60x) to obtain information on exonic rare variants. Due to the family structure and to the availability of whole genome sequence information on 110 individuals from the isolated population we expect to be able to identify putative causative variants for thyroid disorders that may be studied in the remaining affected individuals. Illumina HiSeq 2000; 8 bam
EGAD00001000730 The VBSEQ project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits. Up to 100 Val Borbera samples will be sequenced to a 6x depth. Illumina HiSeq 2000; 110 bam
EGAD00001000731 This study includes Phase 2 whole-genome sequencing data (at 4x depth)of 100 individuals from an Italian genetic isolate population (Val Borbera, abbreviated VBI) of the Italian Network of Genetic Isolates (INGI). The INGI-VBI_SEQ2 project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits. Illumina HiSeq 2000; 100 bam
EGAD00001000732 RNA sequencing to validate findings of somatic pseudogenes acquired during cancer development Illumina HiSeq 2000; 3 cram
EGAD00001000733 The dataset entails 48 RRBS libraries of 24 siblings. 24 individuals are conceived during the Dutch Famine, a severe 6 month famine at the end of World War 2. A same sex sibling was added as a control, allowing partial matching for (early) familial environment and genetics. Illumina Genome Analyzer IIx; 48 bam
EGAD00001000734 Paired end Illumina sequencing of whole exomes of multiple tumour regions. Illumina HiSeq 2000;, Illumina HiSeq 2500;, Illumina Genome Analyzer IIx; 88 bam
EGAD00001000735 Here we present the genomes of three secondary angiosarcomas Illumina HiSeq 2000; 7 bam
EGAD00001000737 Whole exome sequencing data from 30 donors (46 tumors and 30 non-tumoral whole exome sequencing, paired-end, HiSeq 2000, Illumina) collected by the Inserm U674, PI Jessica Zucman-Rossi - Institut National du Cancer (INCa), PI Fabien Calvo, France. Illumina HiSeq 2000; 76 bam
EGAD00001000738 Extension of angiosarcoma whole genome sequencing study Illumina HiSeq 2000; 4 cram
EGAD00001000739 We aim to provide a powerful reference set for genome-wide association studies (GWAS) in African populations. Our pilot study to sequence 100 individuals each from Fula, Jola, Mandinka and Wollof from the Gambia to low coverage has been completed - this first part of the main effort will make available low coverage WGS data for 400 individuals from multiple ethnic groups in Burkina Faso, Cameroon, Ghana and Tanzania. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 57 cram
EGAD00001000740 UK10K_COHORT_ALSPAC REL-2012-06-02: Low-coverage whole genome sequencing; variant calling, genotype calling and phasing Illumina HiSeq 2000 (ILLUMINA) 2,320
EGAD00001000741 UK10K_COHORT_TWINSUK REL-2012-06-02: Low-coverage whole genome sequencing; variant calling, genotype calling and phasing Illumina Genome Analyzer II;, Illumina HiSeq 2000; 1,854
EGAD00001000743 These files contain a total of 20.4M SNVs and the complete information output by the GATK UnifiedGenotyper v1.4 on all 767 GoNL samples. These calls are not trio-aware and all genotypes were reported regardless of their quality. Both filtered and passing calls are reported in these files. Filtered calls include (1) calls failing our VQSR threshold and (2) calls in the GoNL inaccessible genome. 767 vcf
EGAD00001000744 The samples in this panel come from 250 families: 248 parents-child trios and 2 parent-child duos. As the children do not provide additional haplotypes or population information, they were excluded from the panel. The samples present in the release are composed of 248 couples, 2 single individuals and 1 sample composed from the 2 haplotypes from the duo's children transmitted by their missing parent. The composed sample is named gonl-220c_223c. The files contain a total of 18.9M SNVs and 1.1M INDELs in autosomal chromosomes. They were generated by phasing/imputing the SNVs (a) and INDELs (b) using MVNCall. Only sites passing filters are reported. Sites filtered as part of the GoNL inaccessible genome were kept (but flagged as filtered) and still may contain true positive calls but should be used with care as they are located in parts of the genome that are less well captured (systematic under or over-covered or low-mapping quality) 499 vcf
EGAD00001000745 Data supporting the paper Transcriptional diversity during lineage commitment of human blood progenitors Illumina HiSeq 2000; 26 bam,phenotype_file,readme_file
EGAD00001000746 Fernandez-Cuesta et al., RNAseq data Pipline Illumina HiSeq 2000; 25 fastq
EGAD00001000747 Genomic libraries will be generated from total genomic DNA derived from 4000 samples with Acute Myeloid Leukaemia. Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 64 Samples will be individually barcoded and subjected to up to one lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing. Illumina HiSeq 2000; 2,734 cram
EGAD00001000748 In this study we performed whole genome sequencing of plasma DNA (plasma-Seq) of 19 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy. We demonstrated that development of resistance to anti-EGFR therapies is frequently associated with focal amplifications of KRAS, MET, and ERBB2. We also showed that focal KRAS amplifications can be acquired in tumor genomes of patients under cytotoxic chemotherapy. Furthermore, we provide evidence that specific chromosomal polysomies, such as overrepresentations of 12p and 7p, harboring KRAS and EGFR, respectively, determine responsiveness to anti-EGFR therapy. Illumina MiSeq; 19 fastq
EGAD00001000749 Illumina HiSeq 2000; 12 bam
EGAD00001000750 UK10K_RARE_FIND REL-2013-10-31 variant calling Illumina HiSeq 2000; 1,151 tabix,vcf
EGAD00001000752 UK10K_RARE_CILWG REL-2013-09-09 Illumina HiSeq 2000; 4 tabix,vcf
EGAD00001000753 UK10K_RARE_FINDWG REL-2013-09-09 Illumina HiSeq 2000; 4 tabix,vcf
EGAD00001000754 UK10K_RARE_NMWG REL-2013-09-09 Illumina HiSeq 2000; 5 tabix,vcf
EGAD00001000755 UK10K_OBESITY_GS UK10K_EXOME_EXTRAS Illumina HiSeq 2000; 5 tabix,vcf
EGAD00001000756 UK10K_OBESITY_SCOOP UK10K_EXOME_EXTRAS Illumina HiSeq 2000; 1 tabix,vcf
EGAD00001000757 UK10K_RARE_SIR UK10K_EXOME_EXTRAS Illumina HiSeq 2000; 2 tabix,vcf
EGAD00001000758 dataset for BGI bladder cancer project Illumina Genome Analyzer II; 198 fastq
EGAD00001000759 Illumina HiSeq 2000; 86 bam,fastq
EGAD00001000760 dataset for esophageal cancer, 17pairs for whole-genome sequencing and 71pairs for whole-exome sequencing Illumina HiSeq 2000; 176 fastq
EGAD00001000761 In order to establish copy number profiles from the various samples we prepared libraries and subjected them to whole-genome sequencing at a shallow sequencing depth (0.1x) Illumina MiSeq; 14 fastq
EGAD00001000762 We utilized exome sequencing for DNA obtained from saliva (germline DNA) and the four spatially separated tumor foci and 3 corresponding lymph node metastases Illumina HiSeq 2000; 8 fastq
EGAD00001000763 We used targeted deep sequencing to accurately establish the allele frequencies of the mutations identified by exome sequencing Illumina MiSeq; 23 bam
EGAD00001000764 Adrenocortical carcinomas (ACC) are aggressive cancers originating in the cortex of the adrenal glands. Despite the overall poor prognosis, ACC outcome is heterogeneous. CTNNB1 and TP53 mutations are frequent in these tumors, but the complete spectrum of genetic changes remains undefined. Exome sequencing and SNP array analysis of 45 ACC revealed recurrent alterations in known drivers (CTNNB1, TP53, CDKN2A, RB1, MEN1) and genes not previously reported to be altered in ACC (ZNRF3, DAXX, TERT and MED12), which were validated in an independent cohort of 77 ACC. The cell-surface transmembrane E3 ubiquitin ligase ZNRF36 was the gene the most frequently altered (21%), and appears as a potential novel tumor suppressor gene related to the ß-catenin pathway. Our integrated genomic analyses led to the identification of two distinct molecular subgroups with opposite outcome. The C1A group of poor outcome ACC was characterized by numerous mutations and DNA methylation alterations, whereas the C1B group with good prognosis displayed a specific deregulation of two miRNA clusters. Thus, aggressive and indolent ACC correspond to two distinct molecular entities, driven by different oncogenic alterations. Illumina HiSeq 2000; 45 bam
EGAD00001000769 We aim to provide a powerful reference set for genome-wide association studies (GWAS) in African populations. Our pilot study to sequence 100 individuals each from Fula, Jola, Mandinka and Wollof from the Gambia to low coverage has been completed - this first part of the main effort will make available low coverage WGS data for 400 individuals from multiple ethnic groups in Burkina Faso, Cameroon, Ghana and Tanzania. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 38 cram
EGAD00001000770 We aim to provide a powerful reference set for genome-wide association studies (GWAS) in African populations. Our pilot study to sequence 100 individuals each from Fula, Jola, Mandinka and Wollof from the Gambia to low coverage has been completed - this first part of the main effort will make available low coverage WGS data for 400 individuals from multiple ethnic groups in Burkina Faso, Cameroon, Ghana and Tanzania. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 32 cram
EGAD00001000771 We aim to provide a powerful reference set for genome-wide association studies (GWAS) in African populations. Our pilot study to sequence 100 individuals each from Fula, Jola, Mandinka and Wollof from the Gambia to low coverage has been completed - this first part of the main effort will make available low coverage WGS data for 400 individuals from multiple ethnic groups in Burkina Faso, Cameroon, Ghana and Tanzania. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 80 bam,cram
EGAD00001000772 We aim to provide a powerful reference set for genome-wide association studies (GWAS) in African populations. Our pilot study to sequence 100 individuals each from Fula, Jola, Mandinka and Wollof from the Gambia to low coverage has been completed - this first part of the main effort will make available low coverage WGS data for 400 individuals from multiple ethnic groups in Burkina Faso, Cameroon, Ghana and Tanzania. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 77 cram
EGAD00001000773 We aim to provide a powerful reference set for genome-wide association studies (GWAS) in African populations. Our pilot study to sequence 100 individuals each from Fula, Jola, Mandinka and Wollof from the Gambia to low coverage has been completed - this first part of the main effort will make available low coverage WGS data for 400 individuals from multiple ethnic groups in Burkina Faso, Cameroon, Ghana and Tanzania. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 90 cram
EGAD00001000774 This study includes whole-genome sequencing data (at 4x depth) of 100 individuals from an Italian genetic isolate population (Carlantino, abbreviated CARL) of the Italian Network of Genetic Isolates (INGI). The INGI-CARL_SEQ project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits. Illumina HiSeq 2000; 106 cram
EGAD00001000775 Whole exome sequencing of 41 melanomas and normal DNA from Braf mutant mice: 15 tumours from UV exposed mice, 15 tumours from non-exposed mice and 11 from UV exposed, sunscreen-protected mice. Illumina HiSeq 2000; 80 bam
EGAD00001000776 UK10K_COHORT_IMPUTATION REL-2012-06-02: imputation reference panel (20140306); Merged UK10K+1000Genomes Phase 3 imputation reference panel added (20160420) Illumina HiSeq 2000; 3,781 other,readme_file,bam
EGAD00001000777 Dataset contains MeDIP-Seq, MRE-Seq and H3K4me3 ChIP-Seq data on 5 GBM patients. 16 bam
EGAD00001000779 AB SOLiD 4 System; 2 bam
EGAD00001000780 Illumina HiSeq 2000; 18 fastq
EGAD00001000781 Whole genome, high coverage, sequencing of 128 Ashkenazi Jewish controls 128 vcf
EGAD00001000782 Whole-genome sequencing was performed by Illumina Inc (San Diego, CA). Libraries were constructed with ~300bp insert length and paired-end 100bp reads were sequenced on Illumina HiSeq2000. Illumina HiSeq 2000;ILLUMINA 190
EGAD00001000783 Genomic libraries will be generated from total genomic DNA derived from 200+ patients with childhood Transient Myeloproliferative Disorder (TMD) and or Acute Megakaryocytic Leukemia (AMKL) as well some matched constitutional samples (n < 50 ). Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 96 Samples will be individually barcoded and subjected to up to two lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing. Illumina HiSeq 2000; 400 cram
EGAD00001000784 This study aims to target capture sequence regions of interest from DNA derived from breast cancer patients who received neo-adjuvant chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved. Illumina HiSeq 2000; 242 cram
EGAD00001000785 We propose to definitively characterise the somatic genetics of a selection of rare bone cancers through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. Illumina HiSeq 2000; 33 bam,cram
EGAD00001000786 We are interested in the contribution mutations in the Shelterin complex protein POT1 may have to the development of melanoma. We have identified a patient who carries a splice site mutation in POT1 and as part of our analysis of this gene we aim to sequence the transcriptome of this patient to see how this mutation influences splicing. RNA has been obtained from lymphocytes collected from the patient. Illumina MiSeq; 1 cram
EGAD00001000789 UK10K_COHORT_ALSPAC REL-2012-06-02: Phenotype data 1,927 phenotype_file,readme_file
EGAD00001000790 UK10K_COHORT_TWINSUK REL-2012-06-02: Phenotype data 1,854 phenotype_file,readme_file
EGAD00001000791 Exome sequencing of familial and sporadic small cell cancer of ovary cases. Illumina HiSeq 2000;, Illumina HiSeq 2500; 16 fastq
EGAD00001000792 Whole exome sequencing of paediatric glioblastoma with mutations reported in the manuscript: Mutations in ACVR1, FGFR1 and TP53 associate with tumor location in histone H3 K27M pediatric midline high-grade astrocytoma Illumina HiSeq 2000; 38 fastq
EGAD00001000794 Small cell carcinoma of the ovary of hypercalcemic type (SCCOHT) is an extremely rare, aggressive cancer affecting children and young women. We identified germline and somatic inactivating mutations in the SWI/SNF chromatin-remodeling gene SMARCA4 in 75% (9/12) of SCCOHT patients in addition to SMARCA4 protein loss in 82% (14/17) of SCCOHT tumors, but in only 0.4% (2/485) of other primary ovarian tumors. These data implicate SMARCA4 in SCCOHT oncogenesis. Illumina HiSeq 2000; 11 bam
EGAD00001000795 Fernandez-Cuesta et al, 2014, Nature Communication, RNA Sequencing data set Illumina HiSeq 2000; 69 fastq
EGAD00001000796 This project aims to study at least 90 exomes from families with congenital heart disease. The samples have been selected in Leuven in collaboration with Koen Devriendt. Ethic approval has been sought for in Leuven, Belgium and a HDMMC agreement for submitting these samples is in place at the WTSI. The phenotype we wil primarily focus our analysis is severe Left Ventricular Outflow Tract Obstructions (LVOTO) and Atrioventricular Septal Defect (AVSD). The indexed Agilent whole exome pulldown libraries will be sequenced on 75bp PE HiSeq (Illumina). Illumina HiSeq 2000; 167 bam
EGAD00001000797 This project aims to study at least 90 exomes from families with congenital heart disease. The samples have been selected at the Royal, Brompton Hospital in collaboration with Stuart Cook and Piers Daubeney. Ethic approval has been sought for in the UK and a HDMMC agreement for submitting these samples is in place at the WTSI. The phenotype we wil primarily focus our analysis is severe Left Ventricular Outflow Tract Obstructions (LVOTO) and Atrioventricular Septal Defect (AVSD). The indexed Agilent whole exome pulldown libraries will be sequenced on 75bp PE HiSeq (Illumina). Illumina HiSeq 2000; 48 bam
EGAD00001000798 In order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs but it is unclear whether some cell types carry through fewer mutations through reprogramming (either due to mutations present in the primary cells, or mutations accumulated during reprogramming). Through in depth analysis of hiPSCs generated from different somatic cells, it will be possible to assess the variation in genetic stability of different cell types. Illumina MiSeq;, Illumina HiSeq 2000; 28 bam
EGAD00001000799 Atrio-ventricular septal defects (AVSD) are a specific form of congenital heart structural defect that result from abnormal or inadequate fusion of endocardial cushions during cardiac development. This project is focused on identifying rare coding variation that substantially increases risk of AVSD, by exome sequencing of AVSD patients and some of their family members, and comparing to control datasets from other sources. The exome sequencing is performed using Agilent SureSelect 50Mb exome v3 and Hiseq 75bp paired reads with an mean sequencing coverage target of 50X. Illumina HiSeq 2000; 95 bam
EGAD00001000800 This project aims to study exomes from families and trios with congenital heart disease (CHD). The samples have been collected under the Competence Network - Congenital Heart Defects in Berlin, Germany. The phenotypes are mainly left ventricular outflow obstruction (aortic stenosis, bicuspd aortic valve disease coarctation and hypoplastic left heart), but will also include samples with hypoplastic right heart and atrioventricular septal defects. We will perform whole exome sequencing using Agilent sequence capture and Illumina HiSeq sequencing. Illumina HiSeq 2000; 406 bam,cram
EGAD00001000802 UK10K_RARE_CILWG REL-2013-03-06 Illumina HiSeq 2000; 2 tabix,vcf
EGAD00001000803 UK10K_RARE_FINDWG REL-2013-03-06 Illumina HiSeq 2000; 2 tabix,vcf
EGAD00001000804 UK10K_RARE_NMWG REL-2013-03-06 Illumina HiSeq 2000; 1 tabix,vcf
EGAD00001000805 UK10K_RARE_THYWG REL-2013-03-06 Illumina HiSeq 2000; 2 tabix,vcf
EGAD00001000806 Whole Genome Sequencing (WGS) for St. Jude High Grade Glioma (HGG) study Illumina HiSeq 2000 (ILLUMINA) 63 bam
EGAD00001000807 Whole Exome Sequencing (WES) for St. Jude High Grade Glioma (HGG) study Illumina HiSeq 2000; 148 bam
EGAD00001000808 RIKEN collection WGS reads for 321 HCC and blood matched samples from 158 donors submitted to ICGC for release 15 Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 321 fastq
EGAD00001000809 RIKEN collection WGS reads for 61 liver cancer and matched blood samples from 30 donors displaying biliary phenotype Illumina HiSeq 2000; 61 fastq
EGAD00001000810 Dataset for whole exome sequencing of 49 tumor-blood pairs and transcriptome sequencing of 44 tumors for adrenocortical tumors Illumina HiSeq 2000; 106 fastq
EGAD00001000811 Whole exome sequencing of 6 HCCs and matched background liver in children with bile salt export pump deficiency. Illumina HiSeq 2000; 12 fastq
EGAD00001000812 Sequencing of 350 cancer genes in BC samples from patients treated with either Epirubicin or Paclitaxel monotherapy in the neoadjuvant setting. Illumina HiSeq 2000; 364 cram
EGAD00001000813 Fernandez-Cuesta et al., 2014, Nature Communication, Whole genome sequencing was performed using a read length of 2x100 bp for all samples. On average, 110 Gb of sequence were produced per sample, aiming a mean coverage of 30x for both tumour and matched normal. Illumina HiSeq 2000; 29 bam
EGAD00001000814 Whole genome alignments of DIPG patients 40 bam,phenotype_file
EGAD00001000815 Exome-seq, RNA-Seq, SNP array profiling of gastric tumor samples. Illumina HiSeq 2000; 102 fastq
EGAD00001000816 ICGC medulloblastoma whole genome sequencing data, ICGC release 16 44 bam
EGAD00001000817 Alternative splicing plays critical roles in differentiation, development, and cancer (Pettigrew et al., 2008; Chen and Manley, 2009). The recent identification of specific spliceosome inhibitors has generated interest in the therapeutic potential of targeting this cellular process (van Alphen et al., 2009). Using an integrated genomic approach, we have identified PRPF6, an RNA binding component of the pre-mRNA spliceosome, as an essential driver of oncogenesis in colon cancer. Importantly, PRPF6 is both amplified and overexpressed in colon cancer, and only colon cancer cells with high PRPF6 levels are sensitive to its loss. Our data clearly point to an important role for PRPF6 in colon cancer growth and suggest that a better understanding of its role in alternative splicing in colon cancer is warranted. To determine the specific alternative splice forms that PRPF6 regulates in colon cancer, we plan three experiments: 1. The first involves knocking down expression of PRPF6 in two different cancer cell lines with 3 different siRNAs, and then completing RNA-seq to determine the gene expression changes that occur relative to a non-targeting control siRNA. Because of the role for PRPF6 in pre-mRNA splicing, we especially want to quantify the changes in splice-specific forms of all genes genome-wide to identify genes whose splicing is altered upon PRPF6 knockdown. 2. The second involves immunoprecipitating PRPF6 from two different cancer cell lines and isolating any RNA that is bound to PRPF6, since PRPF6 is an RNA-binding protein. We then want to carry out RNA-seq to identify which RNA molecules co-immunoprecipitated with PRPF6. This will help us determine possible functions for PRPF6 in regulating colon cancer growth. 3. The third involves overexpressing PRPF6 in cell lines and then carrying out RNA-seq to identify any changes in splice-specific gene expression. This will allow us to determine whether increased PRPF6 expression is sufficient to drive alternative splicing changes. Illumina HiSeq 2000; 34 fastq
EGAD00001000818 Quiescent Sox2+ cells drive hierarchical growth and relapse in Sonic hedgehog subgroup medulloblastoma 4 bam
EGAD00001000819 We are aiming to investigate repair of a double strand break (DSB) within the genome in the presence and absence of the BLOOM protein. Zinc Finger Nucleases introduce DSBs at specified loci within the genome. Using sequencing we will assess the size of the deletion following repair. Protocol 1. Transfect normal and BLOOM deficient human iPS cells with ZFNs, using AMXA 2. Harvest cells after 5 days 3. Perform column extraction of DNA 4. PCR-amplify the ZFN region 5. Sequence and analyse repair of the DSB This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 6 bam
EGAD00001000820 Fernandez-Cuesta et al, 2014, Nature Communication, Whole exome sequencing data set Illumina HiSeq 2000; 15 bam
EGAD00001000821 Raw sequencing data for all samples in fastq format. Illumina HiSeq 2000; 767 fastq
EGAD00001000822 Whole exome sequencing and miRNA-seq data of PPB. Illumina MiSeq;, Illumina HiSeq 2000; 18 bam
EGAD00001000824 RNA sequencing will be undertaken to reconstruct rearrangements at level of transcription to determine pathogenomic genomic events in chondromyxoid fibroma. Illumina HiSeq 2000; 1 cram
EGAD00001000825 This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer. Illumina HiSeq 2000; 454 cram
EGAD00001000826 We propose to definitively characterise the somatic genetics of Osteosarcoma cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome and transcriptome sequencing. Illumina HiSeq 2000; 10 cram
EGAD00001000827 n order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs and from studies in the mouse, it appears that an epigenetic memory of the starting cell type is carried over to hiPSCs. However a comprehensive comparative study of the characteristics of these hiPSCs has been missing from the literature. Importantly studies which aimed to address these aspects of hiPSCs have used cells from different patients. In order to avoid this important confounding variable and to keep the genetic background constant, tissue samples were procured from the patients and reprogrammed to iPS cells. The methylation status of these iPS cells will be compared. Protocol: Primary cell cultures were generated and reprogrammed to iPS cells. DNA was extracted and immunoprecipitated using anti-methyl cytosine and anti-hydroxymethyl cytosine antibodies. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 4 bam,cram
EGAD00001000828 Fibroblasts have been shown to re-program into induced pluripotent stem (hiPS) cells, through over-expression of pluripotency genes. These hiPS cells show similar characteristics to embryonic stem cells including cell surface markers, epigenetic changes and ability to differentiate into the three germ layers. However it is unclear as to the extent of changes in gene expression through the re-programming process.. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 6 bam
EGAD00001000829 Illumina HiSeq 2000; 16 bam
EGAD00001000830 Illumina HiSeq 2000; 14 bam
EGAD00001000831 Illumina HiSeq 2000; 30 bam
EGAD00001000832 Illumina HiSeq 2000; 16 bam
EGAD00001000833 Illumina HiSeq 2000; 10 bam
EGAD00001000834 Illumina HiSeq 2000; 20 bam
EGAD00001000835 Illumina HiSeq 2000; 8 bam
EGAD00001000836 Illumina HiSeq 2000; 49 bam
EGAD00001000842 RIKEN collection WGS reads for 100 HCC and matched blood samples from 50 donors submitted to ICGC for release 16 Illumina HiSeq 2000; 100 fastq
EGAD00001000843 Illumina HiSeq 2000; 12 fastq
EGAD00001000844 Illumina HiSeq 2000; 22 fastq
EGAD00001000845 44 bam
EGAD00001000847 Shwachman-Diamond syndrome (SDS) is a rare autosomal recessive disorder characterized by exocrine pancreatic insufficiency, bone marrow dysfunction, leukemia predisposition, and skeletal abnormalities. We aim to characterise the structural effects of SDS in patients with this disorder by exome sequencing. Illumina HiSeq 2000; 2 cram
EGAD00001000848 To evaluate the presence of mutations in frequently mutated genes in MPN by performing targeted resequencing of a selected gene panel comprising of 111 genes across 40 samples with MPN. Illumina MiSeq; 48 cram
EGAD00001000849 Illumina HiSeq 2000; 50 bam
EGAD00001000850 Small cell carcinoma of the ovary of hypercalcemic type (SCCOHT) is an extremely rare, aggressive cancer affecting children and young women. We identified germline and somatic inactivating mutations in the SWI/SNF chromatin-remodeling gene SMARCA4 in 75% (9/12) of SCCOHT patients in addition to SMARCA4 protein loss in 82% (14/17) of SCCOHT tumors, but in only 0.4% (2/485) of other primary ovarian tumors. These data implicate SMARCA4 in SCCOHT oncogenesis. Illumina HiSeq 2000; 19 bam
EGAD00001000853 DATA FILES FOR SJEPD Illumina HiSeq 2000; 37 bam
EGAD00001000854 DATA FILES FOR SJEPD Illumina HiSeq 2000; 77 bam
EGAD00001000856 Illumina HiSeq 2000; 1 fastq
EGAD00001000865 WGS of 14 paired samples of Bladder Cancer patient Illumina HiSeq 2000; 28 bam
EGAD00001000868 FFPE CPA accreditation of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing. Illumina HiSeq 2000; 60 cram
EGAD00001000869 It is the ambition of the team formed by members of the Netherlands Cancer Institute (NKI) and the Cancer Genome Project at the Wellcome Trust Sanger Institute (WTSI) to unravel the genomic and phenotypic complexity of human cancers in order to identify optimal drug combinations for personalized cancer therapy. Our integrated approach will entail (i) deep sequencing of human tumours and cognate mouse tumours; (ii) drug screens in a 1000+ fully characterized tumour cell line panel; (iii) high-throughput in vitro and in vivo shRNA and cDNA drug resistance and enhancement screens; (iv) computational analysis of the acquired data, leading to significant response predictions; (v) rigorous validation of these predictions in genetically engineered mouse models and patient-derived xenografts. This integrated effort is expected to yield a number of combination therapies and companion-diagnostics biomarkers that will be further explored in our existing clinical trial networks. Illumina HiSeq 2000; 62 cram
EGAD00001000870 Testing logistics and infrastructure of molecular screening program. Core biopsies taken from invasive recurrent or metastatic breast cancer to evaluate and identify molecular traits rendering them suitable for clinical trials Illumina HiSeq 2500; 52 cram
EGAD00001000871 The purpose of this study is to sequence 500 known cancer genes in 960 newly diagnosed high risk breast cancer patients treated with current standard of care therapies and trastuzumab, for somatic alteration and copy number changes. We will be using next gen sequencing technology to determine the prognostic relevance of these somatic genetic alterations and of teh low frequency events to determine if they are associated with trastuzumab benefit or HER2 positive breast cancer, i.e. treatment interaction. The samples will be analysed adn correlated with clinical variables including outcome. Illumina HiSeq 2000; 993 cram
EGAD00001000872 These samples are to be analysed with the CGP Developed cancer panel and the results will be compared with WGS data from 4 different comercial providers. Illumina HiSeq 2500; 8 cram
EGAD00001000873 Fastq files of 10 samples of condrosarcoma Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 10 fastq
EGAD00001000874 Indel/point mutation of chondrosarcoma 10 vcf
EGAD00001000875 The CRO7 clinical trial recruited patients with clinically operable rectal adenocarcinoma. Patients were randomized to either pre-operative short course surgery followed by chemo-radiotherapy only in those patients at high risk of local relapse. Patients in both arms the received standard %-FU based adjuvant chemotherapy as per local policy. We intend to use FFPE derived DNA from the primary tumours to identify patterns of mutations or copy number alterations that are predictive of local or distant relapse. Illumina HiSeq 2000; 330 cram
EGAD00001000876 Illumina HiSeq 2000; 98 fastq
EGAD00001000877 Complete WGS and RNA-Seq dataset for Australian ICGC ovarian cancer sequencing project 2014-07-07, representing 93 donors. Sequencing was performed on Illumina HiSeq. Alignment of the lane-level fastq data was performed with bwa (WGS data) and RSEM (transcriptome data). For this dataset lane-level .bam files have been merged and de-duplicated to create a single bam file for each sample type (tumour/normal) for each donor. This dataset supersedes all previous datasets for this study. 331 bam
EGAD00001000878 DATA FILES FOR SJRHB RNA-Seq Illumina HiSeq 2000; 42 bam
EGAD00001000879 Genomic libraries will be generated from total genomic DNA derived from 200+ patients with childhood Transient Myeloproliferative Disorder (TMD) and or Acute Megakaryocytic Leukemia (AMKL) as well some matched constitutional samples (n < 50). Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 96 Samples will be individually barcoded and subjected to up to two lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing. Illumina HiSeq 2500; 335 cram
EGAD00001000880 233 bam,vcf
EGAD00001000881 RNA sequencing of Resistant BCC samples. Illumina HiSeq 2000; 11 fastq
EGAD00001000882 Targeted genome sequences of the human X chromosome in 4 colorectal adenomas and 4 matched normal tissues from male patients Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 8 bam
EGAD00001000883 Illumina HiSeq paired-end exome sequencing of a trio and singleton. Illumina HiSeq 2000; 4 bam
EGAD00001000884 In order to elucidate whether newly acquired genetic alterations during serial transplantation of patient derived primary pancreatic cancer cultures contribute to the observed clonal dynamics in vivo, all coding genes of two patient derived primary cultures and derived genetically marked serial xenografts (1°/2°/3°) were sequenced. Illumina HiSeq 2000; 10 fastq
EGAD00001000885 Exome read sequences for 30 tumor-normal pairs for the study "Diverse modes of genomic alterations in Hepatocellular Carcinoma". Illumina HiSeq 2000; 60 fastq
EGAD00001000886 RNA-Sequencing data (raw read sequences) for 23 samples, from 12 patients, for the study "Diverse modes of genomic alterations in Hepatocellular Carcinoma" Illumina HiSeq 2000; 23 fastq
EGAD00001000887 Exome sequencing of Resistant BCC samples. Illumina HiSeq 2000; 23 fastq
EGAD00001000888 NSCLC WGS. AB 5500 Genetic Analyzer; 4 bam
EGAD00001000889 NSCLC targeted. Ion Torrent PGM; 4 bam
EGAD00001000891 We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331 Illumina HiSeq 2000; 62 bam
EGAD00001000892 We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331 Illumina HiSeq 2000; 40 bam
EGAD00001000893 HipSci - Healthy Normals - Exome Sequencing - May 2014 Illumina HiSeq 2000; 15 cram,tabix,vcf,bai,bam
EGAD00001000894 SPECTA comprises a network of participating European clinical sites and NGS screening platforms that can screen individual patients for multiple molecular targets and potentially allow the design of trials that will match the specific biology of the diseases affecting specific patients with cancer. Illumina HiSeq 2500; 64 cram
EGAD00001000896 Illumina HiSeq 2000; 12 bam
EGAD00001000897 HipSci - Healthy Normals - RNA Sequencing - May 2014 Illumina HiSeq 2000; 22 cram,bam,bai
EGAD00001000898 Cancers are ecosystems of genetically related clones, competing across space and time for limited resources. To understand the clonal structure of primary breast cancer, we applied genome and targeted sequencing to 295 samples from 49 patients’ tumors. The extent of subclonal diversification varied considerably among patients and encompassed many spatial patterns, including local growth, intraductal dissemination and clonal intermixture. Landmarks of disease progression, such as acquiring invasive or metastatic potential, arose within detectable subclones of antecedent lesions, suggesting that subclonal mutations could be relevant if actionable. No defined temporal order of mutation was evident, with the commonest genes, including PIK3CA, TP53, BRCA2, PTEN and MYC, mutated early in some, late in others, often exhibiting parallel evolution across subclones. Signatures of homologous recombination deficiency correlated with response to neoadjuvant chemotherapy. Thus, the interplay of mutation, growth and competition drives clonal structures of breast cancer that are complex, variable across patients and clinically relevant. Illumina HiSeq 2000; 42 bam
EGAD00001000899 We propose to definitively characterise the somatic genetics of Metastatic breast cancer through generation of comprehensive catalogues of somatic mutations in Metastatic breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000; 41 bam,cram
EGAD00001000900 Multi-region Illumina whole-exome and/or whole-genome sequencing on tumor regions collected from early-stage NSCLC patients who underwent definitive surgical resection prior to receiving adjuvant therapy. Detected variants were validated on Ion AmpliSeqâ„¢ Custom Panel and/or Comprehensive Cancer Gene Panels. Patients covered by this dataset: L001, L002, L003, L004, L008 and L011. Ion Torrent PGM;, Illumina Genome Analyzer IIx; 28 bam,fastq
EGAD00001000901 The dataset includes the whole exome sequencing data from 32 pairs of gallbladder caner tissues and patient-matched normal tissues. Illumina HiSeq 2500; 64 bam
EGAD00001000902 The dataset includes the targeted gene sequencing data from 51 pairs of gallbladder caner tissues and patient-matched normal tissues. Illumina HiSeq 2500; 102 bam
EGAD00001000903 RNA-Seq data for 4 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 22 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 4 fastq
EGAD00001000904 RNA-Seq data for 7 mature neutrophil sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 7 fastq
EGAD00001000905 DNase-Hypersensitivity data for 5 CD14-positive, CD16-negative classical monocyte sample(s). 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811 Illumina HiSeq 2000; 5 fastq
EGAD00001000906 ChIP-Seq data for 1 mature eosinophil sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 1 fastq
EGAD00001000907 RNA-Seq data for 3 common myeloid progenitor sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 3 fastq
EGAD00001000908 RNA-Seq data for 3 inflammatory macrophage sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 3 fastq
EGAD00001000909 Bisulfite-Seq data for 1 erythroblast sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam,readme_file
EGAD00001000910 Bisulfite-Seq data for 1 precursor lymphocyte of B lineage sample(s). 8 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam,readme_file
EGAD00001000911 RNA-Seq data for 4 erythroblast sample(s). 22 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 4 fastq
EGAD00001000912 RNA-Seq data for 1 CD8-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 1 fastq
EGAD00001000913 ChIP-Seq data for 9 CD14-positive, CD16-negative classical monocyte sample(s). 59 run(s), 55 experiment(s), 55 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 9 fastq
EGAD00001000914 Bisulfite-Seq data for 3 inflammatory macrophage sample(s). 38 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 3 bam,readme_file
EGAD00001000915 RNA-Seq data for 4 megakaryocyte-erythroid progenitor cell sample(s). 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 4 fastq
EGAD00001000916 ChIP-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 1 fastq
EGAD00001000917 Bisulfite-Seq data for 1 hematopoietic multipotent progenitor cell sample(s). 8 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam,readme_file
EGAD00001000918 RNA-Seq data for 3 common lymphoid progenitor sample(s). 15 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 3 fastq
EGAD00001000919 RNA-Seq data for 3 hematopoietic multipotent progenitor cell sample(s). 9 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 3 fastq
EGAD00001000920 Bisulfite-Seq data for 1 alternatively activated macrophage sample(s). 10 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam,readme_file
EGAD00001000921 Bisulfite-Seq data for 1 CD8-positive, alpha-beta T cell sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam,readme_file
EGAD00001000922 RNA-Seq data for 3 granulocyte monocyte progenitor cell sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 3 fastq
EGAD00001000923 Bisulfite-Seq data for 1 macrophage sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam,readme_file
EGAD00001000924 ChIP-Seq data for 2 erythroblast sample(s). 14 run(s), 14 experiment(s), 14 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 2 fastq
EGAD00001000925 ChIP-Seq data for 3 CD4-positive, alpha-beta T cell sample(s). 21 run(s), 21 experiment(s), 21 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 3 fastq
EGAD00001000926 DNase-Hypersensitivity data for 2 inflammatory macrophage sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811 Illumina HiSeq 2000; 2 fastq
EGAD00001000927 Bisulfite-Seq data for 1 Plasma cell sample(s). 11 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam,readme_file
EGAD00001000928 RNA-Seq data for 7 CD14-positive, CD16-negative classical monocyte sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 7 fastq
EGAD00001000929 ChIP-Seq data for 1 macrophage sample(s). 6 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 1 fastq
EGAD00001000930 ChIP-Seq data for 7 mature neutrophil sample(s). 68 run(s), 50 experiment(s), 50 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 7 fastq
EGAD00001000931 DNase-Hypersensitivity data for 1 macrophage sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811 Illumina HiSeq 2000; 1 fastq
EGAD00001000932 Bisulfite-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam
EGAD00001000933 RNA-Seq data for 1 macrophage sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 1 fastq
EGAD00001000934 Bisulfite-Seq data for 2 Multiple myeloma sample(s). 16 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 2 bam,readme_file
EGAD00001000935 Bisulfite-Seq data for 6 mature neutrophil sample(s). 79 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 6 bam,readme_file
EGAD00001000936 ChIP-Seq data for 2 CD8-positive, alpha-beta T cell sample(s). 13 run(s), 13 experiment(s), 13 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 2 fastq
EGAD00001000937 RNA-Seq data for 1 alternatively activated macrophage sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 1 fastq
EGAD00001000938 ChIP-Seq data for 4 alternatively activated macrophage sample(s). 29 run(s), 28 experiment(s), 28 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 4 fastq
EGAD00001000939 RNA-Seq data for 3 hematopoietic stem cell sample(s). 8 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 3 fastq
EGAD00001000940 ChIP-Seq data for 3 inflammatory macrophage sample(s). 21 run(s), 21 experiment(s), 21 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 3 fastq
EGAD00001000941 Bisulfite-Seq data for 6 CD14-positive, CD16-negative classical monocyte sample(s). 86 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 6 bam,readme_file
EGAD00001000942 DNase-Hypersensitivity data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811 Illumina HiSeq 2000; 1 fastq
EGAD00001000943 Bisulfite-Seq data for 1 germinal center B cell sample(s). 8 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam,readme_file
EGAD00001000945 NGS of 10 mucosal melanomas: Whole genome sequencing of 5 mucosal melanomas and matched normal DNA Whole exome sequencing of 5 mucosal melanomas and matched normal DNA Illumina HiSeq 2000; 20 bam
EGAD00001000946 Divergent clonal selection dominates medulloblastoma at recurrence 125 bam
EGAD00001000947 Genomic libraries (500 bps) will be generated from total genomic DNA derived from Colorectal cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions. Illumina HiSeq 2000; 45 cram
EGAD00001000948 A comparison of the somatic variation present in a primary colorectal tumour and three different liver metastases from the same patient. Illumina HiSeq 2000; 6 cram
EGAD00001000949 Validations of variants identified by exome sequencing in sequential samples derived after treatment cycle with AZA. Illumina HiSeq 2000; 170 cram
EGAD00001000950 Whole genome sequencing data for ependymomas (5 tumor-control pairs). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142). 10 bam
EGAD00001000951 Whole exome sequencing data for ependymomas (42 tumor-control pairs). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142). 84 bam
EGAD00001000952 DNA methylation profiling of 8 control samples from adult (4) and fetal brain (4) Illumina HiSeq 2000; 8 fastq
EGAD00001000963 Exome sequencing of sporadic schwannomatosis patients 16 bam
EGAD00001000964 Low-coverage whole genome sequencing of sporadic schwannomatosis patients 16 bam
EGAD00001000965 Cancers are ecosystems of genetically related clones, competing across space and time for limited resources. To understand the clonal structure of primary breast cancer, we applied genome and targeted sequencing to 295 samples from 49 patients’ tumors. The extent of subclonal diversification varied considerably among patients and encompassed many spatial patterns, including local growth, intraductal dissemination and clonal intermixture. Landmarks of disease progression, such as acquiring invasive or metastatic potential, arose within detectable subclones of antecedent lesions, suggesting that subclonal mutations could be relevant if actionable. No defined temporal order of mutation was evident, with the commonest genes, including PIK3CA, TP53, BRCA2, PTEN and MYC, mutated early in some, late in others, often exhibiting parallel evolution across subclones. Signatures of homologous recombination deficiency correlated with response to neoadjuvant chemotherapy. Thus, the interplay of mutation, growth and competition drives clonal structures of breast cancer that are complex, variable across patients and clinically relevant. Illumina HiSeq 2000; 331 bam,cram
EGAD00001000966 Whole genome bisulfite sequencing data for 6 ependymomas plus 3 fetal controls (f1, f2, f4) and 3 adult controls (a2, a3, a4). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142). Illumina HiSeq 2000; 14 readme_file
EGAD00001000967 This dataset contains the fastq sequencing data collected from bone marrow DNA of a chronic myeloid leukaemia patient at time of diagnosis. Illumina HiSeq 2000; 4 fastq
EGAD00001000972 Whole Genome Sequencing to track subclonal heterogeneity in 18 samples from 3 Chronic Lymphocytic Leukemia patients subjected to repeated cycles of therapy. Illumina HiSeq 2500; 18 bam
EGAD00001000973 Van Hippel-Lindau syndrome multi-region exome sequencing of two patients Illumina HiSeq 2000; 21 bam
EGAD00001000974 High-grade serous ovarian cancer (HGSC) is characterized by poor outcome, often attributed to emergence of treatment-resistant sub-clones. We sought to measure the degree of genomic diversity within primary, untreated HGSC to examine the natural state of tumor evolution prior to therapy. We performed exome sequencing, copy number analysis, targeted amplicon deep sequencing and gene expression profiling on thirty-one spatially and temporally separated HGSC tumor specimens (six patients) including ovarian masses, distant metastases, and fallopian tube lesions. We found widespread intra-tumoral variation in mutation, copy number, and gene expression profiles, with key driver alterations in genes present in only a subset of samples (e.g. PIK3CA, CTNNB1, NF1). On average, only 51.5% of mutations were present in every sample of a given case (range: 10.2% to 91.4%), with TP53 as the only somatic mutation consistently present in all samples. Complex segmental aneuploidies, such as whole genome doubling, were present in a subset of samples from the same individual, with divergent copy number changes segregating independently of point mutation acquisition. Reconstruction of evolutionary histories showed one patient with mixed HGSC and endometrioid histology with common etiologic origin in the fallopian tube and subsequent selection of different driver mutations in the histologically distinct samples. In this patient, we observed mixed cell populations in the early fallopian tube lesion, indicating diversity arises at early stages of tumorigenesis. Our results reveal that HGSC exhibit highly individual evolutionary trajectories and diverse genomic tapestries prior to therapy, exposing an essential biological characteristic to inform future design of personalized therapeutic solutions and investigation of drug resistance mechanisms. Illumina MiSeq;, Illumina HiSeq 2000; 131 bam
EGAD00001000975 65 prostate cancer cases transcriptome sequencing Illumina HiSeq 2000; 130
EGAD00001000976 WGS DATA FILES FOR SJPhLike Illumina HiSeq 2000; 80 bam
EGAD00001000977 WGS dataset LCNEC study Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2000; 11
EGAD00001000978 Multi-region whole genome sequencing of an high grade serous ovarian carcinoma sample for characterization of genomic intra-tumoural heterogeneity. Illumina HiSeq 2000; 48 bam
EGAD00001000979 We are developing a protocol to differentiate mouse and human induced pluripotent stem (IPS) and embryonic stem (ES) cells towards the haematopoietic pathway to generate erythrocytes in vitro. This system has many applications such as the study of the role of specific genes and human polymorphisms in infectious diseases such as malaria, as well as haematological diseases such as myelodysplastic syndrome. The nature of the in vitro differentiation process means that a heterogeneous population of cells is generated. In order to understand the types of cells produced with our protocol, we have performed a single cell analysis, which has the power to reveal the different populations of cells and their characteristics. For this, a cDNA library has been made that needs to be sequenced to obtain the gene expression profiles of the different cells. With this information we will be able to assess the quality of the differentiation protocol and improve it in order to produce better cells for the downstream applications. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2500; 192 cram
EGAD00001000980 This study involves a forward genetic screen to identify common insertion sites in drug resistant clones. We will be utilising piggybac transposon systems in order to generate multiple drug resistant clones in a range of human cancer cell lines. Illumina MiSeq; 144 bam,cram
EGAD00001000983 65 prostate cancer cases wgs sequencing Illumina HiSeq 2000; 10
EGAD00001000984 This is the Whole Exome Sequencing (WES) data from 59 samples from 11 patients with lung adenocarcinomas including 48 tumor samples and 11 peripheral white blood cell samples Illumina HiSeq 2000; 59 bam
EGAD00001000985 This is the targeted capture deep sequencing (TCS) data for validation of the mutations discovered in the WES step. There are 58 bam files of TCS data including 48 tumor samples and 10 peripheral blood WBC samples. Illumina HiSeq 2000; 58 bam
EGAD00001000986 Pheochromocytomas and paragangliomas (PCC/PGL) are neural crest derived tumors with a very strong genetic component. We report the first integrated genomic portrayal of a large collection of PCC/PGL. SNP array analysis revealed distinct copy-number patterns associated with genetic background. Whole-exome sequencing showed a low mutation rate of 0.3 mutations per megabase, with few recurrent somatic mutations in genes not previously associated with PCC/PGL. DNA methylation arrays and miRNA sequencing identified DNA methylation changes and miRNA expression clusters strongly associated with mRNA expression profiling. Overexpression of the miRNA cluster 182/96/183 was specific of SDHB-mutated tumors and induced invasive traits, whereas silencing of the imprinted DLK1-MEG3 miRNA cluster appeared as a potential driver in a subgroup of sporadic tumors. Altogether, the complete genomic landscape of PCC/PGL is mainly driven by distinct germline and/or somatic mutations in susceptibility genes and reveals different molecular entities, characterized by a set of unique genomic alterations. Illumina HiSeq 2000; 60 bam
EGAD00001000987 Whole exome sequencing data from tumor and normal samples from carcinosarcoma (malignant mixed mullerian tumor) patients Illumina HiSeq 2000; 44
EGAD00001000988 Validation/deeper sequencing for metastatic prostate cancer samples Illumina HiSeq 2500; 94 cram
EGAD00001000989 Validation/deeper sequencing for metastatic prostate cancer samples Illumina HiSeq 2500; 26 cram
EGAD00001000990 mRNA-Seq on total RNA from primary osteoblastomas and phosphaturic mesenchymal tumours, focussing on fusion transcript expression Illumina HiSeq 2000; 11 cram
EGAD00001000992 HIPO blastemal Wilms (nephroblastoma) characterisation of tumor driving events caused by differential SIX1 binding of the SIX1 Q177R mutatns Illumina HiSeq 2500; 3 fastq
EGAD00001000993 HIPO blastemal Wilms (nephroblastoma) characterisation of tumor driving gene expression events Illumina HiSeq 2000; 40 fastq
EGAD00001000994 HIPO blastemal Wilms (nephroblastoma) characterisation of tumor driving chromosomal aberrations Illumina HiSeq 2000;, Illumina HiSeq 2500; 56 fastq
EGAD00001000995 HIPO blastemal Wilms (nephroblastoma) characterisation of tumor driving DNA alterations Illumina HiSeq 2000; 112 fastq
EGAD00001000996 Whole exome sequencing data for AML and matched normal samples Illumina HiSeq 2500; 16 bam
EGAD00001000997 Whole-exome sequencing of a chronic lymphocytic leukemia (CLL) developed during vemurafenib treatment of a patient with malignant melanoma. Peripheral blood mononuclear cells were separated by Ficoll gradient centrifugation. DNA was extracted from highly purified (>97%) CD19+CD5+ cells obtained from the patient while being under BRAF inhibition versus CD14+ germline control cells (>90% purity). No alterations that could be linked to aberrant RAS activity or paradoxical RAF/MEK/ERK signaling could be identified in the CLL, which shows characteristic copy number alterations. Illumina HiSeq 2500; 2 fastq
EGAD00001000998 Targeted capture of exonic and intronic regions of interest for the study of genomic alterations in multiple myeloma. Illumina HiSeq 2000; 24 cram
EGAD00001001000 Background: The disease course of patients with diffuse low-grade glioma is notoriously unpredictable. Temporal and spatially distinct samples may provide insight into the evolution of clinically relevant copy number aberrations (CNAs). The purpose of this study is to identify CNAs that are indicative of aggressive tumor behaviour and can thereby complement the prognostically favorable 1p/19q co-deletion. Results: Genome-wide, 50 base pair single-end, sequencing was performed to detect CNAs in a clinically well-characterized cohort of 98 formalin-fixed paraffin-embedded low-grade gliomas. CNAs are correlated with overall survival as an endpoint. Seventy-five additional samples from spatially distinct regions and paired recurrent tumors of the discovery cohort were analysed to interrogate the intratumoral heterogeneity and spatial evolution. Loss of 10q25.2-qter is a frequent subclonal event and significantly correlates with an unfavorable prognosis. A significant correlation is furthermore observed in a validation set of 126 and confirmation set of 184 patients. Loss of 10q25.2-qter arises in a longitudinal manner in paired recurrent tumor specimens, whereas the prognostically favorable 1p/ 19q co-deletion is the only CNA that is stable across spatial regions and recurrent tumors. Conclusions: CNAs in low-grade gliomas display extensive intratumoral heterogeneity. Distal loss of 10q is a late onset event and a marker for reduced overall survival in low-grade glioma patients. Intratumoral heterogeneity and higher frequencies of distal 10q loss in recurrences suggest this event is involved in outgrowth to the recurrent tumor. Illumina HiSeq 2000; 175 fastq
EGAD00001001001 2 bam
EGAD00001001002 Exome sequencing data for 8 pairs of seminomas and matched normal Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 16 fastq
EGAD00001001003 Exome sequencing of lymphocyte DNA from 12 affected individuals from six unrelated, non-syndromic Wilms tumor families. Illumina HiSeq 2000; 12 fastq
EGAD00001001004 65 prostate cancer cases wgs sequencing Illumina HiSeq 2000; 130
EGAD00001001006 Dataset for whole exome sequencing of 113 pairs of tumor and normal DNA samples along with 8 cell lines. Illumina HiSeq 2000; 234 fastq
EGAD00001001007 Low depth (4x) Illumina HiSeq raw sequence data for 100 unrelated Zulu from Durban area, South Africa. Illumina HiSeq 2000; 100 bam,cram
EGAD00001001008 Low depth (4x) Illumina HiSeq raw sequence data for 100 unrelated Baganda from rural Uganda. Illumina HiSeq 2000; 100 bam
EGAD00001001009 Exome sequencing of peripheral blood from 4 individuals of a family with familial colorectal cancer type X Illumina HiSeq 2000; 4 fastq
EGAD00001001010 Sequencing of colorectal tumors and normal tissue using Ion AmpliSeq Cancer Hotspot Panel V2 Ion Torrent Proton; 8 bam
EGAD00001001011 Monocyte differentiation into macrophages represents a cornerstone process for host defense. Concomitantly, immunological imprinting of either tolerance or trained immunity determines the functional fate of macrophages and susceptibility to secondary infections. Transcriptomes (RNA-Seq) and epigenomes (ChIP-Seq H3K4me1,H3K4me3,H3K27ac) in four primary cell types: monocytes, in vitro differentiated naive, tolerized and trained macrophages were characterized. Inflammatory and metabolic pathways were modulated in macrophages, including decreased inflammasome activation, and pathways functionally implicated in trained immunity were identified. Strikingly, B-glucan training elicits an exclusive epigenetic signature, revealing a complex network of enhancers and promoters. Analysis of transcription factor motifs in DNase I hypersensitive sites at cell-type specific epigenetic loci unveiled differentiation and treatment specific repertoires. Altogether, this study provides a resource to understand the epigenetic changes that underlie innate immunity in humans. Illumina HiSeq 2000;, NextSeq 500; 57 fastq
EGAD00001001012 The need for a detailed catalogue of local variability for the study of rare diseases within the context of the Medical Genome Project motivated the whole exome sequencing of 267 unrelated individuals, representative of the healthy Spanish population. AB 5500xl Genetic Analyzer; 267 fastq
EGAD00001001013 RNAseq and exome sequencing data of gastric cancer cell lines. Illumina HiSeq 2000; 30
EGAD00001001014 Illumina HiSeq 2000; 2,597 bam
EGAD00001001015 Illumina HiSeq 2000; 76 bam
EGAD00001001016 DATA FILES FOR SJPhLike-RNASeq Illumina HiSeq 2000; 125 bam
EGAD00001001017 DNA extracted from multiple biopsies taken from different areas of primary lung tumours will be subjected to targeted re-sequencing and analysed in order to assess intra-tumour heterogeneity with respect to mutations in a selection of cancer related genes. Illumina HiSeq 2000; 31 bam,cram
EGAD00001001018 The samples will be sequenced for a targeted panel of cancer relevant genes (n ~ 370) and analysed for somatic mutations. This dataset contains all the data available for this study on 2014-09-24 Illumina HiSeq 2000; 374 cram
EGAD00001001019 RNA-seq dataset used for the validation of CDK6 cis-regulatory mutation annotated by OncoCis. NB bam files for manuscript A_Proteomic_Chronology_of_Gene_Expression_through_the_Cell_Cycle_in_Human_Myeloid_Leukemia_Cells are now available at the following link:http://www.ebi.ac.uk/ena/data/view/ERP008483 Illumina HiSeq 2000; 1 bam
EGAD00001001020 DATA FILES FOR SJEWS-WGS Illumina HiSeq 2000; 38 bam
EGAD00001001021 Exome sequencing of 1000 samples from the UK 1958 Birth Cohort. DNA library preps prepared with Illumina TruSeq sample preparation kit. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers. Sequencing was performed with an Illumina HiSeq2000 (SBS Kit v3, one pool per lane) generating 2x101-bp reads. Illumina HiSeq 2500; 1,000 fastq
EGAD00001001022 nccRCC RNA-Seq data of consented samples Illumina HiSeq 2500; 139 fastq
EGAD00001001023 nccRCC Whole Exome sequencing data (consented samples only) Illumina HiSeq 2500; 137 fastq
EGAD00001001024 Fastq files of 52 samples of hepatocellular carcinoma (RCAST, THCC) Illumina HiSeq 2000; 104 fastq
EGAD00001001025 The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 50-80%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing British-Pakistani cohort samples from Birmingham will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consist of low coverage whole exome sequencing on these samples. Illumina HiSeq 2000; 1,156 bam,cram
EGAD00001001026 The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing British-Pakistani cohort samples from Birmingham will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consists of low coverage whole exome sequencing on these samples. Illumina HiSeq 2000; 452 cram
EGAD00001001027 The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing British-Pakistani cohort samples will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consists of low coverage whole exome sequencing on these samples. Illumina HiSeq 2000; 130 cram
EGAD00001001028 DNA belonging to 16 tumour/normal samples were treated with bisulfite, then up to 5 different bisulfite PCRs were performed in each one of the samples. Amplicons form the same sample were pooled and submitted to sequencing on a MiSeq platform. Illumina MiSeq; 18 cram
EGAD00001001029 The dataset regards the sequencing of coding and putative regulatory sequences of 38 genes associated to either sporadic or Mendelian form of Parkinson's disease Illumina HiSeq 2000; 394 bam
EGAD00001001031 These are only the whole exome sequences Illumina HiSeq 2500; 6 bam
EGAD00001001032 DATA FILES FOR SJMEL-WGS Illumina HiSeq 2000; 12 bam
EGAD00001001033 Whole exome sequencing (WES) was performed on genomic DNA derived from two patients with Sotos Syndrome Features. Sequencing (100 base pair paired-end) was performed on an Illumina Hiseq 2000 sequencer after enrichment of 62Mb of exonic and adjacent intronic sequences with TruSeq Exome Enrichment Kit (Illumina, San Diego, CA, USA). Illumina HiSeq 2000; 2 fastq
EGAD00001001034 Whole genome data (Complete genomics platform) for the study EGAS00001000824 24 other
EGAD00001001035 RIKEN collection WGS and RNA-seq reads for 66 HBV-associated HCC and matched blood or liver samples from 22 donors. Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 66 fastq
EGAD00001001036 Illumina HiSeq 2000; 26 fastq
EGAD00001001037 A total of 395 couples were subjected to IVF-PGD treatment, including 129 couples with NGS-based test and 266 couples with SNP array based test for the detection of embryonic chromosomal abnormalities. The NGS test was performed using low coverage whole genome sequencing with HiSeq 2000 platform. And the SNP array test was using Affymetrix Gene Chip Mapping Nsp I 262K. The average age of patients was 32.1 years (age range 20-44 years). Illumina HiSeq 2000; 188 fastq
EGAD00001001038 We mapped the data to the UCSC human reference genome build 37 using BWA 0.5.9-r16. We first mapped each read pair separately using bwa aln. Then we used bwa sampe to map the paired reads together to a BAM9 file. The BAM file was then sorted by genomic position and indexed using PicardTools-1.32 SortSam. To prevent PCR artifacts from influencing the downstream analysis of our data, we used Picard to mark the duplicate reads, which were ignored in downstream analysis. We used GATK IndelRealigner on our data around known indels (from 1KG Pilot). The IndelRealigner creates all possible read alignments using the source and computes the likelihood of the data containing the indel based on the read pileup. Whenever the maximum likelihood contains an indel, the reads are realigned accordingly. Each base is associated with a phred-scaled base quality score. Calibration of Phred scores is crucial as they are used in some of the downstream analysis models. We used GATK to recalibrate the base qualities with respect to (i) the base cycle, (ii) original quality score, and (iii) dinucleotide context. To minimize issues stemming from mapping problems around indels, we decided to undergo a second round of indel realignment using the GATK IndelRealigner by family rather than by individual. For this second round, we considered two sources of possible indels: 1KG Phase 1 indels and indels aligned by BWA in the GoNL data. 769 bam
EGAD00001001039 Genomic characterisation of a large series of cancer cell lines. Illumina HiSeq 2000; 1,072 bam,cram
EGAD00001001040 This is the complete dataset (exome and genome) for the EGAS00001000974 study. Illumina HiSeq 2500; 16 bam
EGAD00001001041 Comparison of genomic rearrangements and DNA methylation patterns between different foci of multiple synchronous (multifocal and multicentric) invasive breast cancers. Illumina Genome Analyzer II;, Illumina HiSeq 2000; 305
EGAD00001001043 Illumina HiSeq 2000; 8 bam
EGAD00001001044 Ion Torrent PGM; 2 bam
EGAD00001001045 DATA FILES FOR SJRB Illumina HiSeq 2000; 20 bam
EGAD00001001046 We propose to biopsy 20 consented BRAF mutant melanoma patients at Addenbrooke's Hospital pre-treatment with vemurafenib and also upon the development of resistant disease, with the aim of using exome sequence and SNP6 data to identify novel sequence variants and copy number alterations that can be used to validate observed resistance mechanisms in our cell line models and also to use these models to inform as to likely candidate small molecule inhibitors to overcome resistance and that could be tested in the clinical trial setting. Illumina HiSeq 2000; 33 cram
EGAD00001001047 Targeted exome sequencing of 375 genes Illumina HiSeq 2500; 31 fastq
EGAD00001001048 Samples from Edwards et al 2015 - doi:10.1186/s12864-015-1685-z Illumina HiSeq 2000 (ILLUMINA) 86 bam
EGAD00001001050 We propose to biopsy 20 consented BRAF mutant melanoma patients at Addenbrooke's Hospital pre-treatment with vemurafenib and also upon the development of resistant disease, with the aim of using exome sequence and SNP6 data to identify novel sequence variants and copy number alterations that can be used to validate observed resistance mechanisms in our cell line models and also to use these models to inform as to likely candidate small molecule inhibitors to overcome resistance and that could be tested in the clinical trial setting. Illumina HiSeq 2000; 8 cram
EGAD00001001051 Illumina HiSeq 2000; 200 fastq
EGAD00001001052 DATA FILES FOR SJTALL Illumina HiSeq 2000; 24 bam
EGAD00001001053 DATA FILES FOR SJOS-WGS-2ndBatch Illumina HiSeq 2000; 27 bam
EGAD00001001054 DATA FILES FOR Ph-likeALL WES Illumina HiSeq 2000; 23 bam
EGAD00001001055 Bam files for the whole exome sequencing from the study on Spatial homogeneity in pediatric brain tumors. Illumina HiSeq 2000; 53
EGAD00001001056 Illumina HiSeq 2000; 7 bam
EGAD00001001057 RNA-seq from normal human tissues (2 x 75 bp) Illumina HiSeq 2000; 3 fastq
EGAD00001001058 Cancer exome reads consisting of FASTQ paired end reads from bone marrow samples Illumina HiSeq 2000; 42 fastq
EGAD00001001059 DATA FILES FOR SJRHB-WES Illumina HiSeq 2000; 56 bam
EGAD00001001060 Illumina HiSeq 2000; 112 bam
EGAD00001001061 This experiment is to inform us of the validity of using pre-made library material to perform a bespoke pulldown experiment to validate the mutations found between the whole genome sequencing of the DNA from the same individuals cancer and normal material. This is to identify the valid and informative mutations in cancer genomes. Illumina MiSeq; 4 bam
EGAD00001001062 Patient (who has had multiple malignancies) has previously been found to harbour a pathogenic p53 variant which is probably mosaic. This finding is based on exome sequencing performed elsewhere. In this study we will resequence the locus in question to ascertain whether the variant is indeed mosaic. Illumina MiSeq; 4 cram
EGAD00001001063 Chondromxoid fibroma is a benign tumour of bone with unknown underlying pathogenesis. To determine pathognomic genomic event in chondromyxoid fibroma whole genome sequencing will be undertaken to reconstruct rearrangements and find underlying mutations. Illumina HiSeq 2000; 2 bam,cram
EGAD00001001064 Extension of angiosarcoma whole genome sequencing study Illumina MiSeq; 4 cram
EGAD00001001066 Dynamics of genomic clones in breast cancer patient xenografts at single cell resolution Illumina MiSeq;, Illumina HiSeq 2000; 188 bam
EGAD00001001071 Samples from the "100" project that are in the ICGC PanCancer project. Illumina HiSeq 2000; 200 bam
EGAD00001001072 Illumina MiSeq; 5 fastq
EGAD00001001073 miRNA-seq Cohort of 140 Formalin Fixed Paraffin Embedded Diffuse Large B-cell Lymphoma Patient Samples 140 bam
EGAD00001001074 miRNA-seq Cohort of 92 Fresh Frozen Diffuse Large B-cell Lymphoma Patient Samples 92 bam
EGAD00001001075 miRNA-seq Cohort of 15 Benign Centroblasts 15 bam
EGAD00001001076 Fastq files of 239 samples of biliary tract cancer Illumina HiSeq 2000; 239 fastq
EGAD00001001079 The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing cohort samples from the Born In Bradford study will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consist of low coverage whole exome sequencing on these samples.Data Access is controlled by the Wellcome Trust Sanger Institute DAC and the Born In Bradford Executive Group. This dataset contains all the data available for this study on 2014-11-20. Illumina HiSeq 2000; 2,702 vcf,cram
EGAD00001001080 MDS patients 5 bam
EGAD00001001081 Healthy reference samples 3 bam
EGAD00001001083 Illumina HiSeq 2000; 2 fastq
EGAD00001001084 Illumina HiSeq 2000; 209 fastq
EGAD00001001085 This dataset includes 2 pairs of tumour/normal whole genome sequence data as well as MEN1 gene targeted sequencing of an additional 87 specimens. Illumina MiSeq;, Illumina HiSeq 2500; 91 bam
EGAD00001001086 These analysis are the BAM files for the LCLs samples of the EUROBATS samples. 765 bai,bam
EGAD00001001087 RNAseq BAM files for the Skin samples of the EUROBATS project. 672 bai,bam
EGAD00001001088 RNAseq BAM files for the blood samples of the EUROBATS project 391 bai,bam
EGAD00001001089 RNAseq BAM files for the Fat samples of the EUROBATS project 685 bai,bam
EGAD00001001090 This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer. Illumina HiSeq 2000; 166 bam,cram
EGAD00001001091 We established and validated a sequence capture based NGS testing approach for PKD1. The presence of six PKD1 pseudogenes and tremendous allelic heterogeneity make molecular genetic testing of PKD1 variants challenging. In the publication accompaying this dataset (An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease, Eisenberger et.al., PLoS one), we demonstrate that the applied standard mapping algorithm specifically aligns reads to the PKD1 locus and overcomes the complication of unspecific capture of pseudogenes. This dataset contains the raw PKD1 reads of all patients from the publication. Illumina HiSeq 1500; 55 fastq
EGAD00001001092 Approximately 80% of clinically clearly diagnosed patients suffering from primary ciliary dyskinesia (PCD) cannot be assigned to a specific gene defect. Despite extensive research on PCD and despite the increasing number of PCD genes and knowledge about their sites of action as e.g structural component or cytoplasmic pre-assembly factor, the biology of motile cilia and the pathomechanism leading to PCD is largely unknown. The aim of this study is to identify novel PCD related genes and processes relevant for motile cilia function. We will perform exome sequencing, aiming on the analysis of family trios. In these families, the diagnosis of PCD is secured, but the underlying gene defects has so far not been identified. Illumina HiSeq 2000; 150 cram
EGAD00001001093 Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing Illumina HiSeq 2000; 2 fastq
EGAD00001001094 200PG : WGS Raw Sequence (fastq) : Raw WG sequence data (fastq) in this dataset are from the 124 CPCGene Tumour/Normal Pairs used in the 200PG Study. https://www.ncbi.nlm.nih.gov/pubmed/28068672 Illumina HiSeq 2500;ILLUMINA, Illumina HiSeq 2500; 247 fastq
EGAD00001001095 Supporting data for ICGC PACA-CA Release 18 Illumina HiSeq 2000;, Illumina HiSeq 2500; 506 bam,fastq
EGAD00001001096 Illumina HiSeq 2000; 419 bam
EGAD00001001098 DATA FILES FOR SJINF RNASeq Illumina HiSeq 2000; 63 bam
EGAD00001001100 DCC Project Code: SKCA-BR Skin Adenocarcinoma - BR Brazil Illumina HiSeq 2500;ILLUMINA 200
EGAD00001001104 MMP-seq tumor samples, UDG treated (FASTQ) Illumina MiSeq; 16 fastq
EGAD00001001105 Whole-exome sequencing in 16 RMS cases Whole-transcriptome sequencing in 8 RMS cases Illumina HiSeq 2000; 38 bam
EGAD00001001106 In the first part of this project, we will differentiate IPS cells from 5 human donors into macrophages, and extract RNA from unstimulated and LPS stimulated macrophages to perform RNA sequencing. We will also extract RNA before and after stimulation in blood- derived macrophages from 5 additional, unrelated healthy samples. In the second part of the project, RNA-seq data will be analysed to compare LPS response of these two macrophage populations. In summary, we will perform 75bp PE RNA-seq on 20 samples (10 pre and post stimulus), on the HiSeq 2500 platform. Samples will be multiplexed at 5 samples / lane, so we will require 4 flow cells in total. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 18
EGAD00001001107 MMP-seq cell lines (FASTQ) Illumina Genome Analyzer IIx; 154 fastq
EGAD00001001108 MMP-seq tumor samples (FASTQ) Illumina Genome Analyzer IIx; 218 fastq
EGAD00001001109 Illumina HiSeq 2000; 46
EGAD00001001110 Illumina HiSeq 2000; 46
EGAD00001001111 Illumina HiSeq 2000; 46
EGAD00001001112 Illumina HiSeq 2000; 46
EGAD00001001113 Illumina HiSeq 2000; 46 bam
EGAD00001001114 DDD DATAFREEZE 2013-12-18: 1133 trios - exome sequence BAM files (Ref: DDD Nature 2015) 3,335 bam,tab
EGAD00001001115 SeqControl Illumina HiSeq 2500; 54 fastq
EGAD00001001116 We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331 Illumina HiSeq 2000; 190 bam
EGAD00001001118 Gastric Cancer (GC) is a highly heterogeneous disease. To identify potential clinically actionable therapeutic targets that may inform individualized treatment strategies, we performed whole-exome sequencing on 78 GCs of differing histologies and anatomic locations, as well as whole-genome sequencing on two GC cases, each with 3 primary tumours and 2 matching lymph node metastases. The data showed two distinct GC subtypes with either high-clonality (HiC) or low-clonality (LoC). Illumina HiSeq 2000; 168 fastq
EGAD00001001119 Whole Genome Bisulfite Sequencing Illumina HiSeq 2000;, Illumina HiSeq 2500; 26 fastq
EGAD00001001120 Whole Genome Sequencing Illumina HiSeq 2000;, Illumina HiSeq 2500; 64 fastq
EGAD00001001121 RNA Sequencing Illumina HiSeq 2000; 26 fastq
EGAD00001001122 FFPE normal panel generation for use with V3 cancer panel 0618521 Illumina HiSeq 2000; 94 cram
EGAD00001001123 Deep sequencing of two skin biopsies to study the landscape of somatic mutations in human adult tissues. Illumina HiSeq 2000; 2 cram
EGAD00001001124 Our aim is to analyze the genome of human melanoma cell lines and short term culture from human melanoma samples in order to identify genes that confer drug resistance to clinically relevant targeted therapies. We will perform whole-exome sequencing, copy number variation analysis and methylome analysis in a collection of human melanoma cell lines and short term culture that will be then screened for drug sensitivity/resistance through a library of clinically relevant drugs and drug combinations. By the combined analysis of the genomic lesion and the drug sensitivity/resistance profile of different cell lines, we will look for genes whose mutation is associated to the sensitivity or resistance to a specific drug in different samples. Illumina HiSeq 2000; 14 cram
EGAD00001001125 Exome sequencing of Untreated BCC samples. Illumina HiSeq 2000; 91 fastq
EGAD00001001126 340 other
EGAD00001001127 ChIP-Seq data for 2 effector memory CD8-positive, alpha-beta T cell sample(s). 10 run(s), 10 experiment(s), 10 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 2 fastq,bam
EGAD00001001128 Bisulfite-Seq data for 3 cytotoxic CD56-dim natural killer cell sample(s). 38 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 3 bam
EGAD00001001129 RNA-Seq data for 10 mature neutrophil sample(s). 10 run(s), 10 experiment(s), 10 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 10 fastq,readme_file,bam
EGAD00001001130 DNase-Hypersensitivity data for 5 CD14-positive, CD16-negative classical monocyte sample(s). 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811 Illumina HiSeq 2000; 5 fastq,readme_file,bam
EGAD00001001131 Bisulfite-Seq data for 1 memory B cell sample(s). 20 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam
EGAD00001001132 RNA-Seq data for 3 inflammatory macrophage sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 3 fastq,bam,readme_file
EGAD00001001133 Bisulfite-Seq data for 2 erythroblast sample(s). 35 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 2 bam,readme_file
EGAD00001001134 Bisulfite-Seq data for 1 precursor lymphocyte of B lineage sample(s). 8 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam,readme_file
EGAD00001001135 Bisulfite-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 2 bam
EGAD00001001136 ChIP-Seq data for 2 endothelial cell of umbilical vein (proliferating) sample(s). 13 run(s), 13 experiment(s), 13 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 2 fastq,bam
EGAD00001001137 RNA-Seq data for 2 CD8-positive, alpha-beta T cell sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 2 fastq,readme_file,bam
EGAD00001001138 ChIP-Seq data for 6 Acute promyelocytic leukemia sample(s). 25 run(s), 23 experiment(s), 23 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 6 fastq,bam
EGAD00001001139 Bisulfite-Seq data for 3 inflammatory macrophage sample(s). 38 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 3 bam,readme_file
EGAD00001001140 RNA-Seq data for 4 megakaryocyte-erythroid progenitor cell sample(s). 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 4 fastq,readme_file,bam
EGAD00001001141 Bisulfite-Seq data for 1 hematopoietic multipotent progenitor cell sample(s). 8 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam,readme_file
EGAD00001001142 RNA-Seq data for 1 endothelial cell of umbilical vein (resting) sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001143 Bisulfite-Seq data for 4 alternatively activated macrophage sample(s). 64 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 4 bam,readme_file
EGAD00001001144 ChIP-Seq data for 1 central memory CD4-positive, alpha-beta T cell sample(s). 6 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001145 RNA-Seq data for 2 CD38-negative naive B cell sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 2 fastq,bam
EGAD00001001146 RNA-Seq data for 3 granulocyte monocyte progenitor cell sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 3 fastq,readme_file,bam
EGAD00001001147 ChIP-Seq data for 7 CD4-positive, alpha-beta T cell sample(s). 46 run(s), 45 experiment(s), 45 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 7 fastq,readme_file,bam
EGAD00001001148 RNA-Seq data for 8 CD14-positive, CD16-negative classical monocyte sample(s). 8 run(s), 8 experiment(s), 8 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 8 fastq,readme_file,bam
EGAD00001001149 ChIP-Seq data for 7 mature neutrophil sample(s). 78 run(s), 60 experiment(s), 60 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 7 fastq,readme_file,bam
EGAD00001001150 Bisulfite-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam
EGAD00001001151 Bisulfite-Seq data for 1 endothelial cell of umbilical vein (proliferating) sample(s). 21 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam
EGAD00001001152 Bisulfite-Seq data for 2 Multiple myeloma sample(s). 16 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 2 bam,readme_file
EGAD00001001153 RNA-Seq data for 1 effector memory CD8-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001154 ChIP-Seq data for 5 CD8-positive, alpha-beta T cell sample(s). 28 run(s), 28 experiment(s), 28 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 5 fastq,readme_file,bam
EGAD00001001155 ChIP-Seq data for 5 alternatively activated macrophage sample(s). 36 run(s), 35 experiment(s), 35 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 5 fastq,bam,readme_file
EGAD00001001156 RNA-Seq data for 6 hematopoietic stem cell sample(s). 13 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 6 fastq,readme_file,bam
EGAD00001001157 Bisulfite-Seq data for 3 CD4-positive, alpha-beta T cell sample(s). 61 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 3 bam
EGAD00001001158 ChIP-Seq data for 4 cytotoxic CD56-dim natural killer cell sample(s). 16 run(s), 16 experiment(s), 16 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 4 fastq,bam
EGAD00001001159 RNA-Seq data for 3 cytotoxic CD56-dim natural killer cell sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 3 fastq,bam
EGAD00001001160 Bisulfite-Seq data for 1 plasma cell sample(s). 11 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam,readme_file
EGAD00001001161 DNase-Hypersensitivity data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001162 Bisulfite-Seq data for 1 Acute myeloid leukemia sample(s). 18 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam
EGAD00001001163 RNA-Seq data for 1 effector memory CD4-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001164 RNA-Seq data for 1 class switched memory B cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001165 RNA-Seq data for 5 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 23 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 5 fastq,readme_file,bam
EGAD00001001166 RNA-Seq data for 1 endothelial cell of umbilical vein (proliferating) sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001167 Bisulfite-Seq data for 3 Acute promyelocytic leukemia sample(s). 24 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 3 bam
EGAD00001001168 ChIP-Seq data for 2 mature eosinophil sample(s). 12 run(s), 12 experiment(s), 12 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 2 fastq,bam
EGAD00001001169 RNA-Seq data for 3 common myeloid progenitor sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 3 fastq,readme_file,bam
EGAD00001001170 RNA-Seq data for 1 conventional dendritic cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001171 RNA-Seq data for 1 memory B cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001172 RNA-Seq data for 1 central memory CD4-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001173 RNA-Seq data for 10 CD4-positive, alpha-beta T cell sample(s). 10 run(s), 10 experiment(s), 10 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 10 fastq,bam
EGAD00001001174 RNA-Seq data for 1 regulatory T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001175 RNA-Seq data for 1 central memory CD8-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001176 Bisulfite-Seq data for 1 class switched memory B cell sample(s). 20 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam
EGAD00001001177 RNA-Seq data for 7 erythroblast sample(s). 29 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 7 fastq,readme_file,bam
EGAD00001001178 RNA-Seq data for 1 Leukemia sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001179 ChIP-Seq data for 10 CD14-positive, CD16-negative classical monocyte sample(s). 73 run(s), 69 experiment(s), 69 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 10 fastq,readme_file,bam
EGAD00001001180 Bisulfite-Seq data for 2 central memory CD8-positive, alpha-beta T cell sample(s). 27 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 2 bam
EGAD00001001181 RNA-Seq data for 7 Acute promyelocytic leukemia sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 7 fastq,bam
EGAD00001001182 ChIP-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001183 ChIP-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 10 run(s), 10 experiment(s), 10 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 2 fastq,bam
EGAD00001001184 RNA-Seq data for 5 common lymphoid progenitor sample(s). 20 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 5 fastq,readme_file,bam
EGAD00001001185 DNase-Hypersensitivity data for 2 monocyte sample(s). 4 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811 Illumina HiSeq 2000; 2 fastq,bam
EGAD00001001186 RNA-Seq data for 3 hematopoietic multipotent progenitor cell sample(s). 9 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 3 fastq,readme_file,bam
EGAD00001001187 ChIP-Seq data for 3 Chronic lymphocytic leukemia sample(s). 6 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 3 fastq,bam
EGAD00001001188 ChIP-Seq data for 7 Acute myeloid leukemia sample(s). 23 run(s), 23 experiment(s), 23 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 7 fastq,bam
EGAD00001001189 Bisulfite-Seq data for 4 CD8-positive, alpha-beta T cell sample(s). 56 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 4 bam,readme_file
EGAD00001001190 DNase-Hypersensitivity data for 1 Acute myeloid leukemia sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001191 RNA-Seq data for 8 monocyte sample(s). 8 run(s), 8 experiment(s), 8 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 8 fastq,bam
EGAD00001001192 Bisulfite-Seq data for 5 macrophage sample(s). 72 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 5 bam,readme_file
EGAD00001001193 DNase-Hypersensitivity data for 2 inflammatory macrophage sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811 Illumina HiSeq 2000; 2 fastq,bam,readme_file
EGAD00001001194 ChIP-Seq data for 2 erythroblast sample(s). 14 run(s), 14 experiment(s), 14 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 2 fastq,bam,readme_file
EGAD00001001195 ChIP-Seq data for 1 effector memory CD8-positive, alpha-beta T cell, terminally differentiated sample(s). 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 1 fastq,bam
EGAD00001001196 ChIP-Seq data for 13 macrophage sample(s). 55 run(s), 55 experiment(s), 55 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000;, NextSeq 500; 13 fastq,readme_file,bam
EGAD00001001197 ChIP-Seq data for 2 monocyte sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000;, NextSeq 500; 2 fastq,bam
EGAD00001001198 DNase-Hypersensitivity data for 14 macrophage sample(s). 18 run(s), 14 experiment(s), 14 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811 Illumina HiSeq 2000; 14 fastq,readme_file,bam
EGAD00001001199 RNA-Seq data for 18 macrophage sample(s). 19 run(s), 18 experiment(s), 18 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 18 fastq,readme_file,bam
EGAD00001001200 Bisulfite-Seq data for 1 effector memory CD8-positive, alpha-beta T cell sample(s). 11 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam
EGAD00001001201 Bisulfite-Seq data for 6 mature neutrophil sample(s). 79 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 6 bam,readme_file
EGAD00001001202 RNA-Seq data for 4 alternatively activated macrophage sample(s). 6 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811 Illumina HiSeq 2000; 4 fastq,bam,readme_file
EGAD00001001203 Bisulfite-Seq data for 1 germinal center B cell sample(s). 8 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 1 bam,readme_file
EGAD00001001204 ChIP-Seq data for 6 inflammatory macrophage sample(s). 35 run(s), 35 experiment(s), 35 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 6 fastq,bam,readme_file
EGAD00001001205 Bisulfite-Seq data for 3 CD38-negative naive B cell sample(s). 29 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 3 bam
EGAD00001001206 Bisulfite-Seq data for 6 CD14-positive, CD16-negative classical monocyte sample(s). 86 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811 Illumina HiSeq 2000; 6 bam,readme_file
EGAD00001001207 ChIP-Seq data for 4 CD38-negative naive B cell sample(s). 14 run(s), 14 experiment(s), 14 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811 Illumina HiSeq 2000; 4 fastq,bam
EGAD00001001208 Targeted capture of cancer gene panel bait set in single cell derived organoids from colon tissue and colorectal cancer from 1 patient. Illumina HiSeq 2000;, Illumina HiSeq 2500; 105 cram
EGAD00001001209 To examined the reproducibility of nucleotide variant calls in replicate sequencing experiments of the same genomic DNA, we performed targeted sequencing of all known human protein kinase genes (kinome) (~3.3 Mb) using the SOLiD v4 platform. This data set contains 17 breast cancer samples that were sequenced in duplicate (n=14) or triplicate (n=3), in order to assess concordance of all calls and single nucleotide variant (SNV) calls. AB SOLiD 4 System; 37 SOLiD_native_csfasta,SOLiD_native_qual
EGAD00001001210 Altered translation response to stress by medulloblastoma-associated DDX3X mutations 28 bam
EGAD00001001212 RNAseq profile of purified plasma cells from multiple myeloma patients and tonsils of healthy donors Illumina HiSeq 2000; 15 fastq
EGAD00001001213 Illumina HiSeq 2000; 88 bam
EGAD00001001214 Deep (>25x mean coverage) whole genome sequencing on 5-10 families drawn from the Scottish Family Health Study with four or more children. Illumina HiSeq 2000; 19 bam
EGAD00001001215 Targeted sequencing follow-up of genomic lesions in multiple myeloma. Illumina HiSeq 2000; 424 cram
EGAD00001001216 The aim of this project is to genotype and sequence single spermatozoa from two men, one in his twenties and the other in his seventies. The resulting data is used to quantify the mutations that have arisen in the gametes of both individuals in order to better understand the effect of aging on mutation rates and modes. Project Outline. In order to quantify mutations, semen from two individuals are sequenced. 48 single sperm cells are isolated from each individual, and their DNA is extracted. The resulting genomes are amplified using PicoPlex, GenomiPhi MDA, Repli-G MDA, and MALBAC. QC step is applied to check the quality of WGA DNA using standard Sequenom plex (26 SNPs). A subset of 32 amplification products which pass the intiall QC, are genotyped using Affymetrix SNP6 chips. 12 of the genotyped amplification products are also sequenced. In addition, one multi-cell sample per individual is sequenced as a reference and for validation purposes. Altogether, 12 single cell sperm genomes and two multi-cell genomes are sequenced, coming to a total of 14 genomes. Of the single cell sperm genomes, 2 are sequenced to 50x coverage, and the other 10 to 25x coverage. Both multi-cell genomes are sequenced to 25x coverage. Illumina HiSeq 2000; 12 cram
EGAD00001001217 15 bam
EGAD00001001218 10 bam
EGAD00001001220 Illumina HiSeq 1000; 10 bam
EGAD00001001221 Illumina HiSeq 2500; 54 fastq
EGAD00001001222 TGCT Whole Exome Sequencing data Illumina HiSeq 2500; 84 bam
EGAD00001001226 smRNA-Seq assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Canada as part of the International Human Epigenome Consortium. 28 bam
EGAD00001001227 Strand-specific mRNA-Seq assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. 32 bam
EGAD00001001228 Whole genome shotgun sequencing assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. 27 bam,vcf
EGAD00001001229 ChIP-Seq (H3K27ac) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA 48 bam
EGAD00001001230 ChIP-Seq (H3K27me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA 48 bam
EGAD00001001231 ChIP-Seq (H3K36me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA 48 bam
EGAD00001001232 ChIP-Seq (H3K4me1) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA 48 bam
EGAD00001001233 ChIP-Seq (H3K4me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA 48 bam
EGAD00001001234 ChIP-Seq (H3K9me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA 48 bam
EGAD00001001235 ChIP-Seq (Input) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. 48 bam
EGAD00001001236 Targetted capture and resequencing of 94 known myeloid genes across MPN trials (PT1 and Voriconazole study) and other MPN samples. Illumina HiSeq 2000; 1,860 cram
EGAD00001001237 This is a pilot project to determine whether the TAPG FFPE DNA's are suitable for deep sequencing. If successful an investigation of SNP distribution in a larger cohort will follow. Illumina HiSeq 2000; 15 cram
EGAD00001001238 Extension analysis to pursue candidate genes of interest in chordoma Illumina HiSeq 2000; 262 cram
EGAD00001001239 Extension analysis to pursue candidate genes of interest in chordoma Illumina HiSeq 2000; 262 cram
EGAD00001001240 VCF files of somatic variants from tumor-normal pairs of Asian lung cancer patients 30 vcf
EGAD00001001242 Pilot study to set up sequencing protocols for targeted pulldown methylation profiling Illumina MiSeq; 2 cram
EGAD00001001243 Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci. Illumina HiSeq 2000; 9 bam,fastq
EGAD00001001244 RNA-sequencing (RNA-seq) was performed with RNA extracted from fresh-frozen human tumor tissue samples. cDNA libraries were prepared from poly-A selected RNA applying the Illumina TruSeq protocol for mRNA. The libraries were then sequenced with a 2 x 100bp paired-end protocol to a minimum mean coverage of 30x of the annotated transcriptome. Illumina HiSeq 2000; 59 fastq
EGAD00001001245 DATA FILES FOR PCGP SJINF WES Illumina HiSeq 2000; 40 bam
EGAD00001001246 DATA FILES FOR PCGP SJMEL WXS Illumina HiSeq 2000; 28 bam
EGAD00001001247 DATA FILES FOR PCGP SJMEL RNASEQ Illumina HiSeq 2000; 7 bam
EGAD00001001248 DATA FILES FOR PCGP SJETP WXS Illumina HiSeq 2000; 13 bam
EGAD00001001249 WES of HCC by HiSeq 2000,total 71 samples including Hepatocellular carcinoma cell lines and nornal sample(Peripheral Blood or the adjacent tissues of cancer) Illumina HiSeq 2000; 71 fastq
EGAD00001001250 Low coverage (4-6x) sequencing on samples from population cohorts (Finrisk, Health2000) will be done at Wellcome Trust Sanger Institute (WTSI) using Illumina HiSeq sequencing technology. We will produce 100bp paired end reads. Variants will be called using the 1000 Genomes Project pipeline. The samples have been selected from a national representative set of 8028 samples from persons of 30 years or older, which were screened for psychotic and bipolar disorders using the Composite International Diagnostic Interview, self-reported diagnoses, medical examination, and national registers. Illumina HiSeq 2000; 731 bam
EGAD00001001251 Low coverage (4-6x) sequencing on samples from population cohorts (Finrisk, Health2000) will be done at Wellcome Trust Sanger Institute (WTSI) using Illumina HiSeq sequencing technology. We will produce 100bp paired end reads. Variants will be called using the 1000 Genomes Project pipeline. The samples have been selected from a national representative set of approximately 30,300 samples and comprises 500 individuals of each gender in the extreme tail of high density lipoprotein (HDL) concentrations. Included individuals were between 25 and 65 years of age. Individuals with a diagnosis of diabetes or BMI>30 were excluded from the study. Illumina HiSeq 2000; 966 bam
EGAD00001001252 DNA was derived from the primary tumour, lung metastasis, and peri-aortic lymph node metastasis. DNA from the spleen was used as a normal control. For WE sequencing we user Hybrid capture (Nimblegen version 3.0) of the lymph node and lung metastases, primary tumour and spleen normal; we generated ~100-fold coverage. 4 bam
EGAD00001001253 DNA was derived from the primary tumour, lung metastasis, and peri-aortic lymph node metastasis. DNA from the spleen was used as a normal control. WG sequencing produced ~30-fold (primary tumour, spleen normal)-50-fold (lung metastasis) coverage 3 bam
EGAD00001001256 Clonal hematopoiesis was investigated in patients with aplastic anemia using next-generation sequencing and single-nucleotide polymorphism (SNP) array-based karyotyping. Illumina HiSeq 2000; 186 bam
EGAD00001001257 Illumina HiSeq 2000; 3 fastq
EGAD00001001258 Illumina HiSeq 2000; 5 fastq
EGAD00001001259 Illumina HiSeq 2000; 2 fastq
EGAD00001001260 Illumina HiSeq 2000; 2 fastq
EGAD00001001261 Bisulfite-Seq of CD14-positive, CD16-negative classical monocyte samples for methylome saturation and COMET analysis Illumina HiSeq 2000; 2 bam,readme_file
EGAD00001001262 Unaligned bam of 31 samples derived from primary tumor Illumina HiSeq 2000;, Illumina Genome Analyzer IIx; 31 bam
EGAD00001001263 Unaligned bam of 31 samples derived from blood Illumina Genome Analyzer IIx; 31 bam
EGAD00001001264 We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000; 223 cram
EGAD00001001265 Genomic architecture of mesothelioma parent study is project 925. This project is set up in parallel to project 925 in order to Whole genome sequence ten of the 59 tumours in that project. HiSeq X Ten; 18 cram
EGAD00001001266 Whole genome sequencing of primary angiosarcoma HiSeq X Ten; 12 cram
EGAD00001001267 Anaplastic meningiomas are a rare, malignant variant of meningioma. At present there is no effective treatment for this cancer. The aim of the study is to identify somatic mutations in anaplastic meningiomas. We plan to sequence a set of 500 known cancer genes in 50 anaplastic meningioma and corresponding peripheral blood DNA samples. Bioinformatics will be used to analyse the results to assess the probability of these mutations being causal and so likely of critical importance for the tumour growth. Identification of these mutations will guide selection of appropriate compounds to effectively treat the disease. HiSeq X Ten; 60 cram
EGAD00001001268 H9 human embryonic stem cells (hESCs) were cultured in feeder-free chemically-defined conditions in medium containing 10ng/ml Activin A and 12ng/ml FGF2 (Vallier L. 2011, Methods in Molecular Biology, 690: 57-66). Chromatin immunoprecipitation was performed as described in Brown S. et al. 2011. Stem Cells 29: 1176-85 by using 5ug of anti-DPY30 antibody (Sigma, cat. number HPA043761). This protocol was performed in control hESCs (expressing a scrambled shRNA) and in hESCs stably expressing an shRNA against DPY30 (Sigma, clone n. TRCN0000131112). This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 4 cram
EGAD00001001269 Exome bam files of 75 Individuals From Multiply Affected Coeliac Families Illumina Genome Analyzer II;, Illumina Genome Analyzer IIx; 75 bam
EGAD00001001271 Around 50 samples of pre-invasive lung cancer lesions showing subsequent clinical and pathological progression or regression HiSeq X Ten; 50 cram
EGAD00001001272 Illumina HiSeq 2000; 15 fastq
EGAD00001001273 Whole genome sequencing was performed with DNA extracted from fresh-frozen tumor and normal material. Short insert DNA libraries were prepared with the TruSeq DNA PCRfree sample preparation kit (Illumina) for paired-end sequencing at a minimum read length of 2x100bp. Human DNA libraries were sequenced to an average coverage of minimum 30x for both tumor and matched normal. Murine DNA libraries of tumor and matched normal were both sequenced to a coverage of 25x. Illumina HiSeq 2000; 100 bam
EGAD00001001274 Brain samples for this dataset were provided by the Medical Research Council Sudden Death Brain and Tissue Bank (Edinburgh, UK). All four individuals sampled were of European descent, neurologically normal during life and confirmed to be neuropathologically normal by a consultant neuropathologist using histology performed on sections prepared from paraffin-embedded tissue blocks. Twelve regions of the central nervous system were sampled from each individual. The regions studied were: cerebellar cortex, frontal cortex, temporal cortex, occipital cortex, hippocampus, the inferior olivary nucleus (sub-dissected from the medulla), putamen, substantia nigra, thalamus, hypothalamus, intralobular white matter and cervical spinal cord. Illumina HiSeq 2000; 48 bam
EGAD00001001275 Illumina HiSeq 2000; 1 fastq
EGAD00001001276 McGill EMC Release 4 for cell type "induced pluripotent stem cell" Illumina HiSeq 2500; 8 fastq
EGAD00001001277 McGill EMC Release 4 in tissue "fat pad" for cell type "fat cell" Illumina HiSeq 2500; 1 fastq
EGAD00001001278 McGill EMC Release 4 in tissue "venous blood" for cell type "B cell" Illumina HiSeq 2500; 41 fastq
EGAD00001001279 McGill EMC Release 4 in tissue "venous blood" for cell type "CD4-positive helper T cell" Illumina HiSeq 2500; 55 fastq
EGAD00001001280 McGill EMC Release 4 in tissue "venous blood" for cell type "CD4-positive, alpha-beta T cell" Illumina HiSeq 2500; 40 fastq
EGAD00001001281 McGill EMC Release 4 in tissue "venous blood" for cell type "eosinophil" Illumina HiSeq 2500; 3 fastq
EGAD00001001282 McGill EMC Release 4 in tissue "venous blood" for cell type "Monocyte" Illumina HiSeq 2500; 82 fastq
EGAD00001001283 McGill EMC Release 4 in tissue "venous blood" for cell type "T cell" Illumina HiSeq 2500; 20 fastq
EGAD00001001284 McGill EMC Release 4 in tissue "Brodmann (1909) area 11" Illumina HiSeq 2500; 1 fastq
EGAD00001001285 McGill EMC Release 4 in tissue "Brodmann (1909) area 44" Illumina HiSeq 2500; 1 fastq
EGAD00001001286 McGill EMC Release 4 in tissue "Brodmann (1909) area 8;Brodmann (1909) area 9" Illumina HiSeq 2500; 1 fastq
EGAD00001001287 McGill EMC Release 4 in tissue "kidney" Illumina HiSeq 2500; 2 fastq
EGAD00001001288 McGill EMC Release 4 in tissue "skeletal muscle tissue" Illumina HiSeq 2500; 29 fastq
EGAD00001001289 McGill EMC Release 4 for assay "Bisulfite-seq": Methylation profiling by high-throughput sequencing Illumina HiSeq 2500; 44 fastq
EGAD00001001290 McGill EMC Release 4 for assay "RNA-seq": Transcriptome profiling by high-throughput sequencing Illumina HiSeq 2500; 261 fastq
EGAD00001001291 McGill EMC Release 4 for assay "mRNA-seq": Transcriptome profiling by high-throughput sequencing Illumina HiSeq 2500; 40 fastq
EGAD00001001292 McGill EMC Release 4 for assay "smRNA-seq": Transcriptome profiling by high-throughput sequencing Illumina HiSeq 2500; 6 fastq
EGAD00001001293 McGill EMC Release 4 for assay "ChIP-Seq Input" Illumina HiSeq 2500; 52 fastq
EGAD00001001294 McGill EMC Release 4 for assay "H3K27me3" Illumina HiSeq 2500; 32 fastq
EGAD00001001295 McGill EMC Release 4 for assay "H3K36me3" Illumina HiSeq 2500; 37 fastq
EGAD00001001296 McGill EMC Release 4 for assay "H3K4me1" Illumina HiSeq 2500; 41 fastq
EGAD00001001297 McGill EMC Release 4 for assay "H3K4me3" Illumina HiSeq 2500; 42 fastq
EGAD00001001298 McGill EMC Release 4 for assay "H3K27ac" Illumina HiSeq 2500; 36 fastq
EGAD00001001299 McGill EMC Release 4 for assay "H3K9me3" Illumina HiSeq 2500; 29 fastq
EGAD00001001300 McGill EMC Release 4 for assay "ATAC-seq": Sequencing of transposase-accessible chromatin as described by Buenrostro et al. (Nature Methods 10, 1213?1218 (2013) doi:10.1038/nmeth.2688) Illumina HiSeq 2500; 1 fastq
EGAD00001001301 Whole exome sequencing data of 5 patients diagnosed with FL that had undergone several relapse episodes without evidence of transformation Illumina HiSeq 2500; 29 bam
EGAD00001001302 Illumina HiSeq 2500; 2 bam
EGAD00001001303 The dataset for the PROP1 study consists of samples of patients with combined pituitary hormone deficiency due to two most prevalent mutations in the PROP1 gene (c.301_302delGA and c.150delA) and healthy relatives and controls. All subjects were genotyped for 21 single nucleotide polymorphisms surrounding the PROP1 gene in order to assess the potential ancestral origin of the respective mutations. The genotype data are displayed in the vcf format. 328 vcf
EGAD00001001304 We used whole-genome bisulfite sequencing (WGBS) to generate unbiased DNA methylation maps of six purified B-cell subpopulations: hematopoietic progenitor cells (HPC); pre-B-II cells (preB2C); naive B cells from peripheral blood (naiBC); germinal center B cells (gcBC); memory B cells from peripheral blood (memBC) and plasma cells from bone marrow (bm-PC). WGBS was performed in 2 biological replicates from each subpopulation. Illumina HiSeq 2000; 10 bam,phenotype_file,readme_file
EGAD00001001305 Dataset contains WES data from 3 astrocytoma patients: blood as control, primary tumor and recurrent tumor 9 bam
EGAD00001001306 Human melanoma samples were collected pre, on, and progression on BRAF inhibitor therapy. RNA was extracted and run on RNA-seq. This has provided insights into different categories of BRAF inhibitor resistance mechanisms. Illumina HiSeq 2000; 38 bam
EGAD00001001307 Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3
EGAD00001001308 Genome and transcriptome sequence data from a primary unknown cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3
EGAD00001001309 Genome and transcriptome sequence data from an appendix cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3
EGAD00001001310 Genome and transcriptome sequence data from a peritoneal mesothelioma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001001311 Genome and transcriptome sequence data from a peritoneal mesothelioma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001001312 Fastq data for whole genome bisulfite sequencing assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;, Illumina HiSeq 2500; 30 fastq
EGAD00001001313 We enriched a panel of cancer associated genes using the Custom Sure Select Target Enrichment Kit. Identified mutations were validated with deep sequencing in order to assess mutated allele frequencies more accurately. Illumina MiSeq; 10 fastq
EGAD00001001314 Sequence data from L1-amplicon libraries prepared from plasma-DNA from a set of 24 female controls and 18 male controls without malignant disease and samples from patients breast (n= 28) and prostate cancer patients (n=61). Illumina MiSeq; 125 fastq
EGAD00001001315 Phenotype determination by SNP-Typing using PCR and snapshotPCR with subsequent fragment analysis. We investigated 400 individuals from Northern Germany and detected up to 12 different SNPs to determine eye, hair and skin colour. More than 1000 different runs on a ABI3130 were performed This dataset includes: - Phenotype information for 400 samples - Summary and complete genotype calls for 12 SNPs on 400 samples. 399 phenotype_file
EGAD00001001316 Exome sequence analysis of individuals with severe early onset inflammatory bowel disease, and their families. Individuals are ascertained through the COLORS in IBD study, which includes centres throughout UK and Europe. Illumina HiSeq 2000; 138 cram
EGAD00001001317 This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 12 cram
EGAD00001001319 The aim of this study is to ascertain whether leukaemic mutations exist within the blood of people with otherwise normal haematopoeisis. To satisfy this aim we plan to look for 7 known leukaemic mutations in the whole blood DNA of a large cohort of blood donors who have normal haematopoesis. Genomic regions around mutational sites have been amplified using a 2 step PCR process which involves barcoding of individual patients Illumina MiSeq; 5,817 cram
EGAD00001001320 This is a study to test ATAC-seq protocols. CD4+ and CD8+ cells have been obtained from three different anatomical compartments. We aim to assay open-chromatin regions across these cells and perform comparative analyses. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina MiSeq; 138 cram
EGAD00001001321 This dataset includes WGS & WTS alignment data generated from 1 ATC tumor, its matched peripheral blood specimen and 3 authenticated ATC cell lines, THJ-16T, THJ-21T and THJ-29T. In addition, it includes WTS data from extra 4 unique anaplastic cell lines, ACT-1, C643, HTh7 and T238. Illumina HiSeq 2000;, Illumina HiSeq 2500; 13 bam
EGAD00001001322 A comprehensive characterisation and analysis of human breast cancers through whole-genome sequencing. Illumina HiSeq 2000; 196 bam
EGAD00001001323 A comprehensive characterisation and analysis of human breast cancers through genome-wide approaches through transcriptomics. Illumina HiSeq 2000; 59 bam
EGAD00001001326 Whole genome sequencing of single adult t-cell leukemia/lymphoma case Illumina HiSeq 2000; 2 bam
EGAD00001001329 Aligned Sequence (bam format), Duplicates removed 28 bam
EGAD00001001330 In this experiment we have sequenced tumour normal pairs from patients presenting with CRC who have a prior history of inflammatory bowel disease. The idea is to identify driver mutations, new genes and novel pathways associated with the development of these malignancies. Illumina HiSeq 2000; 70 cram
EGAD00001001331 The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of large joint (hip and knee) osteoarthritis which culminates in the need for total joint replacement (TJR). In this pilot we will assess the feasibility of the approach in the relevant tissue. We will obtain diseased and non-diseased tissue (cartilage and endochondral bone) following TJR, coupled with a blood sample, from 12 patients. We will characterise the 12 pairs of diseased and non-diseased tissue samples in terms of transcription (RNASeq) The pilot will help assess the feasibility of isolating sufficient levels of starting material for the different approaches, and will instigate the development of analytical approaches to synthesising the resulting data. Illumina HiSeq 2000; 24 cram
EGAD00001001332 Development of a method for separation and parallel sequencing of the genomes and transcriptomes of single cells. Illumina MiSeq;, HiSeq X Ten;, Illumina HiSeq 2500; 700 bam,cram
EGAD00001001333 Whole exome sequencing BAM files for samples from the BRIDGE Consortium with pathogenic or likely pathogenic variants on genes linked to bleeding or platelet disorders. Illumina HiSeq 2000; 28 bam
EGAD00001001334 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000 99
EGAD00001001335 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000;ILLUMINA, Illumina Genome Analyzer II;ILLUMINA 28 bam,srf,cram
EGAD00001001336 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000;ILLUMINA 6 bam
EGAD00001001337 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina MiSeq;ILLUMINA, Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 607
EGAD00001001338 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000;ILLUMINA, Illumina Genome Analyzer II;ILLUMINA 49 bam,srf
EGAD00001001339 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000; 76 bam,cram
EGAD00001001340 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000; 20 cram
EGAD00001001341 We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. Illumina HiSeq 2000; 158 cram
EGAD00001001343 Data from the study of subclonal metastatic expansion in prostate cancer. Whole genome shotgun sequencing of fifteen samples, tumour and whole blood, from the four initial patients. Illumina HiSeq 2000; 15 fastq
EGAD00001001344 Data from the study of subclonal metastatic expansion in prostate cancer. Whole genome shotgun sequencing of six samples, tumour and whole blood, from the three additional patients whose somatic variants were examined in depth. Illumina HiSeq 2000; 6 fastq
EGAD00001001345 Data from the study of subclonal metastatic expansion in prostate cancer. RNA-seq of twelve samples, tumour and benign tissue, from the four initial patients. Illumina HiSeq 2000; 12 fastq
EGAD00001001347 Exome sequencing of a case of lethal EBV-driven LPD Illumina HiSeq 2000; 3 cram
EGAD00001001349 Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells Illumina HiSeq 2000; 4 bam
EGAD00001001350 Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells Illumina HiSeq 2000; 8
EGAD00001001351 Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells Illumina HiSeq 2000; 2 bam
EGAD00001001352 Data files for CONSERTING (WGS) Illumina HiSeq 2000; 38 bam
EGAD00001001353 Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells Illumina HiSeq 2000; 2 bam
EGAD00001001354 Whole exome sequencing of around 700 inflammatory bowel disease cases.This data can only be used for the identification of IBD/immune-mediated disease loci. Illumina HiSeq 2000; 702 cram
EGAD00001001355 DDD DATAFREEZE 2013-12-18: 1133 trios - VCF files (Ref: DDD Nature 2015) 3,335 readme_file,tab,vcf
EGAD00001001356 Neuroblastoma, a clinically heterogeneous pediatric cancer, is characterized by distinct genomic profiles but few recurrent mutations. As neuroblastoma is expected to have high degree of genetic heterogeneity, study of neuroblastoma's clonal evolution with deep coverage whole-genome sequencing of diagnosis and relapse samples will lead to a better understanding of the molecular events associated with relapse. Samples were included in this study if sufficient DNA from constitutional, diagnosis and relapse tumors was available for WGS. Whole genome sequencing was performed on trios (constitutional, diagnose and relapse DNA) from eight patients using Illumina Hi-seq2500 leading to paired-ends (PE) 90x90 for 6 of them and 100x100 for two. Expected coverage for sample NB0175 100x100bp was 30X for tumor and constitutional samples. For the seven other patients expected coverage was 80X for tumor samples with PE 100x100, 100X in the other tumor samples and 50X for all constitutional samples (see table 1). Following alignment with BWA (Li et al., Oxford J, 2009 Jul) allowing up to 4% of mismatches, bam files were cleaned up according to the Genome Analysis Toolkit (GATK) recommendations (Van der Auwera et al., Current Protocols in Bioinformatics, 2013, picard-1.45, GenomeAnalysisTK-2.2-16). Variant calling was performed in parallel using 3 variant callers: GenomeAnalysisTK-2.2-16, Samtools-0.1.18 and MuTect-1.1.4 (McKenna et al., Genome Res, 2010; Li et al., Oxford J, 2009 Aug; Cibulskis et al., Nature, 2013). Annovar-v2012-10-23 with cosmic-v64 and dbsnp-v137 were used for the annotation and RefSeq for the structural annotation. For GATK and Samtools, single nucleotide variants (SNVs) with a quality under 30, a depth of coverage under 6 or with less than 2 reads supporting the variant were filter out. MuTect with parameters following GATK and Samtools thresholds have been used to filter our irrelevant variants. .SNVs within and around exons of coding genes overlapping splice sites.. Then,variants reported in more than 1% of the population in the 1000 genomes (1000gAprl_2012) or Exome Sequencing Project (ESP6500) have been discarded in order to filter polymorphisms. Finally, synonymous variants were filtered out. MuTect focuses on somatic by filtering with constitutional sample. Mpileup comparison between constitutional and somatic DNAs allowed us to focus also on tumor specific SNVs with GATK and Samtools. Finally, every SNV called by our pipeline and also supported in any constitutional samples were filtered our in order to prevent putative constitutional DNA coverage deficiency. Then we analyzed CNVs (copy number variants) with HMMcopy-v0.1.1 (Gavin et al., Genome Res, 2012) and control-FREEC-v6.7 (Boeva et al., Bioinformatics 2011) with a respective window of 2000bp and 1000 bp, and auto-correction of normal contamination of tumor samples for Control-FREEC. Finally we explored Structural variants (SVs) including deletions, inversions, tandem duplications and translocations using DELLY-v0.5.5 with standard parameters (Rausch et al., Oxford J, 2012). In tumors, at least 10 supporting reads were required to make a call and 5 supporting reads for the sample NB0175 with a coverage of only 40X (see table 2). To predict SVs in constitutional samples for subsequent somatic filtering, only 2 supporting reads were required in order not to miss one. To identify somatic events, all the SVs in each normal sample were first flanked by 500 bp in both directions and any SVs called in a tumor sample which was in the combined flanked regions of respective normal sample was removed (see graph 1). Deletions with more than 5 genes impacted or larger than 1Mb and inversions or tandem duplications covering more than 4 genes, were removed. We focused on exonic and splicing events for deletions, inversions, and tandem duplications. For translocation, we keep all SVs that occurred in intronic, exonic, 5'UTR, upstream or splicing regions. Bioinformatics detection of variations with Deep sequencing approach Once PE reads merged and adaptors trimmed by SeqPrep with default parameters, merged reads were aligned via the BWA (Li H. and Durbin R. 2009 PMID 19451168) allowing up to 1 differences in the 22-base-long seeds and reporting only unique alignments. Only reads having a mapping quality 20 or more have been further analysed. Variant calling software was not used, since we aimed to predict variations at low frequencies, observed in less than 1% of reads. Such variants require a custom approach. Using DepthOfCoverage functions of the Genome Analysis Toolkit (GATK) v2.13.2 (McKenna A, et al., 2010 Genome Research PMID: 20644199), we focused on high quality coverage of bases A, C, G and T at the targeted variant position. Depth of coverage of each base following a mapping quality higher than 20 and a base quality higher than 10 have been taken into account in order to focus only on high quality data. Aiming to determine the background level of variability at the studied regions, 10 control samples were included in the analysis. The same approach and filtering criteria have been applied as introduced above over the entire amplicons. In order to highlight variants, for each sample the frequencies of each bases at each amplicon position were then compared to those observed in the set of controls. Statistical analyses were performed with the R statistical software (http://www.R-project.org). Fisher’s exact two-sided tests with a Bonferroni correction were performed to compare percentages of bases between the data sets, i.e. for a given base between a case and the controls. Finally, significant variations were filtered-in once (i) a significant increase in the percentage of avariant base and (ii) a significant decrease in the percentage of it's reference base following our p.values criteria was observed (p.val < 0.05). Illumina HiSeq 2500; 25 bam
EGAD00001001357 Genomic characterisation of a large series of cancer cell lines. Illumina HiSeq 2000; 462
EGAD00001001358 463 newly diagnosed patients from the UK Myeloma XI clinical trial (NCT01554852) underwent whole exome sequencing plus targeted capture of the IGH/K/L and MYC loci. 200 ng of DNA were processed using NEBNext DNA library prepartion kit and hybridised to the SureSelect Human All Exon V5 Plus. Four samples were pooled and run on one lane of a HiSeq 2000 using 76-bp paired end reads. DNA from CD138+ selected bone marrow cells (myeloma tumour) as well as peripheral white blood cells were analysed and somatic mutations detected. Illumina HiSeq 2000; 926 bam
EGAD00001001359 Dataset contains Exome-seq and RNA-seq from 2 GBM patients, as well as RNA-seq from the derived cultured cells (GNS). 6 bam
EGAD00001001360 The majority of neuroblastoma patients have tumors that initially respond to chemotherapy, but a large proportion of patients will experience therapy-resistant relapses. The molecular basis of this aggressive phenotype is unknown. Whole genome sequencing of 23 paired diagnostic and relapsed neuroblastomas showed clonal evolution from the diagnostic tumor with a median of 29 somatic mutations unique to the relapse sample. Eighteen of the 23 relapse tumors (78%) showed RAS-MAPK pathway mutations. Seven events were detected only in the relapse tumor while the others showed clonal enrichment. In neuroblastoma cell lines we also detected a high frequency of activating mutations in the RAS-MAPK pathway (11/18, 61%) and these lesions predicted for sensitivity to MEK inhibition in vitro and in vivo. Our findings provide a rationale for genetic characterization of relapse neuroblastoma and show that RAS-MAPK pathway mutations may function as a biomarker for new therapeutic approaches to refractory disease. 221 other,vcf
EGAD00001001363 To generate an RNA-Seq dataset for organoids apically stimulated with Salmonella Typhimurium. These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2500; 12 cram
EGAD00001001364 This dataset contains whole exome data from 8 esophageal adenocarcinoma tumors, that has been subjected to multiregion sequencing, ranging from 3-8 regions per tumor. In total, 40 tumor samples and 8 normal blood samples have been sequenced on Illumina HiSeq 2500 at a median dept of 90x. Illumina HiSeq 2500; 47 bam
EGAD00001001372 All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate low-coverage sequencing data for 100 Egyptian samples. Illumina HiSeq 2000; 100 cram
EGAD00001001373 The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages, will be sequenced using the standard whole-genome sequencing followed by filtering out of autosomal and X sequences, so that only mtDNA and the Y chromosome will be analysed and released. Illumina HiSeq 2000; 7 bam
EGAD00001001374 The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages will be sequenced using the standard whole-genome sequencing followed by filtering out autosomal and X sequences, so that only mtDNA and the Y chromosome would be analysed and released. Illumina HiSeq 2500; 6
EGAD00001001375 Samples will be from the BRF113683 (BREAK-3) study which is a Phase III Randomized, Open-label Study Comparing GSK2118436 to Dacarbazine (DTIC) in Previously Untreated Subjects With BRAF Mutation Positive Advanced (Stage III) or Metastatic (Stage IV) Melanoma (n=250 enrolled) *NGS [Agilent capture (Sanger V2 panel): 360 genes and 20 gene fusions; Illumina HiSEQ Sequencing] *CNV: [via NGS or Affy SNP 6.0 or Illumina Omni (TBD)] Bioinformatics: Analysis will be performed using core Sanger informatics pipelines similar to those previously described (Papaemmanuil E et al. (2013) Blood. 22:3616 -3627). Briefly, copy number analysis will be performed using the ASCAT algorithm, and base substitutions, small insertions and deletions using the CAVEMAN and Pindel algorithms, respectively. Statistical approaches including generalized linear models will be used to predict clinical variables such as maximum clinical response and duration of response using genetic data. Sanger and EBI to conduct analysis; Raw data and correlation with clinical endpoints to be analyzed by both EBI/Sanger and GSK (unique pipeline analyses to increase call confidence) Illumina HiSeq 2500; 169 cram
EGAD00001001379 Illumina HiSeq 2000; 29 bam
EGAD00001001380 All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate high-coverage sequencing data for 3 Egyptian samples. Illumina HiSeq 2000; 3 cram
EGAD00001001381 Illumina HiSeq 2000; 69 fastq
EGAD00001001382 TwinsUK whole exome sequencing using NimbleGen SeqCap EZ 248 bam,bai
EGAD00001001383 TwinsUK whole exome sequencing using NimbleGen 2.1M SeqCap 242 bam,bai
EGAD00001001384 Mutations that activate the RAF-MEK-ERK signaling pathway, in particular BRAFV600E, occur in many cancers, and mutant BRAF-selective inhibitors have clinical activity in these diseases. Activating BRAF alleles are usually considered to be mutually exclusive with mutant RAS, whereas inactivating mutations in the D594F595G596 motif of the BRAF activation segment can coexist with oncogenic RAS and cooperate via paradoxical MEK/ERK activation. We determined the functional consequences of a largely uncharacterized BRAF mutation, F595L, which was detected along with an HRASQ61R allele by clinical exome sequencing in a patient with histiocytic sarcoma and also occurs in epithelial cancers, melanoma, and neuroblastoma, and investigated its interaction with mutant RAS. We demonstrate that, unlike previously described DFG motif mutants, BRAFF595L is a gain-of-function variant with intermediate activity towards MEK that does not act paradoxically, but nevertheless cooperates with mutant RAS to promote oncogenic signaling. Of immediate clinical relevance, BRAFF595L shows divergent responses to different mutant BRAF-selective inhibitors, whereas signaling driven by BRAFF595L with and without mutant RAS is efficiently blocked by pan-RAF and MEK inhibitors. Mutation data from primary patient samples and cell lines show that BRAFF595L, as well as other BRAF mutations with intermediate activity, frequently coincide with mutant RAS in a broad spectrum of cancers. These data define a novel class of activating BRAF mutations that cooperate with oncogenic RAS in a non-paradoxical fashion to achieve an optimal level of MEK-ERK signaling, extend the spectrum of patients with systemic histiocytic disorders and other malignancies who are candidates for therapeutic blockade of the RAF-MEK-ERK pathway, and underscore the value of comprehensive genetic profiling for understanding the signaling requirements of individual cancers. Illumina HiSeq 2500; 2 fastq
EGAD00001001385 Exome sequencing in 3 Möbius patients AB SOLiD 4 System; 3 bam
EGAD00001001386 Whole Genome Sequencing of Huh7 cell lines Illumina HiSeq 2000; 2 fastq
EGAD00001001387 Using high-throughput sequencing technologies and analytical tools, we conduct an exome sequencing study that will help understand the population genetics of a Croatian island isolate, in a sample of 200 subjects from the Adriatic island of Vis who were selected to reflect islanders with at least four known ancestors in grandparental line who are original islanders. Illumina HiSeq 2000; 193 bam
EGAD00001001389 Genome wide CRISPR screen was performed to find resistance to targeted drugs for melanoma and lung Illumina HiSeq 2500; 15 cram
EGAD00001001390 Human monocytes from a healthy male blood donor were obtained after written informed consent and anonymised. Library preparation was performed essentially as described in the “Whole‐genome Bisulfite Sequencing for Methylation Analysis (WGBS)” protocol as released by Illumina. The library was sequenced on an Illumina HiSeq2500 using 101 bp paired-end sequencing. Read mapping was done with BWA. 1 bam,readme_file
EGAD00001001391 Illumina HiSeq 2000; 3 bam
EGAD00001001393 The aim of this study is to assess translational changes in macrophages over a time course of Salmonella infection. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Illumina HiSeq 2000; 52 cram
EGAD00001001394 Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357 Illumina HiSeq 2000; 101 bam
EGAD00001001395 Background: Invasive lobular breast cancer (ILBC) is the second most common histological subtype after ductal breast cancer (IDBC). In spite of significant clinical and pathological differences, ILBC is still treated as IDBC. Here, we aimed at identifying recurrent genomic alterations in ILBC with potential clinical implications. Methods: Starting from 630 ILBC primary tumors with a median follow up of 10 years, we interrogated oncogenic substitutions and indels of 360 cancer genes and genome-wide copy number alterations in 413 and 170 ILBC samples, respectively, and correlated those findings with clinical, pathological, and outcome features. The Cancer Genome Atlas database was used for comparison of frequency estimates. Results: Besides the high mutation frequency of CDH1 in 65% of the tumors, alterations in one of the three key genes of the PI3K pathway, PIK3CA, PTEN and AKT1, were present in more than half of the cases. ERBB2 and ERBB3 were mutated in 5.1 and 3.6% of the tumors. FOXA1 mutations and ESR1 copy number gains were detected in 9% and 25% of the samples. All these alterations were more frequent in ILBC than IDBC. The histological diversity of ILBC was associated with specific genomic alterations, such as enrichment for ERBB2 mutations in the mixed, non-classic subtype, and for ARID1A mutations and ESR1 gains in the solid subtype. Finally, ERBB2 and AKT1 mutations were associated with short-term risk of relapse, and chromosome 1q and 11p gain with increased and decreased breast cancer free survival, respectively. Conclusion: ERBB2, ERBB3 and AKT1 mutations represent high prevalence therapeutic targets in ILBC. FOXA1 mutations and ESR1 gains urgently deserve dedicated clinical investigation, especially in the context of endocrine treatment. Illumina HiSeq 2000; 541 bam,cram
EGAD00001001397 We sequenced 292 patients who were suffering NSCLC with Whole genome sequencing or Exome sequencing method. Illumina Genome Analyzer II;, Illumina HiSeq 2000; 72 fastq
EGAD00001001398 We sequenced 205 patients who were suffering NSCLC with Exome sequencing method. Illumina Genome Analyzer II;, Illumina HiSeq 2000; 147 fastq
EGAD00001001399 Data represent genome-wide DNA methylation profiles obtained by MethylCap-seq (Diagenode’s MethylCap-kit based purification followed by Illumina GAIIx sequencing), for 70 brain tissue samples, including 65 glioblastoma samples and 5 non-tumoral tissues (obtained from epilepsy surgery). Illumina Genome Analyzer IIx; 70 fastq
EGAD00001001400 Fastq data for whole genome shotgun sequencing assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 27 fastq
EGAD00001001401 Fastq data for smRNA-Seq assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA 28 fastq
EGAD00001001402 Fastq data for stranded mRNA-Seq assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 32 fastq
EGAD00001001403 Fastq data for ChIP-Seq (H3K27ac) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 48 fastq
EGAD00001001404 Fastq data for ChIP-Seq (H3K27me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 48 fastq
EGAD00001001405 Fastq data for ChIP-Seq (H3K36me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 48 fastq
EGAD00001001406 Fastq data for ChIP-Seq (H3K4me1) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 48 fastq
EGAD00001001407 Fastq data for ChIP-Seq (H3K4me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 48 fastq
EGAD00001001408 Fastq data for ChIP-Seq (H3K9me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 48 fastq
EGAD00001001409 Fastq data for ChIP-Seq (Input) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 48 fastq
EGAD00001001410 Whole-exome sequencing of 81 tumor/normal pairs of adult T-cell leukemia/lymphoma Illumina HiSeq 2000; 162 bam
EGAD00001001411 RNA sequencing of 57 tumor samples of adult T-cell leukemia/lymphoma as well as 3 samples of HTLV-1 carrier and 3 samples of healthy volunteers. Illumina HiSeq 2000; 63 bam
EGAD00001001412 Whole genome sequencing of 48 tumor/normal pairs obtained from adult T-cell leukemia/lymphoma. This data set includes 11 full-pass WGS and 37 low-pass WGS data. Illumina HiSeq 2000;, HiSeq X Ten; 96 bam
EGAD00001001413 DDD DATAFREEZE 2013-12-18: 1133 trios - README, family trios, phenotypes, validated DNMs (Ref: DDD Nature 2015) 3,335 readme_file,tab
EGAD00001001415 DATA FILES FOR PCGP Dyer_iPSC WGS Illumina HiSeq 2000; 2 bam
EGAD00001001416 DATA FILES FOR PCGP Dyer_iPSC TEBS Illumina HiSeq 2000; 18 bam
EGAD00001001418 DATA FILES FOR PCGP Dyer_iPSC 5hmc Illumina HiSeq 2000; 8 bam
EGAD00001001421 Clinical Implications of Genomic Alterations in the Tumour and Circulation of Pancreatic Cancer Patients Illumina MiSeq; 125 fastq
EGAD00001001422 HipSci - Bardet-Biedl Syndrome - Exome Sequencing - April 2015 Illumina HiSeq 2000;ILLUMINA 3
EGAD00001001423 Illumina HiSeq 2000; 7 bam
EGAD00001001424 We obtained paired longitudinal specimens from a total of 38 glioblastoma (GBM) patients (34 primary and 4 secondary GBM patients). Treatment-naive initial tumors were available for 35 cases; for the other 3 cases, we used the first available recurrent tumors in lieu of initial tumors. Tumor specimens were subjected to whole-exome sequencing (27 of 38 cases, with the matched normal/blood for 22 of the 27 cases) and transcriptome sequencing (30 of 38 cases). Illumina HiSeq 2000;, Illumina HiSeq 2500; 141 bam
EGAD00001001425 The objectives of this project are the identification of markers related to cancer therapy resistance in the blood of breast cancer patients and to study the genetic changes in cancer cells during this development of resistance. Whole genome amplified DNA from Circulating Tumor Cells (CTCs), selected during the course of systemic treatment from blood of metastatic breast cancer patients, will be exome sequenced . The patients selected for this study did not respond to therapy. Illumina HiSeq 2000; 149 cram
EGAD00001001426 Systematic next generation sequencing efforts are beginning to define the genomic landscape across a range of primary tumours, but we know very little of the mutational evolution that contributes to disease progression. We therefore propose to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in a cohort of matched primary and metastatic colorectal cancers, and additionally to explore the extent to which those mutations identified as recurrent in the metastatic setting are able to subvert normal biological processes using both genetically engineered mouse models and established cancer cell lines. This study will enable us to define to what extent primary tumour profiling can capture the biological processes operative in matched metastases as well as the significance of intratumoural heterogeneity. This dataset contains all the data available for this study on 2015-07-02. Illumina HiSeq 2000; 446 cram
EGAD00001001427 Targeted cancer gene sequencing of samples enrolled in the SSGXVIII trial from Finland. Illumina HiSeq 2000; 312 cram
EGAD00001001428 Identification of human deubiquitylating enzymes whose knock out result in hypersensitivity to DNA damaging agents, by comparing the sequence reads of 'barcode region' from mixed cell culture. Illumina HiSeq 2000; 6 cram
EGAD00001001429 Profiling subclonal architecture and phylogeny in tumors by whole-genome sequence data mining and single-cell genome sequencing HiSeq X Ten; 2