What are Datasets?

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

Total number of Datasets: 2767
Displaying 1 - 2767

Dataset Accession Description Technologysort descending Samples File Types
EGAD00000000019 840 families where both parents have been genotyped together with the child with severe malaria 0
EGAD00000000024 WTCCC2 project samples from National Blood Donors (NBS) Cohort 1
EGAD00001000002 Massive genomic rearrangement acquired in a single catastrophic event during cancer development 11 srf
EGAD00000000023 WTCCC2 project samples from National Blood Donors (NBS) Cohort 1
EGAD00001001658 Genome and transcriptome sequence data from an odontogenic ghost cell carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001001856 100 other
EGAD00010000853 VeraCode GoldenGate GT Assay technology 147
EGAD00010000823 Results of SNP arrays on synchronous CRC samples 1
EGAD00001000277 High Quality Variant Call files, generated by bioscope, converted to vcf format. Complete dataset for all 300 samples. 300 vcf
EGAD00001000001 Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma 18 srf
EGAD00000000020 685 families where both parents have been genotyped together with the child with severe malaria 0
EGAD00010000458 Controls using 450K DNA methylation 151
EGAD00001000202 Neuroblastoma samples (Analyses_vcf files) 204 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
EGAD00000000017 Cord blood control samples from Gambia 0
EGAD00000000018 Severe malaria cases from Gambia 0
EGAD00000000029 Aggregate results from a case-control study on stroke and ischemic stroke. 19,602
EGAD00001000262 OICR PANCREATIC CANCER DATASET 4 bam
EGAD00001000276 OICR PANCREATIC CANCER DATASET 2 10 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
EGAD00010000456 Leukemia samples using 450K DNA methylation 800
EGAD00001000395 Noninvasive Prenatal Molecular Karyotyping from Maternal Plasma 1 bam
EGAD00010000460 GENCORD2 DNA methylation 294
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
EGAD00001000645 ICGC MMML-seq Data Freeze July 2013 whole genome sequencing 42 bam
EGAD00001000648 ICGC MMML-seq Data Freeze July 2013 transcriptome sequencing 31 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
EGAD00001000618 1204 Sardinian males 1,195 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
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
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
EGAD00010000702 SNP-chip genotyping data for one proband in the DDD study (Ref : Carvalho AJHG 2015) 0
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
EGAD00001000660 Analysis .bam files from HiSeq sequencing of Australian ICGC PDAC study samples, submitted 20130826 353 bam
EGAD00001000650 ICGC MMML-seq Data Freeze July 2013 miRNA sequencing 52 bam
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
EGAD00001000709 Dataset of CageKid Blood DNA samples 95 bam
EGAD00001000714 102 bam
EGAD00001000720 Dataset of CageKid tumor-normal paired RNA samples 90 bam
EGAD00001001355 DDD DATAFREEZE 2013-12-18: 1133 trios - VCF files (Ref: DDD Nature 2015) 3,335 readme_file,tab,vcf
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
EGAD00010000574 Pleuropulmonary blastoma samples using 250K 14
EGAD00001000777 Dataset contains MeDIP-Seq, MRE-Seq and H3K4me3 ChIP-Seq data on 5 GBM patients. 16 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
EGAD00001000816 ICGC medulloblastoma whole genome sequencing data, ICGC release 16 44 bam
EGAD00001000814 Whole genome alignments of DIPG patients 40 bam,phenotype_file
EGAD00001000818 Quiescent Sox2+ cells drive hierarchical growth and relapse in Sonic hedgehog subgroup medulloblastoma 4 bam
EGAD00010000534 Illumina HumanMethylation450 BeadChip 0
EGAD00010000528 Illumina HumanHT-12 v4 array 0
EGAD00010000532 Illumina Human Omni1-Quad SNP genotyping array 0
EGAD00010000738 Generation Scotland APOE data 18,336
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
EGAD00010000554 SNP 6.0 arrays of small cell lung cancer 1,032
EGAD00010000556 SNP 6.0 arrays of small cell lung cancer 0
EGAD00010000298 All cases and controls (Hap300) 13,761
EGAD00010000296 1958BC control samples only (Hap550) 2,224
EGAD00010000294 1958BC control samples only (Hap300) 2,436
EGAD00010000292 All cases and Finnish, Dutch, Italian control samples (Hap300) 10,339
EGAD00010000290 NBS control samples only (Hap550) 2,276
EGAD00010000288 All cases and Finnish, Dutch, Italian control samples (Hap550) 6,313
EGAD00001000874 Indel/point mutation of chondrosarcoma 10 vcf
EGAD00001000781 Whole genome, high coverage, sequencing of 128 Ashkenazi Jewish controls 128 vcf
EGAD00010000566 HipSci normal samples using 500K 120
EGAD00010000564 HipSci normal samples using 47K 120
EGAD00010000568 HipSci normal samples using 450K 0
EGAD00010000570 Imputation-based meta-analysis of severe malaria in Kenya. 3,343
EGAD00010000572 Imputation-based meta-analysis of severe malaria in Gambia. 2,870
EGAD00010000580 Gencode control samples using 550K 217
EGAD00010000736 AAD case and control samples from UK and Norway 117
EGAD00010000578 Gencode case samples using 550K 249
EGAD00001000880 233 bam,vcf
EGAD00010000652 Genotyped samples using Illumina HumanOmni2.5 402
EGAD00010000698 PCGP INF ALL SNP6 0
EGAD00010000682 glioma samples tumor using 250K 762
EGAD00010000688 glioma normal samples using 250K 119
EGAD00010000684 glioma normal samples using cytoscan 3
EGAD00010000686 glioma samples tumor using cytoscan 5
EGAD00010000708 Human samples typed on Illumina Omni 5M 124
EGAD00010000704 610k genotyping imputed on Hapmap 3 and 1000G Phase 1 CEU 714
EGAD00001000158 Subgroup-specific structural variation across 1,000 medulloblastoma genomes 23 bam
EGAD00001001210 Altered translation response to stress by medulloblastoma-associated DDX3X mutations 28 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
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
EGAD00001001114 DDD DATAFREEZE 2013-12-18: 1133 trios - exome sequence BAM files (Ref: DDD Nature 2015) 3,335 bam,tab
EGAD00010000658 DLBCL 148 SNP 6.0 Cohort 0
EGAD00010000664 Finnish population cohort genotyping_B 340
EGAD00010000712 ATRT genotyping 0
EGAD00010000662 Finnish population cohort genotyping 7,803
EGAD00010000594 SCOOP severe early-onset obesity cases 1,720
EGAD00010000610 Samples from the Greek island of Crete, MANOLIS cohort 221
EGAD00010000596 PCGP Ph-likeALL GEA 837
EGAD00010000598 PCGP Ph-likeALL SNP6 1,724
EGAD00010000604 DNA methylation data using Illumina 450K 2,195
EGAD00001000946 Divergent clonal selection dominates medulloblastoma at recurrence 125 bam
EGAD00010000552 Neuroblastoma samples 130
EGAD00001001001 2 bam
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
EGAD00010000606 SNP6 data for matched normal samples 8
EGAD00010000608 SNP6 data for seminoma samples 8
EGAD00010000584 WTCCC2 Glaucoma samples using Illumina 670k array 2,765
EGAD00010000602 WTCCC2 Reading and Mathematics ability (RM) samples from UK using the Affymetrix 6.0 array 3,665
EGAD00010000612 Celiac disease North Indian samples using Immunochip 1,227
EGAD00001001887 Exome sequencing VCF files describing mutations during glioma progression. 82 vcf
EGAD00010000858 Achalasia cases & controls 8,151
EGAD00001001860 19 vcf
EGAD00010000616 HumanOmni1-Quad genotyping array 230
EGAD00010000618 Ischemic stroke cases 3,682
EGAD00010000620 Controls 3,683
EGAD00010000622 SNP array data for gastric cancer cell lines 30
EGAD00001001034 Whole genome data (Complete genomics platform) for the study EGAS00001000824 24 other
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
EGAD00010000626 A new beta-globin mutation responsible of a beta-thalassemia (HbVar database ID 2928) was observed in 8 unrelated French families. The mutation carriers originated from Nord-Pas-de-Calais, a Northern French region where the chief town is Lille. 5 unrelated mutation carriers were genotyped for a set of 12 microsatellites from chromosome 11, around the beta-globin gene. Among the 5 mutation carriers, 4 were genotyped for 97 European Ancestry Informative SNPs (EAIMs). 37
EGAD00010000624 A new beta-globin mutation responsible of a beta-thalassemia (HbVar database ID 2928) was observed in 8 unrelated French families. The mutation carriers originated from Nord-Pas-de-Calais, a Northern French region where the chief town is Lille. 5 unrelated mutation carriers were genotyped for a set of 12 microsatellites from chromosome 11, around the beta-globin gene. Among the 5 mutation carriers, 4 were genotyped for 97 European Ancestry Informative SNPs (EAIMs). 0
EGAD00010000630 The TEENAGE study target population comprised adolescent students aged 13–15 years attending the first three classes of public secondary schools located in the wider Athens area of Attica. 436
EGAD00010000634 WTCCC2 People of the British Isles (POBI) samples using Affymetrix 6.0 array 2,930
EGAD00010000632 WTCCC2 People of the British Isles (POBI) samples using Illumina 1.2M array 2,912
EGAD00010000628 The TEENAGE study target population comprised adolescent students aged 13–15 years attending the first three classes of public secondary schools located in the wider Athens area of Attica. 0
EGAD00010000642 CLL Expression Array 144
EGAD00010000644 Affymetrix SNP6.0 cancer cell line exome sequencing data 1,022
EGAD00010000646 DNA methylation analysis of 35 prostate tumor and 6 normal prostate samples 41
EGAD00010000648 nccRCC tumor/normal genotypes 0
EGAD00010000614 40 Druze Trios 120
EGAD00001000845 44 bam
EGAD00001001080 MDS patients 5 bam
EGAD00001001081 Healthy reference samples 3 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
EGAD00001001329 Aligned Sequence (bam format), Duplicates removed 28 bam
EGAD00010000718 BLUEPRINT Gene expression of different B-cell subpopulations 42
EGAD00010000716 BLUEPRINT DNA Methylation of different B-cell subpopulations 35
EGAD00001001075 miRNA-seq Cohort of 15 Benign Centroblasts 15 bam
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
EGAD00001001087 RNAseq BAM files for the Skin samples of the EUROBATS project. 672 bai,bam
EGAD00001001086 These analysis are the BAM files for the LCLs samples of the EUROBATS samples. 765 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
EGAD00010000656 Case samples using SNP 6.0 Array 20
EGAD00010000654 Control samples using SNP 6.0 Arrays 10
EGAD00010000650 Genotypes from Omni2.5 chip 1,213
EGAD00010000847 Genotyping using Affymetrix SNP6.0 49
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
EGAD00010000674 ELSA genome-wide genotypes, excluding estimated related individuals. There are 3 files: .fam, .bim, .bed 7,412
EGAD00010000676 ELSA genome-wide genotypes, including estimated related individuals. There are 3 files: .fam, .bim, .bed 7,452
EGAD00001001126 340 other
EGAD00001000963 Exome sequencing of sporadic schwannomatosis patients 16 bam
EGAD00001000964 Low-coverage whole genome sequencing of sporadic schwannomatosis patients 16 bam
EGAD00001001218 10 bam
EGAD00001001217 15 bam
EGAD00010000694 HCC array for cnv 55
EGAD00010000771 HipSci normal samples REL-2015-04 0
EGAD00001001435 Aligned whole genome bisulfite sequencing data 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. 30 bam
EGAD00010000640 WTCCC2 Visceral Leishmaniasis samples from Sudanl using Illumina 670k 21
EGAD00010000638 WTCCC2 Visceral Leishmaniasis samples from Indial using Illumina 670k 97
EGAD00010000636 WTCCC2 Visceral Leishmaniasis samples from Brazil using Illumina 670k 119
EGAD00010000696 PCGP ETP ALL SNP6 0
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
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
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
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
EGAD00001001240 VCF files of somatic variants from tumor-normal pairs of Asian lung cancer patients 30 vcf
EGAD00010000690 Genome-wide SNP genotyping of African rainforest hunter-gatherers and neighbouring agriculturalists by Illumina HumanOmniExpress 160
EGAD00010000692 Genome-wide DNA methylation epigenotyping of African rainforest hunter-gatherers and neighbouring agriculturalists by Illumina HumanMethylation450 372
EGAD00010000724 Pilot experiment on functional genomics in osteoarthritis (methyl) 0
EGAD00010000730 WTCCC2 Psychosis Endophenotype samples from UK, Germany, Holland, Spain and Australia using the Affymetrix 6.0 array 1
EGAD00001000656 FACS phenotype of 1629 Sardinian samples 1,629 phenotype_file
EGAD00010000710 ATRT genotyping blood 0
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
EGAD00010000722 Pilot experiment on functional genomics in osteoarthritis (coreex) 1
EGAD00010000764 Ovarian tumor samples using Illumina 0
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 bam
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
EGAD00001001413 DDD DATAFREEZE 2013-12-18: 1133 trios - README, family trios, phenotypes, validated DNMs (Ref: DDD Nature 2015) 3,335 readme_file,tab
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
EGAD00010000768 Replication data for HipSci normal samples using both HumanCoreExome-12_v1 and HumanOmni2.5-8 BeadChips 0
EGAD00010000766 We have established a mechanism for the collection of postal DNA samples from consenting National Joint Registry for England and Wales (NJR) patients and have carried out genotyping genome-wide in 903 patients with the condition Developmental Dysplasia of the Hip (DDH) on the Illumina CoreExome array 903
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
EGAD00001001941 Variants derived from mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma. 476 vcf
EGAD00010000791 Illumina HumanOmni2.5-8 BeadChip 1
EGAD00001000702 Complete set of bam files associated with study EGAS00001000622 190 bam
EGAD00010000787 Epigen-Brasil samples using HumanOmni2.5 6,487
EGAD00010000807 Illumina HumanCoreExome genotyping data from the British Society for Surgery of the Hand Genetics of Dupuytren's Disease consortium (BSSH-GODD consortium) collection 4,201
EGAD00001001466 Whole Genome sequencing. 2 ?g of genomic DNA from each sample was used for the construction of two short-insert paired-end sequencing libraries. Both types of libraries were sequenced in paired-end mode on Illumina GAIIx (2 × 151 bp) using Sequencing kit v4 or Illumina HiSeq2000 (2x101 bp) using TruSeq SBS Kit v3. 300 bam
EGAD00001001464 Exome Sequencing. 3 ?g of genomic DNA from each sample were sheared and used for the construction of a paired-end sequencing library as described in the paired-end sequencing sample preparation protocol provided by Illumina41. Enrichment of exonic sequences was then performed for each library using either the Sure Select Human All Exon 50 Mb or All Exon+UTRs v4 kits following the manufacturer’s instructions (Agilent Technologies). Exon-enriched DNA was pulled down by magnetic beads coated with streptavidin (Invitrogen), followed by washing, elution and 18 additional cycles of amplification of the captured library. Enriched libraries were sequenced (2 × 76 bp) in one lane of an Illumina GAIIx sequencer or in two lanes of a HiSeq2000 when using pools of eight samples. 882 bam
EGAD00001002024 Genome and transcriptome sequence data from an anal rectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00010000748 Genotyping using Illumina Human OmniExpress12v1.0 1
EGAD00001001456 1000Genomes imputed data set of 581 cases and 417 controls for male-pattern baldness 1 vcf
EGAD00010000819 Summary statistics from meta-analysis for BP phenotypes 0
EGAD00001001609 Maternal Plasma RNA Sequencing for Genomewide Transcriptomic Profiling and Identification of Pregnancy-Associated Transcripts 14 bam
EGAD00001001616 2 bam
EGAD00001001614 26 bam
EGAD00001001613 10 bam
EGAD00001001615 10 bam
EGAD00010000829 Illumina Infinium 450K array data 70
EGAD00010000827 Illumina Infinium 450K array data 1
EGAD00010000815 ATL tumor samples using Affymetrix 250K SNP array 1
EGAD00010000813 ATL tumor samples using Illumina 450K Methylation array 1
EGAD00010000811 ATL tumor samples using Illumina 610K SNP array 1
EGAD00001001635 Whole genome sequencing detected structural rearrangements of TERT in 17/75 high stage neuroblastoma with 5 cases resulting from chromothripsis. Rearrangements were associated with increased TERT expression and targeted immediate up- and down-stream regions of TERT, placing in 7 cases a super-enhancer close to the breakpoints. TERT rearrangements (23%), ATRX deletions (11%) and MYCN amplifications (37%) identify three almost non-overlapping groups of high stage neuroblastoma, each associated with very poor prognosis. This submission contains all newly sequenced samples only. study_refcenter AMC 42 other
EGAD00001001660 Whole exome sequencing was performed to explore the mutational landscape and potential molecular signature of HPV-positive versus HPV-negative OAC. Four hr-HPV-positive and 8 HPV-negative treatment-naive fresh-frozen OAC tissue specimens and matched normal tissue were analysed to identify somatic genomic mutations 24 bam
EGAD00001001661 Genotype and exome data for an Australian Aboriginal population: a reference panel for health-based research. 72 vcf
EGAD00001002650 Somatic variants called from whole-exome sequencing of meningioma-blood pairs 87 vcf
EGAD00001001663 Low coverage (4x-8x) Illumina HiSeq curated sequence data from 3 African populations from the AGV project; 100 Baganda from Uganda (4x), 100 Zulu from South Africa (4x), and 120 Gumuz, Wolayta, Oromo, Somali and Amhara from Ethiopia (8x). Pre-processed, jointly called and filtered with GATK, refined with Beagle3, phased with SHAPEIT2. 1 vcf
EGAD00001001782 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB8_F 1 other
EGAD00001001785 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW12_F 1 other
EGAD00001001738 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB38_M 1 other
EGAD00001001623 BBMRI - BIOS project - Freeze 1 - Bam files 2,117 bam,contig_fasta
EGAD00001001848 DDD DATAFREEZE 2014-11-04: 4293 trios - VCF files 12,539 vcf
EGAD00001001925 1461 Neuropathological and clinically characterised cases from the MRC Brain Bank 1,461 vcf
EGAD00001001854 Exome sequencing of nine PCC/PGL tumors, SF and FFPE samples 18 bam
EGAD00001001656 Genome and transcriptome sequence data from an atypical chronic lymphocytic leukemia patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001001876 Genome and transcriptome sequence data from a colorectal adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study. These data are included in the manuscript entitled, "Response to Angiotensin Blockade with Irbesartan in a Patient with Metastatic Colorectal Cancer". 4 bam
EGAD00001001655 Genome and transcriptome sequence data from an atypical teratoid rhabdoid tumor patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00010000872 Genotyped case and control sampes using HumanExome Beadchip 1,610
EGAD00001001791 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW15_F 1 other
EGAD00001001801 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW22_M 1 other
EGAD00001001706 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB22_C 1 other
EGAD00001001795 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW18_M 1 other
EGAD00001001748 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB43_C 1 other
EGAD00001001779 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB62_F 1 other
EGAD00001001739 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB40_C 1 other
EGAD00001001722 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB28_F 1 other
EGAD00001001766 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB55_C 1 other
EGAD00001001797 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW20_F 1 other
EGAD00001001828 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW47_M 1 other
EGAD00001001754 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB4_C 1 other
EGAD00001001833 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW4_F 1 other
EGAD00001001829 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW49_C 1 other
EGAD00001001838 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW51_C 1 other
EGAD00001001792 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW15_M 1 other
EGAD00001001762 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB51_M 1 other
EGAD00001001831 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW49_M 1 other
EGAD00001001807 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW27_M 1 other
EGAD00001001780 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB62_M 1 other
EGAD00001001718 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB27_C 1 other
EGAD00001001767 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB55_F 1 other
EGAD00001001781 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB8_C 1 other
EGAD00001001711 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB23_M 1 other
EGAD00001001823 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW46_C 1 other
EGAD00001001778 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB62_C 1 other
EGAD00001001819 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW38_M 1 other
EGAD00001001770 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB57_F 1 other
EGAD00001001743 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB41_F 1 other
EGAD00001001745 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB42_C 1 other
EGAD00001001842 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW52_F 1 other
EGAD00001001813 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW2_M 1 other
EGAD00001001725 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB30_F 1 other
EGAD00001001799 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW22_C 1 other
EGAD00001001835 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW50_C 1 other
EGAD00001001784 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW12_C 1 other
EGAD00001001818 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW38_F 1 other
EGAD00001001708 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB22_M 1 other
EGAD00001001750 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB43_M 1 other
EGAD00001001824 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW46_F 1 other
EGAD00001001830 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW49_F 1 other
EGAD00001001705 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB21_M 1 other
EGAD00001001793 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW18_C 1 other
EGAD00001001834 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW4_M 1 other
EGAD00001001789 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW14_M 1 other
EGAD00001001826 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW47_C 1 other
EGAD00001001768 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB55_M 1 other
EGAD00001001788 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW14_F 1 other
EGAD00001001803 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW24_F 1 other
EGAD00001001756 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB4_M 1 other
EGAD00001001775 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB60_C 1 other
EGAD00001001759 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB50_M 1 other
EGAD00001001721 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB28_C 1 other
EGAD00001001703 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB21_C 1 other
EGAD00001001776 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB60_F 1 other
EGAD00001001695 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB10_F 1 other
EGAD00001001805 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW27_C 1 other
EGAD00001001701 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB1_F 1 other
EGAD00001001796 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW20_C 1 other
EGAD00001001751 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB44_C 1 other
EGAD00001001804 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW24_M 1 other
EGAD00001001765 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB52_M 1 other
EGAD00001001744 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB41_M 1 other
EGAD00001001742 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB41_C 1 other
EGAD00001001816 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW32_M 1 other
EGAD00001001713 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB24_F 1 other
EGAD00001001700 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB1_C 1 other
EGAD00001001714 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB24_M 1 other
EGAD00001001815 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW32_F 1 other
EGAD00001001732 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB33_M 1 other
EGAD00001001699 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB15_M 1 other
EGAD00001001736 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB38_C 1 other
EGAD00001001825 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW46_M 1 other
EGAD00001001843 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW52_M 1 other
EGAD00001001753 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB44_M 1 other
EGAD00001001723 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB28_M 1 other
EGAD00001001741 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB40_M 1 other
EGAD00001001810 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW29_M 1 other
EGAD00001001839 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW51_F 1 other
EGAD00001001755 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB4_F 1 other
EGAD00001001760 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB51_C 1 other
EGAD00001001841 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW52_C 1 other
EGAD00001001822 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW3_M 1 other
EGAD00001001730 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB33_C 1 other
EGAD00001001786 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW12_M 1 other
EGAD00001001798 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW20_M 1 other
EGAD00001001716 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB25_F 1 other
EGAD00001001772 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB58_C 1 other
EGAD00001001717 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB25_M 1 other
EGAD00001001702 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB1_M 1 other
EGAD00001001719 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB27_F 1 other
EGAD00001001731 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB33_F 1 other
EGAD00001001712 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB24_C 1 other
EGAD00001001790 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW15_C 1 other
EGAD00001001758 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB50_F 1 other
EGAD00001001836 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW50_F 1 other
EGAD00001001764 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB52_F 1 other
EGAD00001001800 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW22_F 1 other
EGAD00001001794 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW18_F 1 other
EGAD00001001806 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW27_F 1 other
EGAD00001001697 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB15_C 1 other
EGAD00001001704 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB21_F 1 other
EGAD00001001809 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW29_F 1 other
EGAD00001001724 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB30_C 1 other
EGAD00001001817 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW38_C 1 other
EGAD00001001840 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW51_M 1 other
EGAD00001001727 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB31_C 1 other
EGAD00001001752 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB44_F 1 other
EGAD00001001783 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB8_M 1 other
EGAD00001001771 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB57_M 1 other
EGAD00001001726 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB30_M 1 other
EGAD00001001709 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB23_C 1 other
EGAD00001001811 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW2_C 1 other
EGAD00001001746 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB42_F 1 other
EGAD00001001820 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW3_C 1 other
EGAD00001001757 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB50_C 1 other
EGAD00001001715 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB25_C 1 other
EGAD00001001710 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB23_F 1 other
EGAD00001001761 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB51_F 1 other
EGAD00001001821 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW3_F 1 other
EGAD00001001694 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB10_C 1 other
EGAD00001001696 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB10_M 1 other
EGAD00001001707 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB22_F 1 other
EGAD00001001787 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW14_C 1 other
EGAD00001001814 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW32_C 1 other
EGAD00001001728 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB31_F 1 other
EGAD00001001747 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB42_M 1 other
EGAD00001001827 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW47_F 1 other
EGAD00001001733 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB35_C 1 other
EGAD00001001769 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB57_C 1 other
EGAD00001001763 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB52_C 1 other
EGAD00001001837 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW50_M 1 other
EGAD00001001802 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW24_C 1 other
EGAD00001001737 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB38_F 1 other
EGAD00001001749 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB43_F 1 other
EGAD00001001812 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW2_F 1 other
EGAD00001001698 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB15_F 1 other
EGAD00001001729 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB31_M 1 other
EGAD00001001773 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB58_F 1 other
EGAD00001001735 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB35_M 1 other
EGAD00001001720 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB27_M 1 other
EGAD00001001734 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB35_F 1 other
EGAD00001001774 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB58_M 1 other
EGAD00001001808 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW29_C 1 other
EGAD00001001740 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB40_F 1 other
EGAD00001001777 50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB60_M 1 other
EGAD00010000871 CLL and normal B cell samples using 450K 226
EGAD00001001899 HDAC and PI3K Antagonists Cooperate to Inhibit Growth of MYC-driven Medulloblastoma 102 bam
EGAD00001001943 Here, we studied well-phenotyped individuals from the Flemish Gut Flora Project (FGFP, N=1,106, Belgium) and the effect of environments on microbiome. The 69 major significant phenotypes found in this study are provided. 1,106 phenotype_file
EGAD00001001305 Dataset contains WES data from 3 astrocytoma patients: blood as control, primary tumor and recurrent tumor 9 bam
EGAD00001001987 March 2016 update of Whole genome bisulfite sequencing assay data (bams) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium. 18 bam
EGAD00001002683 A Hematogenous Route for Medulloblastoma Leptomeningeal Metastases 22 bam
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 bam
EGAD00001002255 Sequencing Data for DEEP Paper: "reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T-Cells" Sample: 51_Hf01_BlCM_Ct (human, female, Blood, CD4+ central memory cell, normal control) Sequencing types are: total RNA, Whole Genome Bisulfite, ChipSeq (H3K27ac, H3K9me3, H3k36me3, H3K4me1, H3k27me3, H3K4me3, Input), reChipSeq (H3K27me3, H3K4me3) 1 readme_file,bam
EGAD00001002001 Mapped data (bam files) for high-throughput whole genome sequence data for 83 modern Aboriginal Australians 83 bam,bai
EGAD00001002016 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LICA-FR. 12 bam,bai,readme_file
EGAD00001002014 Isolated populations have unique population genetics characteristics that can help boost power in genetic association studies for complex traits. Leveraging these advantageous characteristics requires an in-depth understanding of parameters that have shaped sequence variation in isolates. This study performs a comprehensive investigation of these parameters using low-depth whole genome sequencing (WGS) across multiple isolates. 6,840 sample_list,vcf
EGAD00001002011 RNA sequencing data of whole blood samples from smoking and non-smoking mothers and their children at gestation/birth and follow-up years. 64 bam
EGAD00001002032 Genome and transcriptome sequence data from an adenoid cystic carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002012 ChIPseq data of whole blood samples from smoking and non-smoking mothers and their children at gestation/birth and follow-up years. 16 bam
EGAD00001002005 Using whole exome sequencing (WES), we identified homozygosity for a missense variant, VPS11: c.2536T>G (p.C846G), as the genetic cause of a leukoencephalopathy syndrome in two individuals from two unrelated Ashkenazi Jewish (AJ) families. Both patients exhibited highly concordant disease progression characterized by infantile onset leukoencephalopathy with brain white matter abnormalities, severe motor impairment, cortical blindness, intellectual disability, and seizures. 2 vcf
EGAD00001002043 Genome and transcriptome sequence data from a recurrent glioma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002038 Genome and transcriptome sequence data from a peripheral T-cell lymphoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 4 bam
EGAD00001002037 Genome and transcriptome sequence data from an adrenal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002036 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002022 Genome and transcriptome sequence data from a colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002017 Genome and transcriptome sequence data from a breast primary patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002034 Genome and transcriptome sequence data from a pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002023 Genome and transcriptome sequence data from a lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002030 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002033 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002039 Genome and transcriptome sequence data from an ovarian cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002028 Genome and transcriptome sequence data from a pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002048 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002040 Genome and transcriptome sequence data from a squamous cell carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002031 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002020 Genome and transcriptome sequence data from a metastatic NPC patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002029 Genome and transcriptome sequence data from an ovarian granulosa patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002044 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002018 Genome and transcriptome sequence data from a melanoma skin cancer - squamous cell carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002047 Genome and transcriptome sequence data from a breast ductal carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002045 Genome and transcriptome sequence data from a lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002042 Genome and transcriptome sequence data from an endometrial cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002049 Genome and transcriptome sequence data from an adrenal cortical carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002021 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002019 Genome and transcriptome sequence data from a patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002046 Genome and transcriptome sequence data from a liposarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002035 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002026 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 4 bam
EGAD00001002025 Genome and transcriptome sequence data from a colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002041 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002027 Genome and transcriptome sequence data from a colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002126 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PRAD-UK. 116 bam,bai,readme_file
EGAD00001002120 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: ORCA-IN. 26 readme_file,bai,bam
EGAD00001002123 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: MALY-DE. 202 readme_file,bai,bam
EGAD00001002121 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BTCA-SG. 24 readme_file,bai,bam
EGAD00001002129 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BRCA-EU. 158 readme_file,bai,bam
EGAD00001002154 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PAEN-AU. 98 readme_file,bai,bam
EGAD00001002155 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LIRI-JP. 524 readme_file,bai,bam
EGAD00001002157 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: MELA-AU. 140 readme_file,bai,bam
EGAD00001002156 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: ESAD-UK. 198 readme_file,bai,bam
EGAD00001002132 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PACA-AU. 192 readme_file,bai,bam
EGAD00001002122 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BRCA-UK. 90 readme_file,bai,bam
EGAD00001002119 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LAML-KR. 18 readme_file,bai,bam
EGAD00001002130 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: CLLE-ES. 194 readme_file,bai,bam
EGAD00001002127 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PBCA-DE. 496 readme_file,bai,bam
EGAD00001002128 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PRAD-CA. 244 readme_file,bai,bam
EGAD00001002124 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: EOPC-DE. 113 readme_file,bai,bam
EGAD00001002153 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PAEN-IT. 74 bam,bai,readme_file
EGAD00001002125 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BOCA-UK. 148 readme_file,bai,bam
EGAD00001002192 Additional sequencing data for 173 donors in EGAS00001000154, a study of Pancreatic Ductal Adenocarcinoma. WGS libraries were used for high-cellularity cases, WXS sequencing to high depth on low-cellularity cases. HiSeq 2xxx platform was used in all cases. The analysis files associated with this dataset are merged, de-duplicated bams aligned against GRCh37, one tumour and one normal bam per donor. 346 bam
EGAD00001002649 Variants called from RNA-seq data of meningioma tumors. 25 vcf
EGAD00001002247 The GoT2D study includes ~2800 samples, half T2D cases and half T2D controls, of Northern European ancestry sequenced over 3 three technologies: deep whole exome sequencing, low-pass (4x) whole genome sequencing, and OMNI 2.5M genotyping. Samples were ascertained to be phenotypically "extreme" (e.g. leaner, younger cases and older, more obese controls). Genotypes (SNVs, INDELs, and SVs) were called separately for each technology and then integrated via genotype refinement into a single phased reference panel; samples and variants were then excluded based on QC procedures described in Fuchsberger et al. Please note that 2 of the samples in the GoT2D vcf do not have phenotype data. 2,872 phenotype_file,vcf
EGAD00001002246 The T2D-GENES/GoT2D 13K exome sequencing study includes ~13,000 samples, half T2D cases and half T2D controls, from five ancestries (~5K Europeans, ~2K each of African-American, East-Asian, South-Asian, and Hispanic). Samples underwent deep exome sequencing, with SNVs and INDEls called according to GATK best practices; variant sites were then filtered according to the GATK best practices, and then samples and variants underwent further filtering based on aggregate genotype quality as described in Fuchsberger et al. (e.g. low call rate, excess heterozygosity for samples, low call rate or coverage for variants). Please note that one of the samples in the T2D-GENES vcf does not have phenotype data. 13,007 phenotype_file,vcf
EGAD00010000777 HipSci bardet-biedl syndrome samples REL-2014-11 1
EGAD00001002109 TSACP TruSeq Amplicon Panel dataset for the TraIT cell line use case 5 other,bam
EGAD00001002069 Complete genomics data for VCaP and PC346c. 2 other
EGAD00001002071 qDNAseq shallow sequencing dataset of the cell line use case. 5 other,bam
EGAD00001002115 Targeted sequencing of 173 genes in 2433 primary breast tumours. Data includes 2433 tumour samples, 523 adjacent normal (breast) samples and 127 blood samples. Libraries were prepared with Illumina's Nextera custom enrichment kit targetting all the exons of the most frequently mutated breast cancer genes. Libraries were multiplexed (48 libraries per lane) and sequenced on Illumina HiSeq 2000 (100bp paired-end reads). Somatic mutations were calling with a custom pipeline. We identified 40 mutation-driver (Mut-driver) genes, and determined associations between mutations, driver CNA profiles, clinical-pathological parameters and survival. We assessed the clonal states of Mut-driver mutations, and estimated levels of intra-tumour heterogeneity using mutant-allele fractions. The results emphasize the importance of genome-based stratification of breast cancer, and have important implications for designing therapeutic strategies. Referece: Pereira et al. (2016) The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes. Nature Communications 3,083 bam,bai
EGAD00001002220 Enteropathy-associated T-cell lymphoma (EATL), a rare and aggressive intestinal malignancy of intraepithelial T lymphocytes, comprises two disease variants (EATL-I and EATL-II) differing in clinical characteristics and pathological features. Here we report findings derived from whole exome sequencing of 15 EATL-II tumor-normal tissue pairs. 15 vcf
EGAD00001001977 DDD DATAFREEZE 2014-11-04: 4293 trios - phenotypic and family descriptions 12,539 phenotype_file
EGAD00001002277 Variation in the Glucose Transporter gene SLC2A2 is associated with glycaemic response to metformin 1 phenotype_file
EGAD00001002142 Paired PCR-free whole genome sequencing data of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. The data was generated with mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions. Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions. 24 bam,vcf,bai
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
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
EGAD00001002265 A pulldown experiment with Agilent SureSelect probes designed on regions that were more likely to contain de novo mutations. 266 candidate sites were selected based on whole genome sequencing data. The probes also included the exons of genes that have been identified as neurodevelopmental disorder genes in DDD (the DDG2P genes) 1,336 targets. In addition, the design included the standard iPLEX sites. 4 bam,bai
EGAD00001002662 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LINC-JP. 62 readme_file,bai,bam
EGAD00001002131 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: RECA-EU. 190 bam,bai,readme_file
EGAD00001002664 ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: CMDI-UK. 98 readme_file,bai,bam
EGAD00010001029 1
EGAD00001002278 58 vcf
EGAD00010000781 HipSci bardet-biedl syndrome samples REL-2015-04 1
EGAD00010000817 HipSci neonatal diabetes mellitus samples REL-2015-04 1
EGAD00010000783 HipSci bardet-biedl syndrome samples REL-2014-11 1
EGAD00010000785 HipSci neonatal diabetes mellitus samples REL-2014-11 1
EGAD00010000744 Subset 2 of osteoarthritis cases genotyped on Illumina 610k from the arcOGEN Consortium (http://www.arcogen.org.uk/) with consent for osteoarthritis studies only. 2,326
EGAD00010000742 Subset 1 of osteoarthritis cases genotyped on Illumina610k from the arcOGEN Consortium (http://www.arcogen.org.uk/) with broader consent. 5,383
EGAD00010000740 Osteoarthritis cases genotyped on Illumina HumanOmniExpress from the arcOGEN Consortium (http://www.arcogen.org.uk/) with broader consent. 674
EGAD00001002537 Genome and transcriptome sequence data from a cholangiocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002534 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002541 Genome and transcriptome sequence data from a liposarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002535 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002539 Genome and transcriptome sequence data from an oligodendroglioma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002548 Genome and transcriptome sequence data from a lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002531 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002556 Genome and transcriptome sequence data from an ovarian cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002554 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002552 Genome and transcriptome sequence data from a Ewing sarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002549 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002555 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002544 Genome and transcriptome sequence data from an ovarian cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002538 Genome and transcriptome sequence data from a uterine sarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002545 Genome and transcriptome sequence data from a duodenal malignancy patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002540 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002547 Exome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002550 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 bam
EGAD00001001657 Genome and transcriptome sequence data from a parotid gland cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002553 Genome and transcriptome sequence data from an unknown cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002543 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002546 Genome and transcriptome sequence data from a melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002533 Genome and transcriptome sequence data from an ovarian cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002542 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002557 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002652 50 ng of genomic double stranded DNA was enzymatically sheared to an average size of 200 bp. Further processing was performed using Illumina Nextera Rapid Capture Custom Kit (Illumina) and 100 bp paired-end sequencing was performed with 24 samples per lane on a Illumina HiSeq 2000 (Illumina) to reach a coverage of 100-1000x. 284 bam,bai
EGAD00001002653 Genomic DNA from leukemic and remission bone marrow mononuclear cells was isolated with the QIAamp DNA Blood Extraction Kit (Qiagen, Venlo, The Netherlands). Libraries were prepared with the Illumina TruSeq DNA Sample Prep and TruSeq Exome Enrichment Kits (Illumina, San Diego, CA, USA) according to the manufacturer's recommendations. 100 bp paired-end sequencing was performed on a HiSeq 2000 (Illumina) to about 80x coverage. 57 bam,bai
EGAD00001001632 miRNA seq data of 13 cases (MMML) 13 bam
EGAD00001001619 miRNA seq data of 43 cases out of dataset EGAD00001000650 (MMML) 43 readme_file,bam
EGAD00001002665 Mapped sequence reads in BAM format for 64 individuals reporting Kanak ancestry recruited in New Caledonia sequenced at four times target coverage using the Illumina HiSeq 4000 platform. 64 bam,bai
EGAD00001002637 Genome and transcriptome sequence data from a metastatic colon cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002580 Genome and transcriptome sequence data from a right breast carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002609 Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002604 Genome and transcriptome sequence data from a clear cell carcinoma of ovary patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002568 Genome and transcriptome sequence data from a metastatic endometrial cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002639 Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002628 Genome and transcriptome sequence data from a squamous cell carcinoma of anus patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002579 Genome and transcriptome sequence data from a carcinoma of left lower outer quadrant patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002636 Genome and transcriptome sequence data from a metastatic pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002622 Genome and transcriptome sequence data from a metastatic colorectal adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002623 Genome and transcriptome sequence data from a cholangiocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002559 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002558 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002575 Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002648 Genome and transcriptome sequence data from a metastatic pancreatic adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002611 Genome and transcriptome sequence data from an adenocarcinoma of unknown primary cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002573 Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002598 Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001001967 Genome and transcriptome sequence data from an adenocarcinoma of right lung patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002621 Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002647 Genome and transcriptome sequence data from a metastatic pancreatic carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002638 Genome and transcriptome sequence data from a metastatic prostate cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002642 Genome and transcriptome sequence data from a metastatic cholangiocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002584 Genome and transcriptome sequence data from a vulvar metastatic melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002593 Genome and transcriptome sequence data from a leiomyosarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002592 Genome and transcriptome sequence data from a pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002588 Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002617 Genome and transcriptome sequence data from a small cell/neuroendocrine carcinoma of the lung patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002631 Genome and transcriptome sequence data from a serous endometrial cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002630 Genome and transcriptome sequence data from a metastatic gastric adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002601 Genome and transcriptome sequence data from an invasive ductal carcinoma of left breast patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001001968 Genome and transcriptome sequence data from a non-small cell lung carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002606 Genome and transcriptome sequence data from an adenocarcinoma of unknown primary cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002589 Genome and transcriptome sequence data from a metastatic neuroendocrine carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002577 Genome and transcriptome sequence data from an adenocarcinoma of primary unknown cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002565 Genome and transcriptome sequence data from an ovarian cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 5 bam
EGAD00001002603 Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002576 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002627 Genome and transcriptome sequence data from an adenoid cystic carcinoma of the trachea patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002620 Genome and transcriptome sequence data from a myxoid liposarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002567 Genome and transcriptome sequence data from a rectosigmoid adenocarcinoma (colorectal cancer) patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002645 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002632 Genome and transcriptome sequence data from a testicular cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002634 Genome and transcriptome sequence data from a metastatic rectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002582 Genome and transcriptome sequence data from a squamous cell carcinoma of anal canal patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002600 Genome and transcriptome sequence data from an adnexal tumor probable of Wolffian origin patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002560 Genome and transcriptome sequence data from a cervical cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002610 Genome and transcriptome sequence data from an invasive carcinoma of left breast patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002570 Genome and transcriptome sequence data from a leiomyosarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002561 Genome and transcriptome sequence data from a metastatic cervical cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002646 Genome and transcriptome sequence data from an epithelioid mesothelioma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002599 Genome and transcriptome sequence data from a medullary thyroid carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002641 Genome and transcriptome sequence data from a metastatic small cell carcinoma of unknown primary cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002586 Genome and transcriptome sequence data from a squamous cell carcinoma of vulva patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002583 Genome and transcriptome sequence data from a retroperitoneal leiomyosarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002607 Genome and transcriptome sequence data from a pancreatic cancer (likely PNET) patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002635 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002590 Genome and transcriptome sequence data from an adenomacarcinoma of vulva patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002625 Genome and transcriptome sequence data from a Ewing sarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002587 Genome and transcriptome sequence data from a metastatic breast carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002572 Genome and transcriptome sequence data from an infiltrating ductal carcinoma of right breast patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002619 Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002564 Genome and transcriptome sequence data from an adenocarcinoma of lung patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002571 Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002614 Genome and transcriptome sequence data from a thymic carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002640 Genome and transcriptome sequence data from a clival chordoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002643 Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002574 Genome and transcriptome sequence data from a ductal carcinoma of left breast patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002615 Genome and transcriptome sequence data from a metastatic colorectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002585 Genome and transcriptome sequence data from a metastatic melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002581 Genome and transcriptome sequence data from a metastatic myxofibrosarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002633 Genome and transcriptome sequence data from an endometrial carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002612 Genome and transcriptome sequence data from an esophageal adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002644 Genome and transcriptome sequence data from a multifocal hepatocellular carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002608 Genome and transcriptome sequence data from a pleomorphic spindle cell sarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001001969 Genome and transcriptome sequence data from a non-small cell lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002597 Genome and transcriptome sequence data from a pancreatic ductal adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002596 Genome and transcriptome sequence data from a porocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002605 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002566 Genome and transcriptome sequence data from a uveal melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002594 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
EGAD00001002591 Genome and transcriptome sequence data from a neuroendocrine tumor likely pancreatic origin patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002624 Genome and transcriptome sequence data from a squamous cell carcinoma of unknown primary cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002618 Genome and transcriptome sequence data from a metastatic rectal cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002616 Genome and transcriptome sequence data from a superficial pleomorphic liposarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002578 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002629 Genome and transcriptome sequence data from a metastatic colon cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002626 Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002595 Genome and transcriptome sequence data from a metastatic adenocarcinoma of the GE junction patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002569 Genome and transcriptome sequence data from a primary unknown cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002602 Genome and transcriptome sequence data from a metastatic breast carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002536 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002613 Genome and transcriptome sequence data from a breast carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001001965 Genome and transcriptome sequence data from a lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001001966 Genome and transcriptome sequence data from a non-small cell lung carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001001961 Genome and transcriptome sequence data from a lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 4 bam
EGAD00001002562 Genome and transcriptome sequence data from an osteogenic sarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001001963 Genome and transcriptome sequence data from a non small cell lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001002563 Genome and transcriptome sequence data from a follicular lymphoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 2 bam
EGAD00001001962 Genome and transcriptome sequence data from a lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002532 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002551 Genome and transcriptome sequence data from a breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001001964 Genome and transcriptome sequence data from a non-small cell lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study 3 bam
EGAD00001002729 Haplotype Reference Consortium Release 1.1 - subset for release via the EGA 11,227 other,vcf,readme_file,tabix,vcf_aggregate
EGAD00001002739 Aligned sequence data from 14 Prostate cancer samples with BRCA2 mutations 49 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
EGAD00001000723 Relative Spatial Homogeneity of Embryonal Brain Tumors of Childhood 60 bam
EGAD00001002771 61 bam
EGAD00001002684 Whole genome sequencing of 98 tumour-normal pairs for the PAEN-AU pancreatic neuroendocrine cancer project. 196 bam
EGAD00001002743 These samples comprise both melanoma cases and controls sequenced for a selection of loci linked to disease susceptibility. These bams are a subset of the sequencing restricted specifically to the GRCh37 coding areas of the BAP1 gene. 3,186 bam
EGAD00001002748 DDD DATAFREEZE 2014-11-04: 4293 trios - exome sequence CRAM files 12,548 cram,bam
EGAD00001003101 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. 267 vcf
EGAD00001003105 Aligned sequence data for 124 CPCGene Tumour/Normal Pairs 184
EGAD00010000230 WTCCC2 samples from Hypertension Cohort - Illuminus 2,943
EGAD00010000232 WTCCC2 samples from Type 2 Diabetes Cohort - Illuminus 2,975
EGAD00010000236 WTCCC2 samples from Coronary Artery Disease Cohort - Illuminus, GenoSNP 3,125
EGAD00010000385 MRCA sample using 300K Illumina 300K - GenomeStudio 394
EGAD00010000150 WTCCC2 project samples from Ankylosing spondylitis Cohort Illumina_670k - Illuminus 2,005
EGAD00001000150 Targeted re-sequencing of 97 genes in T-ALL 454 GS FLX Titanium 33 sff
EGAD00001000224 Enrichment of CRC 454 GS FLX Titanium; 2 bam
EGAD00001000225 Deep sequencing of KRAS 454 GS FLX Titanium; 8 fastq
EGAD00001000708 AZIN1 amplicon sequencing data of the EGAS00001000495 project. 454 GS FLX Titanium; 69 fastq
EGAD00001000272 Genomic Alterations in Gingivo-buccal Cancer: ICGC-India Project_YR01 454 GS FLX Titanium;, Illumina HiSeq 2000; 200 bam
EGAD00001000220 Deep sequencing of CTCs 454 GS FLX Titanium;, Illumina MiSeq; 3 bam
EGAD00001000888 NSCLC WGS. AB 5500 Genetic Analyzer; 4 bam
EGAD00001001436 AB 5500 Genetic Analyzer; 4 bam
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
EGAD00001001596 Whole Exome Sequencing data from the germline of the patient as well as the tumors in bone marrow (T-ALL), Liver (Histiocytic Sarcoma) and ileum (non-Langerhans Cell Histiocytosis). AB 5500xl Genetic Analyzer; 4 bam
EGAD00001002242 This dataset contains RNA-seq and Hi-C data files of induced pluripotent stem (iPS) cells and iPS cell-derived neural progenitors (NPCs) derived from a germline chromothripsis patient and both parents. iPS cells of the patient (cell lines 14 and 15), the father (lines 23 (with two replicates) and 32) and mother (line 30) were differentiated to NPCs and RNA was collected on day 0, day 7 and day 10 of differentiation. In addition, Hi-C data for two iPS cell-derived NPC lines from the patient (14 and 15) and two lines from the father (23 and 32) was generated. AB 5500xl Genetic Analyzer;, Illumina HiSeq 2500; 21 bam
EGAD00001000096 Pancreatic adenocarcinoma QCMG 20120201 AB SOLiD 4 System 166 bam
EGAD00001000632 AB SOLiD 4 System; 12 SOLiD_native_csfasta,SOLiD_native_qual,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
EGAD00001000779 AB SOLiD 4 System; 2 bam
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
EGAD00001000293 Sequencing data for Australian Ovarian Cancer study submitted 20121116 AB SOLiD 4 System; 72 bam
EGAD00001001385 Exome sequencing in 3 Möbius patients AB SOLiD 4 System; 3 bam
EGAD00001000323 Sequencing data for Australian Pancreatic Cancer study submitted 20130102 AB SOLiD 4 System;, Illumina HiSeq 2000; 200 bam
EGAD00001002266 The contribution of genetic predisposing factors to the development of pediatric acute lymphoblastic leukemia (ALL), the most frequently diagnosed cancer in childhood, has not been fully elucidated. Children presenting with multiple de novo leukemias are more likely to suffer from genetic predisposition. Here, we selected five of these patients and analyzed the mutational spectrum of normal and malignant tissues. AB SOLiD 4 System;ABI_SOLID, AB 5500xl Genetic Analyzer;ABI_SOLID 14 bam
EGAD00001000049 Pancreatic adenocarcinoma QCMG 20110901 AB SOLiD System 3.0, AB SOLiD 4 System 26 bam,fastq
EGAD00001000201 MDACC-endo AB SOLiD System 3.0; 28 bam
EGAD00001000115 Mutational landscapes of primary triple negative breast cancers - WGS ABI_SOLID 32 bam
EGAD00010000262 WTCCC2 project Schizophrenia (SP) samples Affyemtrix 6.0 - CHIAMO 3,019
EGAD00010000526 SNP 6.0 arrays of small cell lung cancer Affymetrics_SNP_6.0- 63
EGAD00010000546 SNP 6.0 arrays of carcinoid samples Affymetrics_SNP_6.0- 74
EGAD00010000544 Cusihg's syndrome tumor samples using 250K Affymetrix 250K Nsp-GTYPE 16
EGAD00010000542 Cusihg's syndrome normal samples using 250K Affymetrix 250K Nsp-GTYPE 16
EGAD00010000714 aplastic anemia samples tumor using 250K Affymetrix 250K Nsp-GTYPE 440
EGAD00000000037 NcOEDG Stockholm 2 samples Affymetrix 5.0 514
EGAD00000000004 WTCCC1 project Coronary Artery Disease (CAD) samples Affymetrix 500K 1,998
EGAD00000000009 WTCCC1 project Type 2 Diabetes (T2D) samples Affymetrix 500K 1,999
EGAD00000000005 WTCCC1 project Inflammatory Bowel Disease (IBD) samples Affymetrix 500K 2,005
EGAD00000000007 WTCCC1 project Rheumatooid arthritis (RA) samples Affymetrix 500K 1,999
EGAD00000000001 WTCCC1 project samples from 1958 British Birth Cohort Affymetrix 500K 1,504
EGAD00000000006 WTCCC1 project Hypertension (HT) samples Affymetrix 500K 2,001
EGAD00000000003 WTCCC1 project Bipolar Disorder (BD) samples Affymetrix 500K 1,998
EGAD00000000008 WTCCC1 project Type 1 Diabetes (T1D) samples Affymetrix 500K 2,000
EGAD00000000002 WTCCC1 project samples from UK National Blood Service Affymetrix 500K 1,500
EGAD00000000036 NcOEDG Stockholm 1 samples Affymetrix 500K 484
EGAD00000000039 NcOEDG Malmo - Lund samples Affymetrix 500K 1,374
EGAD00000000016 WTCCC project Tuberculosis (TB) samples Affymetrix 500K 1,498
EGAD00000000015 WTCCC project African control samples Affymetrix 500K 1,496
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
EGAD00000000021 WTCCC2 project samples from 1958 British Birth Cohort Affymetrix 6.0 3,000
EGAD00000000025 WTCCC2 project Ulcerative Colitis (UC) samples Affymetrix 6.0 2,869
EGAD00000000119 Genotypes from cell lines derived from breast carcinoma tissue Affymetrix 6.0 51
EGAD00000000047 Signal data for from 3 recurrent and 1 ovarian primary Granulosa Cell Tumour samples Affymetrix 6.0 4
EGAD00010000950 WTCCC2 Bacteraemia Susceptibility (BS) smaples using Affymetrix 6.0 Affymetrix 6.0 4,924
EGAD00010000282 Pharmacogenomic response to Statins samples (Genotypes/Phenotypes) Affymetrix 6.0 - CHIAMO 4,134
EGAD00010000490 Affymetrix Genome-Wide Human SNP Array 6.0 data Affymetrix 6.0- 19
EGAD00010000936 Affymetrix Exon Array dataset Affymetrix GeneChip Human Exon 1.0 ST 2
EGAD00010000238 CLL Expression array Affymetrix GeneChip Human Genome U133 plus 2.0 64
EGAD00010000901 Russian Tuberculosis samples using Affymetrix 6.0 Affymetrix Genome-Wide Human SNP Array 6.0 Genotypes 11,937
EGAD00010000886 samples using Affymetrix HG_U133_+2 Affymetrix HG_U133_+2 99
EGAD00010000280 CLL Expression array Affymetrix snp 6.0 4
EGAD00010000266 Metabric breast cancer samples (Genotype raw data) Affymetrix SNP 6.0 543
EGAD00010000215 Segmented (CBS) copy number aberrations (CNA); validation set Affymetrix SNP 6.0 995
EGAD00010000217 Segmented (HMM) copy number aberrations (CNA); discovery set Affymetrix SNP 6.0 997
EGAD00010000213 Segmented (CBS) copy number aberrations (CNA); discovery set Affymetrix SNP 6.0 997
EGAD00010000216 Segmented (CBS) copy number variants (CNV); validation set Affymetrix SNP 6.0 995
EGAD00010000164 Affymetrix 6.0 CEL files Affymetrix SNP 6.0 1,992
EGAD00010000214 Segmented (CBS) copy number variants (CNV); discovery set Affymetrix SNP 6.0 997
EGAD00010000050 Matched tumor-negative pancreas tissues Affymetrix SNP 6.0 15
EGAD00010000051 Cell line derived from microdissected primary pancreatic ductal adenocarcinoma tissues Affymetrix SNP 6.0 15
EGAD00010000158 Affymetrix 6.0 cel files Affymetrix SNP 6.0 1,001
EGAD00010000558 SNP 6.0 arrays of small cell lung cancer Affymetrix SNP 6.0 54
EGAD00010000942 Breast lesions assayed with Affymetrix SNP 6.0 Affymetrix SNP 6.0 125
EGAD00010000915 Affymetrix SNP6.0 breast cancer genome sequencing data Affymetrix SNP6.0 344
EGAD00010000252 CLL Expression Arrays Affymetrix U219 137
EGAD00010000472 CLL Expression Array Affymetrix U219 219
EGAD00010000875 CLL Expression Array Affymetrix U219 1,008
EGAD00010000096 DBA case samples using 250K Nsp Affymetrix_250K(Nsp) - gtype 27
EGAD00010000480 ccRCC case samples using 250K Nsp Affymetrix_250K(Nsp) - gtype 240
EGAD00010000484 ccRCC control samples using 250K Nsp Affymetrix_250K(Nsp) - gtype 234
EGAD00010000419 Han Chinese samples using Affymetrix (cases) Affymetrix_6.0 62
EGAD00010000421 Han Chinese samples using Affymetrix (controls) Affymetrix_6.0 187
EGAD00010000148 tumour samples using Affymetrix Genome-Wide SNP6.0 arrays Affymetrix_GenomeWide_SNP6.34 104
EGAD00010000452 Chondrosarcoma case sample genotype using Affymetrix SNP6.0 Affymetrix_SNP6 36
EGAD00010000395 Myeloma case sample genotype using Affymetrix SNP6.0 Affymetrix_SNP6 19
EGAD00010000488 Chondroblastoma case sample genotype using Affymetrix SNP6.0 Affymetrix_SNP6- 7
EGAD00010000498 Affymetrix SNP6.0 genotype data for prostate cancer patients Affymetrix_SNP6- 18
EGAD00010000442 Affymetrix SNP 6.0 CEL files Affymetrix_SNP6_raw 1,302
EGAD00010000440 Segmented copy number data Affymetrix_SNP6_raw 1,302
EGAD00010000502 Case samples using SNP Array 6.0 Affymetrix_U133plus2- 35
EGAD00010000504 Control samples using SNP Array 6.0 Affymetrix_U133plus2- 35
EGAD00010000500 Case samples using U133 Plus 2.0 Array Affymetrix_U133plus2- 35
EGAD00010000462 SJLGG Case samples using Gene Expression Array Affymetrix_U133v2 75
EGAD00010000937 ACGH 180K dataset Agilent 180K 5
EGAD00010000935 ACGH 244K dataset Agilent 244K 10
EGAD00010000938 mRNA Array Agilent 44K dataset Agilent 44K 16
EGAD00010000486 ccRCC case samples using expression array Agilent Human Whole Genome 4x44k v2 - Feature Extraction 101
EGAD00010000917 399 tumors profiled using Agilent miRNA microarrays (Product Number G4872A, design ID 046064). The arrays are based on miRBase release 19.0 and 2006 human miRNAs are represented. 150 ng total RNA was used as input. Agilent miRNA microarrays 399
EGAD00010000438 Normalized miRNA expression data Agilent ncRNA 60k 1,480
EGAD00010000444 Agilent ncRNA 60k txt files Agilent ncRNA 60k 1,480
EGAD00010000934 Agilent miRNA dataset Agilent SurePrint Human miRNA Microarray 2
EGAD00010000881 Digital images of ovarian cancer sections Aperio 91
EGAD00010001099 Digital images of ovarian cancer metastases Aperio 127
EGAD00010000270 Metabric breast cancer samples (Images) Aperio image - H&E stained tissue_section 564
EGAD00010000536 21 unlinked autosomal microsatellite loci for 30 Central Asian populations Applied Biosystems 3100 automated sequencer-GeneMarker v.1.6 (Softgenetics) 1,702
EGAD00010000538 28 unlinked autosomal microsatellite loci for 20 African and 4 philippine populations Applied Biosystems 3100 automated sequencer-GeneMarker v.1.6 (Softgenetics) 1,702
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
EGAD00001000060 Acral melanoma study whole genomes Complete Genomics 3 CompleteGenomics_native
EGAD00010000220 Ovarian & matched normal (Genotypes) Complete Genomics - CG Build 1.4.2.8 2
EGAD00001000196 Neuroblastoma samples Complete Genomics; 203 CompleteGenomics_native
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
EGAD00001000174 DATA_SET_Coverage_bias_sensitivity_of_variant_calling_for_4_WG_seq_tech Complete Genomics;, unspecified; 4 bam
EGAD00010000052 Monozygotic twins that are discordant for schizophrenia (Genotyping) CompleteGenomics build 1.4.2.8 - CG Build 1.4.2.8 36
EGAD00001000048 monozygotic twin discordant for schizophrenia CompleteGenomics build 1.4.2.8 - CG Build 1.4.2.8 2 CompleteGenomics_native
EGAD00010000921 samples using Affymetrix CYTOSCANHD CYTOSCANHD 12
EGAD00010000514 Case samples using SNP 6.0 Array GenomeWideSNP_6-BirdseedV2 12
EGAD00010000510 Matched control samples using HumanOmni1-Quad GenomeWideSNP_6-BirdseedV2 12
EGAD00010000512 Case samples using HumanOmni1-Quad GenomeWideSNP_6-BirdseedV2 12
EGAD00010000508 Matched control samples using SNP 6.0 Array GenomeWideSNP_6-BirdseedV2 12
EGAD00010000470 CLL Expression Array GPL570 20
EGAD00010000425 Han Chinese samples using Immunochip HanChinese_Immunochip 192
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
EGAD00001001271 Around 50 samples of pre-invasive lung cancer lesions showing subsequent clinical and pathological progression or regression HiSeq X Ten; 50 cram
EGAD00001001346 PREDICT/Predicting individual response and resistance to VEGFR/mTOR pathway therapeutic intervention using biomarkers discovered through tumour functional genomics. HiSeq X Ten; 164 cram
EGAD00001001889 ***THIS DATA CAN ONLY BE USED FOR NON-COMMERCIAL CANCER RESEARCH*** Sequencing of organoid cell lines derived from oesophageal tumour sections taken from patients diagnosed with primary oesophageal cancer who underwent tumour resection surgery. HiSeq X Ten; 9 cram
EGAD00001001897 15x whole genome sequencing in samples from the Cretan Greek isolate collection HELIC MANOLIS HiSeq X Ten; 1,482 cram
EGAD00001001898 The study will investigate serial samples from the same patient taken at the time of MGUS or SMM diagnosis, and later at the time of evolution towards MM. Samples will be sequenced by whole genome along with a matched normal to obtain the highest possible amount of information toinvestigate genomic changes at disease evolution. HiSeq X Ten; 131 cram
EGAD00001001429 Profiling subclonal architecture and phylogeny in tumors by whole-genome sequence data mining and single-cell genome sequencing HiSeq X Ten; 2 cram
EGAD00001001440 This project entailed generation of high depth WGS (30x) of 100 individuals from the general Greek population. HiSeq X Ten; 100 cram
EGAD00001001447 Whole genome sequencing of single cell derived organoids from normal colon tissue and colorectal cancer. HiSeq X Ten; 19 cram
EGAD00001001458 Whole genome sequencing of EBV-transformed B cells in order to determine whether EBV induction of activation-induced cytidine deaminase (AID) produces genome-wide mutations and/or chromosomal rearrangements. HiSeq X Ten; 12 cram
EGAD00001001629 Whole-genome somatic rearrangement and point mutation analysis in cell lines with induced telomere fusions. HiSeq X Ten; 20 cram
EGAD00001001846 2 BRAFV600E cell lines that have been made resistance to 1. the BRAF inhibitor PLX4720 and 2. the combination therapy of dabrafenib and trametinib seem to have a internal duplication in the kinase domain. We would like to know if this is caused by a translocation. HiSeq X Ten; 4 cram
EGAD00001001634 This dataset includes the whole genomes, sequenced to high depth (30x) of 25 individuals from Papua New Guinea. The individuals were chosen from several geographically distinct Papuan groups, focusing on the highland regions: Bundi, Kundiawa, Mendi, Marawaka and Tari. HiSeq X Ten; 25 cram
EGAD00001001995 Whole genome sequencing (30X) using Hiseq X TEN on 4 HCC cell lines, primary HCCs and early-passage PDCs. HiSeq X Ten; 12 fastq
EGAD00001002227 In collaboration with Dr David Savage, we have identified a patient with a very unusual phenotype, lacking almost all visceral fat, but showing a massive accumulation of white fat tissue behind her neck and significantly elevated liver fat. Whole exome sequencing of the proband and her unaffected parents and brother has been run previously, however no causative variant has been found and the sequencing coverage was generally poor. We propose to conduct whole genome sequencing of all 4 family members at a depth of 30X. HiSeq X Ten; 3 cram
EGAD00001002206 Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into the evolutionary processes that shape both human adaptation and variation in disease. Populations from Africa have the highest levels of genetic diversity. This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals. A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The GDA Project focus on sequencing the whole genome of less studied, genetically diverse groups within Africa with the objective of detailed characterisation of genetic variation within Africa. As part of this effort we propose to sequence at high depth (30x) on the Illumina X Ten platform nine individuals, including family trios wherever possible, from three distinct ethno-linguistic groups. This set of nine high depth genomes will serve as a high-confidence set to validate calling and filtering of variants in lower depth data. Additionally, it will complement existing data from the Human Genome Diversity Project (HGDP). A family-based design might also serve other projects (e.g. estimating TMRCA or mutation rate). HiSeq X Ten; 9 cram
EGAD00001002209 Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into the evolutionary processes that shape both human adaptation and variation in disease. Populations from SSA have the highest levels of genetic diversity. This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals. A systematic assessment of genetic diversity within SSA would facilitate genomic epidemiological studies in the region. The African Genome Variation Project (AGVP) is an international collaboration that aims to produce a comprehensive catalogue of human genetic variation in SSA. This resource has extended our understanding of population history, patterns of genetic diversity within and among populations in SSA, as well as providing a global resource to help design, implement and interpret genomic studies. The Genome Diversity in Africa Project (GDAP) will extend and expand the African Genome Variation (AGV) project. Using a sequencing-based approach, GDA project aims to produce a comprehensive catalogue of human genetic variation in SSA, including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. This resource will make a substantial contribution to understanding patterns of genetic diversity within and among populations in SSA, as well as providing a global resource to help design, implement and interpret genomic studies in SSA populations and studies comprising globally diverse populations, complementing existing genomic resources. Specifically, we plan to carry out low and high depth whole genome sequencing of up to 2000 individuals across Africa (100 individuals from each ethnolinguistic group), and complement these data with 2.5M Illumina genotyping. We have already completed sequencing of 700 individuals across SSA, we are now adding an additional 540 samples from various ethno-linguistic groups within Africa, including populations from Burkina Faso, Morocco, Ghana, Nigeria, Kenya and South Africa. Our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from SSA accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across SSA; 3) develop a cost-efficient, next-generation genotype array for diverse populations across SSA; and 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. HiSeq X Ten; 25 cram
EGAD00001002146 The dataset contains the whole genome sequencing data of a family with two unaffected parents and two probands that showed Hereditary spastic paraplegias symptoms. Sequencing reads were aligned to human genome (GRCh38) using BWA-MEM, followed by indel-realignment and PCR-duplicates marking. Alignment results are available for download in BAM format. HiSeq X Ten; 4 bam
EGAD00001002223 Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into the evolutionary processes that shape both human adaptation and variation in disease. Populations from SSA have the highest levels of genetic diversity. This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals. A systematic assessment of genetic diversity within SSA would facilitate genomic epidemiological studies in the region. The African Genome Variation Project (AGVP) is an international collaboration that aims to produce a comprehensive catalogue of human genetic variation in SSA. This resource has extended our understanding of population history, patterns of genetic diversity within and among populations in SSA, as well as providing a global resource to help design, implement and interpret genomic studies. The Genome Diversity in Africa Project (GDAP) will extend and expand the African Genome Variation (AGV) project. Using a sequencing-based approach, GDA project aims to produce a comprehensive catalogue of human genetic variation in SSA, including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. This resource will make a substantial contribution to understanding patterns of genetic diversity within and among populations in SSA, as well as providing a global resource to help design, implement and interpret genomic studies in SSA populations and studies comprising globally diverse populations, complementing existing genomic resources. Specifically, we plan to carry out low coverage (4x) whole genome sequencing of up to 2000 individuals across Africa (100 individuals from each ethnolinguistic group), and complement these data with 2.5M Illumina genotyping. We have already completed sequencing of 700 individuals across SSA, we are now adding an additional 500 samples from up to 5 ethno-linguistic groups within Africa, including populations from Burkina Faso, Cameroon, Morocco, Ghana and Seychelles. Our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from SSA accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across SSA; 3) develop a cost-efficient, next-generation genotype array for diverse populations across SSA; and 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. HiSeq X Ten; 25 cram
EGAD00001002222 Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into the evolutionary processes that shape both human adaptation and variation in disease. Populations from SSA have the highest levels of genetic diversity. This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals. A systematic assessment of genetic diversity within SSA would facilitate genomic epidemiological studies in the region. The African Genome Variation Project (AGVP) is an international collaboration that aims to produce a comprehensive catalogue of human genetic variation in SSA. This resource has extended our understanding of population history, patterns of genetic diversity within and among populations in SSA, as well as providing a global resource to help design, implement and interpret genomic studies. The Genome Diversity in Africa Project (GDAP) will extend and expand the African Genome Variation (AGV) project. Using a sequencing-based approach, GDA project aims to produce a comprehensive catalogue of human genetic variation in SSA, including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. This resource will make a substantial contribution to understanding patterns of genetic diversity within and among populations in SSA, as well as providing a global resource to help design, implement and interpret genomic studies in SSA populations and studies comprising globally diverse populations, complementing existing genomic resources. Specifically, we plan to carry out low coverage (4x) whole genome sequencing of up to 2000 individuals across Africa (100 individuals from each ethnolinguistic group), and complement these data with 2.5M Illumina genotyping. We have already completed sequencing of 700 individuals across SSA, we are now adding an additional 500 samples from up to 5 ethno-linguistic groups within Africa, including populations from Burkina Faso, Cameroon, Morocco, Ghana and Seychelles. Our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from SSA accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across SSA; 3) develop a cost-efficient, next-generation genotype array for diverse populations across SSA; and 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. HiSeq X Ten; 25 cram
EGAD00001002198 This set of samples is composed of eight young people (7-16 years old) that have developed melanoma with first-degree relatives that have also developed cancer, which suggests a genetic component to their disease. Here we want to sequence these samples in order to find the causative mutations. As these samples do not carry any of the high-penetrance mutations known to date, finding the genes(s) responsible will offer new insights into the genetic mechanisms underlying predisposition to melanoma. HiSeq X Ten;, Illumina HiSeq 2000; 7 cram
EGAD00001001900 DNA sequencing reads of human adult stem cell cultures from liver, colon and small intestine. Including biopsy or blood samples of the donors. HiSeq X Ten;, Illumina HiSeq 2500; 55 bam
EGAD00001002719 This dataset contains whole-genome sequencing data files from colon organoid cultures, which were mutated using CRISPR-Cas9 for specific genes (APC, KRAS, TP53 and SMAD4) to generate in vitro transformed cancer cells. After introducing each mutation, the resulting cultures were subjected to whole-genome sequencing. In addition, some cultures were xenotransplanted in recipient mice. The resulting primary tumors and corresponding metastases were subjected to whole-genome sequencing. HiSeq X Ten;ILLUMINA 15 bam
EGAD00001003097 High-coverage sequencing data from 47 Yemenis samples HiSeq X Ten;ILLUMINA 47 cram
EGAD00001002696 Recurrent breast cancer is almost universally fatal. We characterize 170 patients locally relapsed or distant metastatic cancers using massively parallel sequencing. We identify that the relapse-seeding clone disseminates late from the primary tumor. TP53 and AKT1 appear to be enriched in ER-positive cancers predisposed to relapse. Mutation acquisition continues at relapse as the same mutation signatures continue to operate and new signatures, such as that caused by radiotherapy appear de novo. In 49% of cases we identify drivers mutations private to the relapse and these are sampled from a wider range of cancer genes, including SWI-SNF complex and JAK-STAT signaling. HiSeq X Ten;ILLUMINA, Illumina HiSeq 2000;ILLUMINA 60 bam,cram
EGAD00001002742 Whole-genome sequencing data from Chad and Lebanon. HiSeq X Ten;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 15 cram
EGAD00000000120 WTCCC2 project Multiple Sclerosis (MS) samples Human670-QuadCustom v1 11,375
EGAD00010000963 Healthy volunteers recruited in Samoa HumanCore-24 BeadChip 24
EGAD00010000959 Healthy volunteers recruited in Fiji HumanCore-24 BeadChip 854
EGAD00010000961 Rheumatic heart disease cases recruited in Fiji HumanCore-24 BeadChip 535
EGAD00010000953 Healthy adult volunteers and newborns recruited in various countries across Oceania. HumanCore-24 BeadChip 937
EGAD00010000957 Rheumatic heart disease cases recruited in New Caledonia HumanCore-24 BeadChip 465
EGAD00010000960 Definite and borderline rheumatic heart disease cases and patients with mild non-diagnostic valvulopathy recruited in Samoa HumanCore-24 BeadChip 126
EGAD00010000954 Healthy volunteers recruited in New Caledonia HumanCore-24 BeadChip 356
EGAD00010000516 Samples from the Pomak Villages in Greece, Pomak isolate HumanExome_12v1.1_A -GenCall, zCall 1,046
EGAD00010000518 Samples from the Greek island of Crete, MANOLIS cohort HumanExome_12v1.1_A -GenCall, zCall 1,280
EGAD00010000377 DNA methylation analysis of 6 primary lymphoma samples HumanMethylation450k Bead Chip - Genome Studio 6
EGAD00010000379 DNA methylation analysis of 2 peripheral blood samples HumanMethylation450k Bead Chip - Genome Studio 2
EGAD00010000427 DNA methylation analysis of 4 peripheral blood samples HumanMethylation450k Bead Chip - Genome Studio 4
EGAD00010000429 DNA methylation analysis of 4 primary lymphoma samples HumanMethylation450k Bead Chip - Genome Studio 4
EGAD00010000908 Illumina SNP-arrays for matching retinoblastoma-blood pairs and retinoblastoma cell lines. HumanOmni1 Quad BeadChip 132
EGAD00010000919 samples using Illumina HUMANOMNI1QUAD HUMANOMNI1QUAD 2
EGAD00010000920 samples using Illumina HUMANOMNIEXPRESS HUMANOMNIEXPRESS 50
EGAD00010000522 Samples from the Greek island of Crete, MANOLIS cohort HumanOmniExpress-12 v1.1 BeadChip-GenCall 1,364
EGAD00010000958 Healthy volunteers recruited in Fiji with higher density genotyping HumanOmniExpressExome-8 BeadChip 32
EGAD00010000962 Healthy volunteers and missing phenotype individuals recruited in New Caledonia with higher density genotyping HumanOmniExpressExome-8 BeadChip 30
EGAD00010000955 Rheumatic heart disease cases recruited in Fiji with higher density genotyping HumanOmniExpressExome-8 BeadChip 32
EGAD00010000956 Rheumatic heart disease cases recruited in New Caledonia with higher density genotyping HumanOmniExpressExome-8 BeadChip 34
EGAD00010000940 Gambian specimens with trachomatous scarring WHO grade C2/C3 Illiumina Omni 2.5 1,531
EGAD00010001032 RNA Expression using Illumina HT12 v3 Illlumina HT12 v3 153
EGAD00010000144 Healthy volunteer collection of European Ancestry Illumin OmniExpress v1.0 - Illumina GenomeStudio 288
EGAD00010000476 blood-based gene expression from breast cancer cases and age-matched controls in case-control serie 1 (CC1) Illumina 110
EGAD00010000474 blood-based gene expression from breast cancer cases and age-matched controls in case-control serie 2 (CC2) Illumina 98
EGAD00010000478 blood-based gene expression from breast cancer cases and age-matched controls in case-control serie 3 (CC3) Illumina 118
EGAD00010000773 HipSci normal samples REL-2014-11 Illumina 580
EGAD00010000892 Healthy individuals from Italy Illumina 300
EGAD00010000909 HipSci normal ES lines REL-2016-04 Illumina 2
EGAD00010000775 HipSci normal samples REL-2014-11 Illumina 580
EGAD00010000910 HipSci normal ES lines REL-2016-04 Illumina 2
EGAD00010000911 HipSci normal ES lines REL-2016-04 Illumina 2
EGAD00010000779 HipSci neonatal diabetes mellitus samples REL-2014-11 Illumina 9
EGAD00010001139 HipSci - Healthy Normals - Methylation Array - October 2016 Illumina 181
EGAD00010000284 NBS control samples only (Hap300) Illumina (Various) 2,500
EGAD00010000286 All cases and controls (Hap550) Illumina (various) 11,950
EGAD00000000022 WTCCC2 project samples from 1958 British Birth Cohort Illumina 1.2M 3,000
EGAD00010000383 MRCA sample using 100K Illumina 100K - GenomeStudio 394
EGAD00000000011 WTCCC1 project Autoimmune Thyroid Disease (ATD) samples Illumina 15K 900
EGAD00000000014 WTCCC1 project samples from 1958 British Birth Cohort Illumina 15K 1,504
EGAD00000000010 WTCCC1 project Ankylosing Spondylitis (AS) samples Illumina 15K 957
EGAD00000000012 WTCCC1 project Multiple Sclerosis (MS) samples Illumina 15K 975
EGAD00000000013 WTCCC1 project Breast cancer (BC) samples Illumina 15K 1,004
EGAD00010000939 Illumina 1M SNP Array dataset Illumina 1M SNP Array 2
EGAD00010000951 SNP array data for 668 cancer cell lines Illumina 2.5M 668
EGAD00010000130 Cerebellar ataxia, mental retardation, and disequilibrium syndrome (CAMRQ) samples Illumina 300 Duo V2 - Bead Studio, Illumina 2
EGAD00010000381 MRCE sample using 300K Illumina 300K - GenomeStudio 543
EGAD00010000946 Human samples, 450k analysis Illumina 450k 127
EGAD00010000916 BASIS breast cancer DNA methylation Illumina 450k Illumina 450k 457
EGAD00010001001 Primary renal cell carcinoma (RCC), RCC metastases and cell lines by Illumina 450K Illumina 450K 62
EGAD00010001025 BLUEPRINT DNA methylation profiles of monocytes, T cells and B cells in type 1 diabetes-discordant monozygotic twins Illumina 450K 302
EGAD00010001003 This data set contains two data files. First data file (file name: PREDO_GA_EGA_methylation_data.csv) includes methylation data from 485512 sites accross human genome from 96 individuals acquired from Illumina 450K -chip. The other data file (file name: PREDO_GA_EGA_phenotypes.csv) contains the gestation ages and the genders of the 96 samples. Illumina 450K-chip (methylation data) 96
EGAD00010000464 Down syndrome SNP genotyping data Illumina 550K - Illumina Genome Studio 338
EGAD00000000104 Gabriel samples from the Russian UFA cohort Illumina 610-Quad 0
EGAD00000000098 Gabriel samples from the Swiss SALPADIA cohort Illumina 610-Quad 0
EGAD00000000090 Gabriel samples from the Russian KMSU cohort Illumina 610-Quad 0
EGAD00000000105 Gabriel samples from the multicenter occupational cohort Illumina 610-Quad 0
EGAD00000000087 Gabriel samples from the multicenter GAIN cohort Illumina 610-Quad 0
EGAD00000000092 Gabriel samples from the German MAGIS cohort Illumina 610-Quad 0
EGAD00000000083 Gabriel samples from the French EGEA Cohort Illumina 610-Quad 0
EGAD00000000088 Gabriel samples from the Karelia Allergy Study Illumina 610-Quad 0
EGAD00000000076 Gabriel samples from the Australian Bussleton Cohort Illumina 610-Quad 0
EGAD00000000095 Gabriel samples from the Dutch PIAMA cohort Illumina 610-Quad 0
EGAD00000000093 Gabriel samples from the German MAGIS cohort Illumina 610-Quad 0
EGAD00000000082 Gabriel samples from the French EGEA Cohort Illumina 610-Quad 0
EGAD00000000102 Gabriel samples from the Russian TOMSK cohort Illumina 610-Quad 0
EGAD00000000106 Gabriel samples from the multicenter occupational cohort Illumina 610-Quad 0
EGAD00000000085 Gabriel samples from the German Gabriel Advanced Survey Illumina 610-Quad 0
EGAD00000000108 Gabriel samples from the UK AUGOSA cohort Illumina 610-Quad 0
EGAD00000000075 Gabriel samples from the Swedish BAMSE Cohort Illumina 610-Quad 0
EGAD00000000107 Gabriel samples from the multicenter occupational cohort Illumina 610-Quad 0
EGAD00000000091 Gabriel samples from the Russian KMSU cohort Illumina 610-Quad 0
EGAD00000000101 Gabriel samples from the Russian TOMSK cohort Illumina 610-Quad 0
EGAD00000000074 Gabriel samples from the Swedish BAMSE Cohort Illumina 610-Quad 0
EGAD00000000103 Gabriel samples from the Russian UFA cohort Illumina 610-Quad 0
EGAD00000000086 Gabriel samples from the multicenter GAIN cohort Illumina 610-Quad 0
EGAD00000000077 Gabriel samples from the Australian Bussleton Cohort Illumina 610-Quad 0
EGAD00000000097 Gabriel samples from the Swiss SALPADIA cohort Illumina 610-Quad 0
EGAD00000000110 Gabriel aggregate data from the asthma study samples Illumina 610-Quad 0
EGAD00000000084 Gabriel samples from the German Gabriel Advanced Survey Illumina 610-Quad 0
EGAD00000000089 Gabriel samples from the Karelia Allergy Study Illumina 610-Quad 0
EGAD00000000094 Gabriel samples from the UK MRCA cohort Illumina 610-Quad 0
EGAD00000000109 Gabriel samples from the UK SEVERE cohort Illumina 610-Quad 0
EGAD00000000096 Gabriel samples from the Dutch PIAMA cohort Illumina 610-Quad 0
EGAD00000000026 Randomly-selected, unrelated individuals Illumina 610-Quad 518
EGAD00010000912 SEA 610K Illumina 610K 1
EGAD00000000057 WTCCC project samples from the Parkinson's disase cohort Illumina 610K Quad 1,705
EGAD00000000056 WTCCC project samples from the primary biliary cirrhosis cohort Illumina 610K Quad 1,705
EGAD00000000060 Samples from the UK Glomerulonephritis DNA bank Illumina 610K Quad, Illumina Hap300 1,705
EGAD00010000913 SEA 660K Illumina 660K 3
EGAD00000000035 NcOEDG Helsinki 4 samples Illumina CNV370 693
EGAD00000000115 Summary data from GWAS analysis on 856 cases and 2836 control Illumina CytoSNP-12 3,719
EGAD00010001075 Argentine samples using 250K Illumina Exome 250K 391
EGAD00001000100 Renal Matched Pair Cell Line Exome Sequencing Illumina Genome Analyzer II 10 bam
EGAD00001000026 Investigation of the genetic basis of the rare syndrome Post-Transfusion Purpura (PTP) Illumina Genome Analyzer II 5 bam,srf
EGAD00001000094 Cancer Genome Libraries Tests Illumina Genome Analyzer II 16 bam
EGAD00001000003 Gencode Exome Pilot Illumina Genome Analyzer II 7 srf
EGAD00001000092 Cancer Exome Resequencing Illumina Genome Analyzer II 58 bam
EGAD00001000104 Acute Lymphoblastic Leukemia Exome sequencing 2 Illumina Genome Analyzer II 97 bam
EGAD00001000095 Acute Myeloid Leukemia Sequencing Illumina Genome Analyzer II 9 bam
EGAD00001000089 Acute Lymphoblastic Leukemia Exome sequencing Illumina Genome Analyzer II 20 bam
EGAD00001000018 Identifying causative mutations for Thrombocytopenia with Absent Radii Illumina Genome Analyzer II 5 bam
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
EGAD00001000111 CML Discovery Project Illumina Genome Analyzer II 6 bam
EGAD00001000029 Grey Platelet Syndrome (GPS) Illumina Genome Analyzer II 5 srf
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
EGAD00001000040 Bleeding Illumina Genome Analyzer II 6 bam
EGAD00001000058 Exome Sequencing analysis Illumina Genome Analyzer II 21 Illumina_native_qseq
EGAD00001000057 RNA-Seq analysis Illumina Genome Analyzer II 15 Illumina_native_qseq
EGAD00001000063 Triple Negative Breast Cancer sequencing Illumina Genome Analyzer II 6 bam
EGAD00000000053 Sequencing data from Breast Cancer samples Illumina Genome Analyzer II 1
EGAD00001000102 Myeloproliferative Disorder Sequencing Illumina Genome Analyzer II 6 bam
EGAD00001000098 FRCC Exome sequencing Illumina Genome Analyzer II 16 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
EGAD00001000033 "SNV detection from formalin fixed paraffin embedded (FFPE) samples" Illumina Genome Analyzer II 6 bam
EGAD00001000036 "Copy number variant detection in multiple foci of three prostate cancer tumors" Illumina Genome Analyzer II 9 bam
EGAD00000000051 Sequencing data from matching Renal Carcinoma samples Illumina Genome Analyzer II 25
EGAD00001000090 Glioma cell lines rearrangement screen Illumina Genome Analyzer II 3 bam
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
EGAD00001000031 Human Colorectal Cancer Exome Sequencing Illumina Genome Analyzer II 16 srf
EGAD00001000038 Hyperfibrinolysis Illumina Genome Analyzer II 5 bam
EGAD00001000093 Breast Cancer Exome Resequencing Illumina Genome Analyzer II 21 bam
EGAD00001000091 Non Tumour Renal Cell Line Sequencing Illumina Genome Analyzer II 1 bam
EGAD00001000037 An evaluation of different strategies for large-scale pooled sequencing study design. Illumina Genome Analyzer II 7 bam,srf
EGAD00001000013 CLL Cancer Whole Genome Sequencing Illumina Genome Analyzer II 19 srf
EGAD00001000059 Screening for human epigenetic variation at CpG islands Illumina Genome Analyzer II 116 bam
EGAD00001000041 Various Platelet Disorders Illumina Genome Analyzer II 7 bam
EGAD00001000064 Cell Line Sub Clone Rearrangement Screen Illumina Genome Analyzer II 6 bam
EGAD00001000097 Matched breast cancer fusion gene study Illumina Genome Analyzer II 46 bam,srf
EGAD00001000066 Breast Cancer Follow Up Series Illumina Genome Analyzer II 288 bam
EGAD00001000105 MuTHER adipose tissue small RNA expression Illumina Genome Analyzer II 130 bam
EGAD00001000103 Myeloproliferative Disorder Sequencing Illumina Genome Analyzer II 4 bam
EGAD00001000019 Lethal malformation syndrome Illumina Genome Analyzer II 6 srf
EGAD00001000112 Identifying Novel Fusion Genes in Myeloma Illumina Genome Analyzer II 6 bam
EGAD00001000099 Meningioma Exome Illumina Genome Analyzer II 26 bam
EGAD00001000065 Mixed Leukemia Rearrangement Screen Illumina Genome Analyzer II 5 bam
EGAD00000000046 RNA-SEQ data from 3 recurrent and 1 ovarian primary Granulosa Cell Tumour samples Illumina Genome Analyzer II 4
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
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
EGAD00001000088 ER-, HER2-, PR- breast Cancer genome sequencing Illumina Genome Analyzer II 6 bam
EGAD00000000052 Sequencing data from natching Pancreatic Carcinoma samples Illumina Genome Analyzer II 25
EGAD00001000025 Determination of the molecular nature of the Vel blood group by exome sequencing Illumina Genome Analyzer II 4 srf
EGAD00001000022 Exome sequencing in patients with cardiac arrhythmias Illumina Genome Analyzer II 20 srf
EGAD00001000050 Tandem duplication of chromosomal segments is common in ovarian and breast cancer genomes Illumina Genome Analyzer II 13 bam
EGAD00001000084 Matched Ovarian Cancer Sequencing Illumina Genome Analyzer II 23 bam
EGAD00001000004 CLL cancer Sample Sequencing Illumina Genome Analyzer II, Illumina Genome Analyzer 5 srf
EGAD00001000101 ADCC Exome Sequencing Illumina Genome Analyzer II, Illumina HiSeq 2000; 125 bam
EGAD00001000118 Osteosarcoma Exome Sequencing Illumina Genome Analyzer II, Illumina HiSeq 2000; 102 bam
EGAD00001000106 Primary Myelofibrosis Myeloproliferative Disease exome sequencing Illumina Genome Analyzer II, Illumina HiSeq 2000; 67 bam
EGAD00001000068 Multifocal Breast Project Illumina Genome Analyzer II, Illumina HiSeq 2000; 22 bam,srf
EGAD00001000045 Somatic mutation of SF3B1 in myelodysplasia with ring sideroblasts and other cancers Illumina Genome Analyzer II, Illumina HiSeq 2000; 33 bam,cram,srf
EGAD00001000212 Functional characterisation of CpG islands in human tissues Illumina Genome Analyzer II; 26 bam
EGAD00001000348 Exome sequencing of Bilateral Anophthalmia cases- Pilot Study Illumina Genome Analyzer II; 16 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
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
EGAD00001000213 Screening for abnormal CGI methylation in primary colorectal tumours Illumina Genome Analyzer II; 21 bam
EGAD00001000052 UK10K_NEURO_MUIR REL-2011-01-28 Illumina Genome Analyzer II; 104 vcf,bam,bam
EGAD00001001453 The project is to evaluate the genomic binding sites of the histone demethylase JARID1C. This gene was recently identified in CGP as a novel recessive cancer gene in human renal cell carcinoma. Illumina Genome Analyzer II; 4 bam
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
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
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
EGAD00001000197 Progressive Hearing Loss Illumina Genome Analyzer II; 8 bam
EGAD00001000258 Deep RNA sequencing in CLL Illumina Genome Analyzer II; 107 fastq
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
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
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
EGAD00001000758 dataset for BGI bladder cancer project Illumina Genome Analyzer II; 198 fastq
EGAD00001001443 RNASeq sequencing. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired-end mode with a read length of 2 × 76 bp. We generated more than 20 million paired-end reads for each sample in a fraction of a sequencing lane on HiSeq2000 (Illumina Inc.) following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files. Illumina Genome Analyzer II; 199 fastq
EGAD00001001645 Illumina Genome Analyzer II; 28 bam
EGAD00001001626 RNA-Seq Illumina GAII dataset for the TraIT cell-line use case (added reverse and forward reads). Illumina Genome Analyzer II; 6 fastq,bam
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
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
EGAD00001000083 Recurrent Somatic Mutations in CLL Illumina Genome Analyzer II;, Illumina Genome Analyzer IIx 61 fastq
EGAD00001001269 Exome bam files of 75 Individuals From Multiply Affected Coeliac Families Illumina Genome Analyzer II;, Illumina Genome Analyzer IIx; 75 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
EGAD00001000295 UK10K_RARE_HYPERCHOL REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 120 vcf
EGAD00001000186 UK10K_RARE_HYPERCHOL REL-2012-02-22 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 71 vcf
EGAD00001000167 UK10K_RARE_HYPERCHOL REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 48 vcf
EGAD00001000207 UK10K_RARE_HYPERCHOL REL-2012-07-05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 88 vcf
EGAD00001000178 UK10K_RARE_CHD REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 46 vcf
EGAD00001000294 UK10K_RARE_CHD REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 124 vcf
EGAD00001000210 UK10K_RARE_CHD REL-2012-07-05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 124 vcf
EGAD00001000192 UK10K_RARE_CHD REL-2012-02-22 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 46 vcf
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
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
EGAD00001000307 UK10K_RARE_COLOBOMA REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 117 vcf
EGAD00001000206 UK10K_RARE_COLOBOMA REL-2012-07-05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 123 vcf
EGAD00001000179 UK10K_RARE_COLOBOMA REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 75 vcf
EGAD00001000185 UK10K_RARE_COLOBOMA REL-2012-02-22 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 98 vcf
EGAD00001000152 UK10K_RARE_THYROID REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 27 vcf
EGAD00001000208 UK10K_RARE_THYROID REL-2012-07-05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 65 vcf
EGAD00001000187 UK10K_RARE_THYROID REL-2012-02-22 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 65 vcf
EGAD00001000329 UK10K_RARE_THYROID REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 113 vcf
EGAD00001000297 UK10K_RARE_FIND REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 124 vcf
EGAD00001000171 UK10K_RARE_FIND REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 44 vcf
EGAD00001000209 UK10K_RARE_FIND REL-2012-07-05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 121 vcf
EGAD00001000190 UK10K_RARE_FIND REL-2012-02-22 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 90 vcf
EGAD00001000322 UK10K_NEURO_MUIR REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 166 vcf
EGAD00001000170 UK10K_NEURO_MUIR REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 167 vcf
EGAD00001000236 EGAD00001000236_UK10K_NEURO_MUIR_REL_2012_07_05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 167 vcf
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
EGAD00001000194 UK10K_COHORT_TWINS REL-2011-12-01 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 1,713 vcf
EGAD00001000188 UK10K_RARE_SIR REL-2012-02-22 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 63 vcf
EGAD00001000334 UK10K_RARE_SIR REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 111 vcf
EGAD00001000218 UK10K_RARE_SIR REL-2012-07-05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 81 vcf
EGAD00001000153 UK10K_RARE_SIR REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 38 vcf
EGAD00001000191 UK10K_RARE_CILIOPATHIES REL-2012-02-22 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 128 vcf
EGAD00001000296 UK10K_RARE_CILIOPATHIES REL-2012-11-27 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 108 vcf
EGAD00001000168 UK10K_RARE_CILIOPATHIES REL-2012-01-13 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 50 vcf
EGAD00001000217 UK10K_RARE_CILIOPATHIES REL-2012-07-05 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 150 vcf
EGAD00001000198 Gene Discovery in Age-Related Hearing Loss Illumina Genome Analyzer II;, Illumina HiSeq 2000; 20 bam
EGAD00001000417 UK10K_RARE_HYPERCHOL REL-2013-04-20 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 125 vcf
EGAD00001000413 UK10K_RARE_CHD REL-2013-04-20 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 125 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
EGAD00001000420 UK10K_RARE_THYROID REL-2013-04-20 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 124 vcf
EGAD00001000419 UK10K_RARE_SIR REL-2013-04-20 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 121 vcf
EGAD00001000414 UK10K_RARE_CILIOPATHIES REL-2013-04-20 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 122 vcf
EGAD00001000425 GENCORD2 RNA-seq BAM files using BWA Illumina Genome Analyzer II;, Illumina HiSeq 2000; 568 bam
EGAD00001000443 UK10K_NEURO_MUIR REL-2013-04-20 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 175 vcf
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
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
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
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
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
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
EGAD00001001398 We sequenced 205 patients who were suffering NSCLC with Exome sequencing method. Illumina Genome Analyzer II;, Illumina HiSeq 2000; 147 fastq
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
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 Genome Analyzer II;, Illumina HiSeq 2000; 28 bam,srf,cram
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 Genome Analyzer II;, Illumina HiSeq 2000; 49 bam,srf
EGAD00001002237 The disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription; co-ordinated secondary alterations in transcriptional pathways; and increased transcriptional noise. To catalogue the rules governing how somatic mutation Overall, 59% of 6980 exonic substitutions were expressed. Compared to other classes, nonsense mutations showed lower expression levels than expected with patterns characteristic of nonsense-mediated decay. 14% of 4234 genomic rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusion transcripts and premature poly-adenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes may drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data therefore reveals the rules by which transcriptional machinery interprets somatic mutation. Illumina Genome Analyzer II;, Illumina HiSeq 2000; 59 bam,srf
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
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
EGAD00001000023 Recurrent Somatic Mutations in CLL Illumina Genome Analyzer IIx 11 fastq
EGAD00001000044 Recurrent Somatic Mutations in CLL Illumina Genome Analyzer IIx 212 fastq
EGAD00001000032 Hepatitis C IL28B pooled resequencing study with 100 responders and 100 non-responders Illumina Genome Analyzer IIx 4 Illumina_native
EGAD00001000042 Whole-Exome-Seq-Dataset Illumina Genome Analyzer IIx 30 bam
EGAD00001000043 RNA-Seq-Dataset Illumina Genome Analyzer IIx 16 bam
EGAD00001000061 Acral melanoma study whole exomes Illumina Genome Analyzer IIx 3 fastq
EGAD00001000132 Mutational landscapes of primary triple negative breast cancers - RNA seq Illumina Genome Analyzer IIx, Illumina Genome Analyzer IIx; 80 bam
EGAD00001000113 Mutational landscapes of primary triple negative breast cancers - Exomes Illumina Genome Analyzer IIx, Illumina Genome Analyzer IIx; 108 bam
EGAD00001000279 ICGC MMML-seq Data Freeze November 2012 whole exome sequencing Illumina Genome Analyzer IIx; 4 bam
EGAD00001000177 Whole Genome Methylation in CLL Illumina Genome Analyzer IIx; 6 fastq
EGAD00001000303 ICGC prostate cancer whole genome mate-pair sequencing Illumina Genome Analyzer IIx; 22 bam
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
EGAD00001000703 SCLC - Whole genome sequencing data Publication Peifer et al., 2012, Nature Genetics Illumina Genome Analyzer IIx; 29 bam
EGAD00001001263 Unaligned bam of 31 samples derived from blood Illumina Genome Analyzer IIx; 31 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
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
EGAD00001001108 MMP-seq tumor samples (FASTQ) Illumina Genome Analyzer IIx; 218 fastq
EGAD00001001107 MMP-seq cell lines (FASTQ) Illumina Genome Analyzer IIx; 154 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
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
EGAD00001000642 Illumina HiScanSQ; 2 bam
EGAD00001000643 Illumina HiScanSQ; 2 bam
EGAD00001002112 RNA-seq data from 195 pediatric BCP-ALL cases. Alignment: TopHat 2.0.7. Reference genome: hg19. Illumina HiScanSQ; 195 fastq
EGAD00001001220 Illumina HiSeq 1000; 10 bam
EGAD00001002892 The data contains genome sequencing of clear cell renal cell carcinomas and normal kidney tissues. The samples were collected from patients from different European countries. Illumina HiSeq 1000;ILLUMINA 21 fastq
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
EGAD00001000160 DATA FILES FOR SJACT Illumina HiSeq 2000 16 bam
EGAD00001000081 Splenic Marginal Zone Lymphoma with villous lymphocytes exome sequencing Illumina HiSeq 2000 1 bam
EGAD00001000075 Gastric and Esophageal tumour rearrangement screen Illumina HiSeq 2000 32 bam
EGAD00001000165 DATA FILES FOR SJINF Illumina HiSeq 2000 46 bam
EGAD00001000085 Somatic Histone H3 mutations Illumina HiSeq 2000 14 bam
EGAD00001000087 An exome sequencing pilot study of HIV elite-long term non progressors and rapid progressors Illumina HiSeq 2000 25 bam
EGAD00001000072 Fanconi Anemia transformation to AML Illumina HiSeq 2000 6 bam
EGAD00001000149 A Comprehensive Catalogue of Somatic Mutations from a Human Cancer Genome Illumina HiSeq 2000 2 srf
EGAD00001000053 Exome sequencing in patients with Calcific Aortic Valve Stenosis Illumina HiSeq 2000 20 bam
EGAD00001000159 DATA FILES FOR SJOS Illumina HiSeq 2000 37 bam
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
EGAD00001000163 DATA FILES FOR SJPHALL Illumina HiSeq 2000 18 bam
EGAD00001000054 Mutational Screening of Human Acute Myleloid Leukaemia Samples Illumina HiSeq 2000 10 bam
EGAD00001000131 Genetic landscape of hepatocellular carcinoma Illumina HiSeq 2000 48 bam
EGAD00001000136 CML blast phase rearrangement screen Illumina HiSeq 2000 6 bam
EGAD00001000069 Lung Rearrangement Study Illumina HiSeq 2000 48 bam
EGAD00001000030 Analysis of genomic integrity of disease-corrected human induced pluripotent stem cells by exome sequencing Illumina HiSeq 2000 4 bam
EGAD00001000086 Analysis of genomic integrity of disease-corrected human induced pluripotent stem cells by exome sequencing Illumina HiSeq 2000 16 bam
EGAD00001000077 CRLF2 sequencing project Exomes Illumina HiSeq 2000 26 bam
EGAD00001000162 DATA FILES FOR SJEPD Illumina HiSeq 2000 44 bam
EGAD00001000135 Neuroblastoma whole genome sequencing Illumina HiSeq 2000 80 bam
EGAD00001000076 CRLF2 sequencing project Illumina HiSeq 2000 13 bam
EGAD00001000121 Breast Cancer Whole Genome Sequencing Illumina HiSeq 2000 6 bam
EGAD00001000161 DATA FILES FOR SJLGG Illumina HiSeq 2000 33 bam
EGAD00001000071 Kaposi sarcoma exome Illumina HiSeq 2000 20 bam
EGAD00001000133 The landscape of cancer genes and mutational processes in breast cancer Illumina HiSeq 2000, Illumina Genome Analyzer II 199 bam
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
EGAD00001000110 Breast Cancer Exome Sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II 179 bam
EGAD00001000154 Single-cell genome sequencing reveals DNA-mutation per cell cycle Illumina HiSeq 2000, Illumina Genome Analyzer II 12 bam,srf
EGAD00001000039 Platelet collagen defect Illumina HiSeq 2000, Illumina Genome Analyzer II 11 bam
EGAD00001000074 Integrative Oncogenomics of Multiple Myeloma Illumina HiSeq 2000, Illumina Genome Analyzer II 174 bam,srf
EGAD00001000107 SCAT osteosarcoma sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II 114 bam
EGAD00001000062 ADCC Rearrangement Screen Illumina HiSeq 2000, Illumina Genome Analyzer II 14 bam,srf
EGAD00001000082 20 Matched Pair Breast Cancer Genomes Illumina HiSeq 2000, Illumina Genome Analyzer II 42 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
EGAD00001000119 Chordoma Exome Sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 50 bam
EGAD00001000123 Polycythemia Vera Myeloproliferative Disease exome sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 119 bam,srf
EGAD00001000021 Paroxysmal neurological disorders Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 97 bam,srf
EGAD00001000108 Paroxysmal neurological disorders Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 327 bam,srf
EGAD00001000117 Myelodysplastic Syndrome Exome Sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 152 bam,srf
EGAD00001000116 Acute Lymphoblastic Leukemia Sequencing Illumina HiSeq 2000, Illumina Genome Analyzer II, Illumina HiSeq 2000; 61 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
EGAD00001000046 Gastric Cancer Exome Sequencing Illumina HiSeq 2000, Illumina Genome Analyzer IIx 43 fastq
EGAD00001000027 ICGC Germany PedBrain Medulloblastoma Pilot_2_LM Illumina HiSeq 2000, Illumina Genome Analyzer IIx 8 bam
EGAD00001000122 DATA_SET_ICGC_PedBrainTumor_Medulloblastoma Illumina HiSeq 2000, Illumina Genome Analyzer IIx 206 bam
EGAD00001000128 Familial Thrombocytosis germline exome sequencing Illumina HiSeq 2000, Illumina HiSeq 2000; 4 bam
EGAD00001000070 TMD_AMLK Exome Study Illumina HiSeq 2000, Illumina HiSeq 2000; 50 bam,cram
EGAD00001000047 An exome sequencing pilot study of HIV elite-long term non progressors and rapid progressors. **ACCESS TO THIS DATASET IS ONLY PROVIDED FOR HIV RELATED RESEARCH** Illumina HiSeq 2000, Illumina HiSeq 2000; 49 bam,cram
EGAD00001000127 Burden of Disease in Sarcoma Illumina HiSeq 2000, Illumina HiSeq 2000; 220 bam,cram
EGAD00001000145 Matched Pair Cancer Cell line Whole Genomes Illumina HiSeq 2000, Illumina HiSeq 2000; 58 bam
EGAD00001000130 Breast Cancer Matched Pair Cell Line Whole Genomes Illumina HiSeq 2000, Illumina HiSeq 2000; 22 bam
EGAD00001000144 Lung Cancer Whole Genomes Illumina HiSeq 2000, Illumina HiSeq 2000; 18 bam
EGAD00001000067 Cancer Single Cell Sequencing Illumina HiSeq 2000, Illumina HiSeq 2000; 16 bam,srf
EGAD00001000129 Essential Thrombocythemia Myeloproliferative Disease exome sequencing Illumina HiSeq 2000, Illumina HiSeq 2000; 189 bam
EGAD00001000125 Chondrosarcoma Exome Illumina HiSeq 2000, Illumina HiSeq 2000; 104 bam
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
EGAD00001000078 ALK inhibitors in the context of ALK-dependent cancer cell lines Illumina HiSeq 2000, Illumina HiSeq 2000; 16 bam,cram
EGAD00001000142 Renal Follow Up Series Illumina HiSeq 2000, Illumina HiSeq 2000; 637 bam
EGAD00001000126 HER2 positive Breast Cancer Illumina HiSeq 2000, Illumina HiSeq 2000; 101 bam,cram
EGAD00001000124 Sequencing Acute Myeloid Leukaemia Illumina HiSeq 2000, Illumina HiSeq 2000; 4 bam
EGAD00001000143 Xenograft Seqeuncing Illumina HiSeq 2000, Illumina HiSeq 2000; 16 bam
EGAD00001000079 PREDICT Illumina HiSeq 2000, Illumina HiSeq 2000; 186 bam,cram
EGAD00001000164 DATA FILES FOR SJRHB Illumina HiSeq 2000, Illumina HiSeq 2000; 29 bam
EGAD00001000147 Osteosarcoma Whole Genome Illumina HiSeq 2000, Illumina HiSeq 2000; 108 bam,cram
EGAD00001000073 MDSMPN Rearrangement Screen Illumina HiSeq 2000, Illumina HiSeq 2000; 11 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
EGAD00001000227 EGAD00001000227_UK10K_NEURO_ABERDEEN_REL_2012_07_05 Illumina HiSeq 2000; 347 vcf
EGAD00001000315 UK10K_NEURO_ABERDEEN REL-2012-11-27 Illumina HiSeq 2000; 313 vcf
EGAD00001000271 Pilot study Pilocytic Astrocytoma ICGC PedBrain, whole genome sequencing of 5 tumors and matched blood Illumina HiSeq 2000; 10 bam
EGAD00001000887 Exome sequencing of Resistant BCC samples. Illumina HiSeq 2000; 23 fastq
EGAD00001000881 RNA sequencing of Resistant BCC samples. Illumina HiSeq 2000; 11 fastq
EGAD00001000269 OLD DATA FILES FOR SJMB - Superseded by EGAD00001001864 Illumina HiSeq 2000; 68 bam
EGAD00001000319 UK10K_NEURO_GURLING REL-2012-11-27 Illumina HiSeq 2000; 48 vcf
EGAD00001000237 EGAD00001000237_UK10K_NEURO_GURLING_REL_2012_07_05 Illumina HiSeq 2000; 43 vcf
EGAD00001000336 UK10K_OBESITY_SCOOP REL-2012-11-27 Illumina HiSeq 2000; 784 vcf
EGAD00001000241 EGAD00001000241_UK10K_OBESITY_SCOOP_REL_2012_07_05 Illumina HiSeq 2000; 674 vcf
EGAD00001000151 UK10K OBESITY REL-2011-07-14 Illumina HiSeq 2000; 88 vcf
EGAD00001000181 UK10K_OBESITY_SCOOP REL-2012-01-13 Illumina HiSeq 2000; 212 vcf
EGAD00001000193 UK10K_OBESITY_SCOOP REL-2012-02-22 Illumina HiSeq 2000; 573 vcf
EGAD00001000318 UK10K_NEURO_FSZ REL-2012-11-27 Illumina HiSeq 2000; 119 vcf
EGAD00001000184 UK10K_NEURO_FSZ_REL_2012_01_13 Illumina HiSeq 2000; 120 vcf
EGAD00001000240 UK10K_NEURO_FSZ_REL_2012_07_05 Illumina HiSeq 2000; 120 vcf
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
EGAD00001000214 Whole genome sequencing of colon samples Illumina HiSeq 2000; 11 fastq
EGAD00001000306 ICGC prostate cancer whole genome sequencing Illumina HiSeq 2000; 22 bam
EGAD00001000270 DATA_SET_EOP-PCA-LargeAndSmallTumors1 Illumina HiSeq 2000; 18 bam
EGAD00001000235 EGAD00001000235_UK10K_NEURO_IOP_COLLIER_REL_2012_07_05 Illumina HiSeq 2000; 170 vcf
EGAD00001000321 UK10K_NEURO_IOP_COLLIER REL-2012-11-27 Illumina HiSeq 2000; 158 vcf
EGAD00001002158 This is an in vitro genome-wide CRISPR/cas9 screen in human glioblastoma stem cells, screening for genes essential for survival of these cells. These cells express cas9 and have been transfected with a guide RNA library causing gene knockouts. We will analyse the sequencing data for depletion of guide RNAs. Illumina HiSeq 2000; 6 cram
EGAD00001000345 Exome sequencing of 12 DNA samples obtained from patients with structural brain malformations. Illumina HiSeq 2000; 9 bam
EGAD00001000310 UK10K_NEURO_ASD_BIONED REL-2012-11-27 Illumina HiSeq 2000; 76 vcf,bam
EGAD00001000228 EGAD00001000228_UK10K_NEURO_ASD_BIONED_REL_2012_07_05 Illumina HiSeq 2000; 59 vcf
EGAD00001001125 Exome sequencing of Untreated BCC samples. Illumina HiSeq 2000; 91 fastq
EGAD00001000261 Retinoblastoma whole genome sequencing Illumina HiSeq 2000; 8 bam
EGAD00001000256 UK10K_NEURO_UKSCZ REL-2012-07-05 Illumina HiSeq 2000; 595 vcf
EGAD00001000335 UK10K_NEURO_UKSCZ REL-2012-11-27 Illumina HiSeq 2000; 527 vcf
EGAD00001000182 UK10K_NEURO_UKSCZ REL-2012-01-13 Illumina HiSeq 2000; 95 vcf
EGAD00001000317 UK10K_NEURO_EDINBURGH REL-2012-11-27 Illumina HiSeq 2000; 214 vcf
EGAD00001000233 EGAD00001000233_UK10K_NEURO_EDINBURGH_REL_2012_07_05 Illumina HiSeq 2000; 219 vcf
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
EGAD00001000347 These samples include exome sequences of family members with dyslipidemias from Finnish origin. Illumina HiSeq 2000; 95 bam
EGAD00001001862 RNA-seq of PDXs Illumina HiSeq 2000; 12 fastq
EGAD00001001693 Fastq files of RNAseq of 182 samples of biliary tract cancer Illumina HiSeq 2000; 182 fastq
EGAD00001001872 Targeted exome sequencing of patient derived xenografts from primary colorectal tumours and liver metastases. Illumina HiSeq 2000; 333 cram
EGAD00001001873 AML emerges as a consequence of accumulating independent genetic aberrations that direct regulation and/or dysfunction of genes resulting in aberrant activation of signalling pathways, resistance to apoptosis and uncontrolled proliferation. Given the significant heterogeneity of AML genomes, AML patients demonstrate a highly variable response rate and poor median survival in response to current chemotherapy regimens. For the past 4 years we have conducted gene expression profiling on purified bone marrow populations equating to normal haematopoietic stem and progenitor cells from healthy subjects and patients with de novo AML in order to identify AML signatures of aberrantly expressed genes in cancer versus normal. We are now applying a series of bioinformatic methodologies combined with clinical and conventional diagnostic data to establish novel genomics strategies for improved prognostication of AML. Additionally, we use our AML signatures to unravel oncogenic signalling pathway activities in AML patients and test inhibitory drugs for these pathways inn preclinical therapeutic programmes. We consider that superimposing GEP and clinical data for our AML patient cohort with additional data on their mutational status will significantly improve the prognostic power of the study as well as unravel yet unknown mutations associated with aberrant signalling activities of oncogenic pathways. Illumina HiSeq 2000; 215 cram
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
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
EGAD00001000223 RNA sequencing of SCLC tumor/normal sample pairs and cell lines Illumina HiSeq 2000; 79 fastq
EGAD00001000222 Exome capture sequencing of SCLC tumor/normal pairs and cell lines Illumina HiSeq 2000; 103 fastq
EGAD00001000221 Whole genome sequencing of SCLC tumor/normal samples Illumina HiSeq 2000; 4 fastq
EGAD00001001053 DATA FILES FOR SJOS-WGS-2ndBatch Illumina HiSeq 2000; 27 bam
EGAD00001001052 DATA FILES FOR SJTALL Illumina HiSeq 2000; 24 bam
EGAD00001001955 HipSci-RNAseq_REL-2016-01_RNA sequencing_Monogenic Diabetes Illumina HiSeq 2000; 39 other,cram,bai,bam
EGAD00001000259 DATA FILES FOR SJAMLM7 Illumina HiSeq 2000; 8 bam
EGAD00001000183 UK10K_NEURO_FSZNK REL-2012-01-13 Illumina HiSeq 2000; 273 vcf
EGAD00001000234 EGAD00001000234_UK10K_NEURO_FSZNK_REL_2012_07_05 Illumina HiSeq 2000; 281 vcf
EGAD00001000332 UK10K_NEURO_FSZNK REL-2012-11-27 Illumina HiSeq 2000; 258 vcf
EGAD00001000382 Whole Exome Sequencing of Permanent Neonatal Diabetes Patients Illumina HiSeq 2000; 25 bam
EGAD00001000232 EGAD00001000232_UK10K_NEURO_ASD_TAMPERE_REL_2012_07_05 Illumina HiSeq 2000; 54 vcf
EGAD00001000314 UK10K_NEURO_ASD_TAMPERE REL-2012-11-27 Illumina HiSeq 2000; 48 vcf
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
EGAD00001000249 This is the bam file generated after alignment using BWA program for the SAIF genome Illumina HiSeq 2000; 1 bam
EGAD00001000254 This dataset contain the raw files generated for SAIF genome project Illumina HiSeq 2000; 1 fastq
EGAD00001000381 Illumina paired-end sequencing of whole- exome pulldown DNA from Severe Insulin Resistant patients. Illumina HiSeq 2000; 3 bam
EGAD00001000602 Illumina HiSeq 2000; 1 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
EGAD00001000229 EGAD00001000229_UK10K_NEURO_ASD_FI_REL_2012_07_05 Illumina HiSeq 2000; 85 vcf
EGAD00001000173 UK10K_NEURO_ASD_FI REL-2012-01-13 Illumina HiSeq 2000; 85 vcf
EGAD00001000311 UK10K_NEURO_ASD_FI REL-2012-11-27 Illumina HiSeq 2000; 84 vcf
EGAD00001000231 EGAD00001000231_UK10K_NEURO_ASD_SKUSE_REL_2012_07_05 Illumina HiSeq 2000; 320 vcf
EGAD00001000313 UK10K_NEURO_ASD_SKUSE REL-2012-11-27 Illumina HiSeq 2000; 305 vcf
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
EGAD00001000278 ICGC MMML-seq Data Freeze November 2012 whole genome sequencing Illumina HiSeq 2000; 12 bam
EGAD00001000281 ICGC MMML-seq Data Freeze November 2012 transcriptome sequencing Illumina HiSeq 2000; 6 bam
EGAD00001000356 ICGC MMML-seq Data Freeze March 2013 transcriptome sequencing Illumina HiSeq 2000; 23 bam
EGAD00001000355 ICGC MMML-seq Data Freeze March 2013 whole genome sequencing Illumina HiSeq 2000; 46 bam
EGAD00001000298 UK10K_RARE_NEUROMUSCULAR REL-2012-11-27 Illumina HiSeq 2000; 130 vcf
EGAD00001000180 UK10K_RARE_NEUROMUSCULAR REL-2012-01-13 Illumina HiSeq 2000; 47 vcf
EGAD00001000189 UK10K_RARE_NEUROMUSCULAR REL-2012-02-22 Illumina HiSeq 2000; 86 vcf
EGAD00001000219 UK10K_RARE_NEUROMUSCULAR REL-2012-07-05 Illumina HiSeq 2000; 117 vcf
EGAD00001000274 DATA_SET_TRANSCIPTOME_Comparing_sequencing_four_proto-typical_Burkitt_lymphomas_BL_IG-MYC_translocation Illumina HiSeq 2000; 4 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
EGAD00001000393 Illumina HiSeq 2000; 30 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 vcf
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
EGAD00001000320 UK10K_NEURO_IMGSAC REL-2012-11-27 Illumina HiSeq 2000; 111 vcf
EGAD00001000239 EGAD00001000239_UK10K_NEURO_IMGSAC_REL_2012_07_05 Illumina HiSeq 2000; 114 vcf
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
EGAD00001000268 DATA FILES FOR SJCBF Illumina HiSeq 2000; 34 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
EGAD00001000352 DATA FILES FOR SJLGG Illumina HiSeq 2000; 7 bam
EGAD00001000353 DATA FILES FOR SJLGG Illumina HiSeq 2000; 45 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
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
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
EGAD00001000242 EGAD00001000242_UK10K_NEURO_ASD_MGAS_REL_2012_07_05 Illumina HiSeq 2000; 60 vcf
EGAD00001000312 UK10K_NEURO_ASD_MGAS REL-2012-11-27 Illumina HiSeq 2000; 96 vcf
EGAD00001000328 ICGC PedBrain: RNA sequencing Illumina HiSeq 2000; 28 fastq
EGAD00001000275 Data set for Whole-genome-Sequencing of adult medulloblastoma Illumina HiSeq 2000; 10 bam
EGAD00001000248 RNAseq Pulldown Illumina HiSeq 2000; 6 bam
EGAD00001000230 EGAD00001000230_UK10K_NEURO_ASD_GALLAGHER_REL_2012_07_05 Illumina HiSeq 2000; 72 vcf
EGAD00001000316 UK10K_NEURO_ASD_GALLAGHER REL-2012-11-27 Illumina HiSeq 2000; 75 vcf
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
EGAD00001000203 Otosclerosis gene discovery Illumina HiSeq 2000; 10 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
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
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
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
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
EGAD00001000246 Integrative Oncogenomics of multiple myeloma Illumina HiSeq 2000; 106 bam
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
EGAD00001000255 Testing the feasibility of genome scale sequencing in routinely collected FFPE cancer specimens versus matched fresh frozen samples Illumina HiSeq 2000; 32 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
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
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
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
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
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
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
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
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
EGAD00001000243 Melanoma-TIL Study Exomes Illumina HiSeq 2000; 43 bam,cram
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
EGAD00001000199 ORCADES_WGA Illumina HiSeq 2000; 400 bam
EGAD00001000309 UK10K_OBESITY_GS REL-2012-11-27 Illumina HiSeq 2000; 424 vcf
EGAD00001000300 UK10K_OBESITY_GS_REL_2012_07_05 Illumina HiSeq 2000; 430 bam
EGAD00001000613 UK10K_NEURO_ASD_MGAS REL-2013-04-20 Illumina HiSeq 2000; 97 vcf
EGAD00001000604 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 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
EGAD00001000204 Hearing loss in adults from South Carolina Illumina HiSeq 2000; 10 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
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
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
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
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
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
EGAD00001000200 Dilgom Exome Illumina HiSeq 2000; 130 bam
EGAD00001000251 De novo mutations in schizophrenia Illumina HiSeq 2000; 611 bam
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
EGAD00001000245 Pulldown cytosine deaminases Illumina HiSeq 2000; 20 bam
EGAD00001000247 Integrative Oncogenomics of multiple myeloma Illumina HiSeq 2000; 51 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
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
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
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; 190 bam
EGAD00001000304 ICGC prostate cancer miRNA sequencing Illumina HiSeq 2000; 8 fastq
EGAD00001000434 UK10K_NEURO_ASD_BIONED REL-2013-04-20 Illumina HiSeq 2000; 77 vcf
EGAD00001000418 UK10K_RARE_NEUROMUSCULAR REL-2013-04-20 Illumina HiSeq 2000; 140 vcf
EGAD00001000305 ICGC prostate cancer RNA sequencing Illumina HiSeq 2000; 12 fastq
EGAD00001000433 UK10K_NEURO_ABERDEEN REL-2013-04-20 Illumina HiSeq 2000; 392 vcf
EGAD00001000432 UK10K_OBESITY_SCOOP REL-2013-04-20 Illumina HiSeq 2000; 985 vcf
EGAD00001000442 UK10K_NEURO_IOP_COLLIER REL-2013-04-20 Illumina HiSeq 2000; 172 vcf
EGAD00001000430 UK10K_NEURO_UKSCZ REL-2013-04-20 Illumina HiSeq 2000; 554 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
EGAD00001000437 UK10K_NEURO_ASD_TAMPERE REL-2013-04-20 Illumina HiSeq 2000; 55 vcf
EGAD00001000435 UK10K_NEURO_ASD_FI REL-2013-04-20 Illumina HiSeq 2000; 84 vcf
EGAD00001000431 UK10K_OBESITY_GS REL-2013-04-20 Illumina HiSeq 2000; 428 vcf
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
EGAD00001000441 UK10K_NEURO_IMGSAC REL-2013-04-20 Illumina HiSeq 2000; 113 vcf
EGAD00001000436 UK10K_NEURO_ASD_GALLAGHER REL-2013-04-20 Illumina HiSeq 2000; 77 vcf
EGAD00001000597 Illumina HiSeq 2000; 212 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
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
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
EGAD00001000616 Pilocytic Astrocytoma ICGC PedBrain whole genome sequencing Illumina HiSeq 2000; 192 bam
EGAD00001000286 Whole-exome study of congenital macrothrombocytopenia Illumina HiSeq 2000; 21 fastq
EGAD00001000601 Illumina HiSeq 2000; 1 bam
EGAD00001000617 Pilocytic Astrocytoma ICGC PedBrain RNA sequencing Illumina HiSeq 2000; 73 fastq
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
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
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
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
EGAD00001000429 UK10K_OBESITY_TWINSUK REL-2013-04-20 Illumina HiSeq 2000; 68 vcf
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
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
EGAD00001000427 Illumina HiSeq 2000; 30 bam
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
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
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
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
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
EGAD00001000657 DATA FILES FOR Histone Capture bams Illumina HiSeq 2000; 962 bam
EGAD00001000655 DATA FILES FOR Histone-NSD2_RNASeq Illumina HiSeq 2000; 8 bam
EGAD00001000654 DATA FILES FOR BALL-PAX5 Illumina HiSeq 2000; 153 bam
EGAD00001000659 Illumina HiSeq 2000; 12 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
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
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
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
EGAD00001000675 RNA-seq for monocytes and neutrophils Illumina HiSeq 2000; 12 fastq
EGAD00001000674 DNaseI-seq for monocytes Illumina HiSeq 2000; 4 fastq
EGAD00001000673 WGBS-seq for monocytes and neutrophils Illumina HiSeq 2000; 12 bam,readme_file
EGAD00001001326 Whole genome sequencing of single adult t-cell leukemia/lymphoma case Illumina HiSeq 2000; 2 bam
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
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
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
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
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
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
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
EGAD00001001260 Illumina HiSeq 2000; 2 fastq
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
EGAD00001000291 Exome sequencing identifies mutation of the ribosome in T-cell acute lymphoblastic leukemia Illumina HiSeq 2000; 128 bam
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
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
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
EGAD00001000292 Whole genome sequencing analysis was performed on 6 patients within matched germline, follicular lymphoma and transformed follicular lymphoma. Illumina HiSeq 2000; 20 bam
EGAD00001000667 Illumina HiSeq 2000; 72 bam
EGAD00001000711 Illumina HiSeq 2000; 42 bam
EGAD00001000713 Illumina HiSeq 2000; 12 bam
EGAD00001000712 Illumina HiSeq 2000; 72 bam
EGAD00001002238 ChIP-Seq (H3K4me3, H3K4me1, H3K9me3, H3K27ac, H3K27me3, H3K36me3, Input) data for HL60 cell line generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency. Illumina HiSeq 2000; 1 bam,fastq
EGAD00001000710 Whole Genome Bisulfite-seq of four B cell samples Illumina HiSeq 2000; 4 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
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
EGAD00001000856 Illumina HiSeq 2000; 1 fastq
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
EGAD00001000672 Whole-genome Bisulfite sequencing of two multiple myeloma samples and one pooled sample of plasma cells. Illumina HiSeq 2000; 3 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
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