DAC Accession Contact Person Email Access Information
EGAC00001000000 Data Sharing datasharing@sanger.ac.uk http://www.ebi.ac.uk/ega/dacs/EGAC00001000000

This DAC controls 230 datasets:

Dataset Accessionsort ascending Technology Samples Description
EGAD00010000644 1022 Affymetrix SNP6.0 cancer cell line exome sequencing data
EGAD00010000488 Affymetrix_SNP6- 7 Chondroblastoma case sample genotype using Affymetrix SNP6.0
EGAD00010000452 Affymetrix_SNP6 36 Chondrosarcoma case sample genotype using Affymetrix SNP6.0
EGAD00010000395 Affymetrix_SNP6 19 Myeloma case sample genotype using Affymetrix SNP6.0
EGAD00001003885 Illumina HiSeq 2500;ILLUMINA 19 The genetic basis of many rare childhood cancers remains unknown. These include a spectrum of infant soft tissue tumors without canonical gene fusions, encompassing congenital mesoblastic nephroma (CMN) of the kidney and infantile fibrosarcoma (IFS). Here, we integrated whole genome and transcriptome sequencing and identified diagnostic markers and novel therapeutic strategies.
EGAD00001003884 HiSeq X Ten;ILLUMINA 37 The genetic basis of many rare childhood cancers remains unknown. These include a spectrum of infant soft tissue tumors without canonical gene fusions, encompassing congenital mesoblastic nephroma (CMN) of the kidney and infantile fibrosarcoma (IFS). Here, we integrated whole genome and transcriptome sequencing and identified diagnostic markers and novel therapeutic strategies.
EGAD00001003811 Illumina HiSeq 2500;ILLUMINA 81 Our project will examine the role of PIK3CA mutations and their sensitivity to endocrine therapies and its role, with the addition of complete ovarian suppression. We plan to test our hypotheses using tumour samples collected from patients enrolled in the SOFT/IBCSG24-02 clinical study (Suppression of Ovarian Function Trial - (NCT00066690). SOFT is a phase III trial that randomised 3066 premenopausal women to evaluate if adding ovarian suppression to adjuvant endocrine therapy will improve clinical outcomes. This dataset contains all the data available for this study on 2017-11-22.
EGAD00001003703 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 628 The incidence of acute myeloid leukemia (AML) increases with age and mortality exceeds 90% when diagnosed after age 60. Only 10-15% of cases evolve from a pre-existing myeloproliferative or myelodysplastic disorder; the remaining cases arise de novo without a detectable prodrome and are diagnosed upon development of bone marrow failure. Analysis of diagnostic blood samples has demonstrated that de novo AML is preceded by the accumulation of somatic mutations in pre-leukemic hematopoietic stem and progenitor cells (preL-HSPCs) that subsequently undergo clonal expansion. If individuals in this pre-leukemic phase could be identified, methods for determination of risk and monitoring for progression to overt AML could be developed. However recurrent AML mutations also accumulate during aging in healthy individuals who never develop AML, referred to as age related clonal hematopoiesis (ARCH). To distinguish individuals with preL-HSPCs at high risk of developing AML from those with ARCH, we undertook deep targeted sequencing of genes recurrently mutated in AML in blood samples from 133 individuals in the European Prospective Investigation into Cancer and Nutrition (EPIC) study taken on average 6 years before they developed AML (pre-AML group), together with 683 matched healthy individuals (Control group). Pre-AML cases displayed accelerated age-correlated accumulation of somatic mutations.The identity, number and variant allele frequency (VAF) of mutations differed between the two groups, and were incorporated into a computational model of AML risk prediction that accurately distinguished pre-AML cases from controls on average 7 years prior to AML development. Our findings provide proof of concept that early prediction of AML development is feasible in high-risk populations, paving the way for early disease detection, monitoring, and potentially prevention.
EGAD00001003445 HiSeq X Ten;ILLUMINA 164 Clear cell renal cancer is characterized by near-universal loss of the short arm of chromosome 3 (3p). This event arises through unknown mechanisms, but critically results in the loss of several tumor suppressor genes. We analyzed whole genomes from 95 biopsies across 33 patients with clear cell renal cancer (ccRCC) recruited into the Renal TRACERx study. We find novel hotspots of point mutations in the 5'-UTR of TERT, targeting a MYC-MAX repressor, that result in telomere lengthening. The most common structural abnormality generates simultaneous 3p loss and 5q gain (36% patients), typically through chromothripsis. Using molecular clocks, we estimate this occurs in childhood or adolescence, generally preceding emergence of the most recent common ancestor by years to decades. Similar genomic changes recent common ancestor by years to decades. Similar genomic changes are seen in inherited kidney cancers. Modeling differences in age-incidence between inherited and sporadic cancers suggests that the number of cells with 3p loss capable of initiating sporadic tumors is no more than a few hundred. Targeting essential genes in deleted regions of chromosome 3p could represent a potential preventative strategy for renal cancer.
EGAD00001003425 Illumina MiSeq;ILLUMINA 177 A EGFR mutant NSCLC cell line which is sensitive to AZD9291 inhibition was mutagenised with the chemical mutagen ENU and then drug selected using a AZD9291. Single cell derived colonies were then manually picked and expanded in drug. Resistance was confirmed in a 14 day assay and DNA was collected. These then underwent targeted amplicon-based sequencing to confirm candidate resistance effectors hypothesised from currently available literature. This dataset contains all the data available for this study on 2017-07-05.
EGAD00001003334 Illumina HiSeq 2000;ILLUMINA 573 Targeted exome sequencing of patient derived xenografts from primary colorectal tumours and liver metastases. This dataset contains all the data available for this study on 2017-05-11.
EGAD00001003332 Illumina MiSeq;ILLUMINA 4 PCR and MiSeq validation for early embryonic substitution candidates from 400 Breast cancer patients This dataset contains all the data available for this study on 2017-05-11.
EGAD00001003330 Illumina HiSeq 2000;ILLUMINA 416 The samples will be sequenced for a targeted panel of cancer relevant genes (n ~ 370) and analysed for somatic mutations. This dataset contains all the data available for this study on 2017-05-11.
EGAD00001003321 Illumina HiSeq 2000;ILLUMINA 523 Systematic next generation sequencing efforts are beginning to define the genomic landscape across a range of primary tumours, but we know very little of the mutational evolution that contributes to disease progression. We therefore propose to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in a cohort of matched primary and metastatic colorectal cancers, and additionally to explore the extent to which those mutations identified as recurrent in the metastatic setting are able to subvert normal biological processes using both genetically engineered mouse models and established cancer cell lines. This study will enable us to define to what extent primary tumour profiling can capture the biological processes operative in matched metastases as well as the significance of intratumoural heterogeneity. This dataset contains all the data available for this study on 2017-05-04.
EGAD00001003320 Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA 106 Transcriptome sequencing of tumour tissue, adjacent normal tissue and derived organoids/tumoroids from colorectal cancer This dataset contains all the data available for this study on 2017-05-04.

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