DAC

Wellcome Trust Case Control Consortium Data Access Committee

Dac ID Contact Person Email Access Information
EGAC00000000001 Giselle Kerry datasharing [at] sanger [dot] ac [dot] uk http://www.wtccc.org.uk/info/access_to_data_samples.html

This DAC controls 21 datasets:

Dataset ID Description Technology Samples
EGAD00001001018 The samples will be sequenced for a targeted panel of cancer relevant genes (n ~ 370) and analysed for somatic mutations. This dataset contains all the data available for this study on 2014-09-24 Illumina HiSeq 2000 374
EGAD00001001426 Systematic next generation sequencing efforts are beginning to define the genomic landscape across a range of primary tumours, but we know very little of the mutational evolution that contributes to disease progression. We therefore propose to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in a cohort of matched primary and metastatic colorectal cancers, and additionally to explore the extent to which those mutations identified as recurrent in the metastatic setting are able to subvert normal biological processes using both genetically engineered mouse models and established cancer cell lines. This study will enable us to define to what extent primary tumour profiling can capture the biological processes operative in matched metastases as well as the significance of intratumoural heterogeneity. This dataset contains all the data available for this study on 2015-07-02. Illumina HiSeq 2000 446
EGAD00001001459 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 2015-08-05. Illumina HiSeq 2000 76
EGAD00001001600 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 2015-09-03. Illumina MiSeq 2
EGAD00001001872 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 2016-01-06. Illumina HiSeq 2000 333
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. This dataset contains all the data available for this study on 2016-01-27. HiSeq X Ten 131
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 HiSeq 2000 58
EGAD00001003321 This dataset contains all the data available for this study on 2017-05-04. Illumina HiSeq 2000 523
EGAD00001003334 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. Illumina HiSeq 2000 573
EGAD00001003811 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. Illumina HiSeq 2500 81
EGAD00001003884 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. HiSeq X Ten 37
EGAD00001003885 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. Illumina HiSeq 2500 19
EGAD00001003923 The discovery of the BRAF V600E mutation in almost all cases of hairy-cell leukemia has led to the widespread adoption of the BRAF inhibitor vemurafenib for treatment of chemotherapy-resistant cases. Impressive responses are reported; however, acquired resistance is common. Whilst diverse mechanisms of vemurafenib resistance have been elucidated in melanoma, the basis of resistance in HCL is unclear. Here we apply whole genome and deep targeted sequencing to investigate resistance mechanisms and potential therapeutic strategies in a patient with aquired resistance to vemurafenib. Illumina HiSeq 2500 15
EGAD00001004000 Targeted gene screen of cell line tumours for testing the new V4 Colorectal gene panel. . This dataset contains all the data available for this study on 2018-03-07. Illumina HiSeq 2500 53
EGAD00001004001 Targeted gene screen of FFPEs, cell lines and primary CRC tumours for testing the new V4 Colorectal gene panel. . This dataset contains all the data available for this study on 2018-03-07. Illumina HiSeq 2500 92
EGAD00001004086 We will take a bone marrow aspirate and peripheral blood samples from a healthy patient aged around 60, and use flow cytometry to isolate 100 HSCs, 50 MEPs, and 50 GMPs. We will grow these up into colonies, then whole genome sequence each colony. Somatic mutations will act as a unique barcode for each clone. We will then design a panel for targeted resequencing of the mutations that we find. It will then be possible to look for these mutations in the peripheral blood over several years, to see the dynamics of how HSCs contribute to the peripheral blood in health. This dataset contains all the data available for this study on 2018-04-19. HiSeq X Ten,Illumina HiSeq 2500 207
EGAD00001004087 We took a bone marrow aspirate and peripheral blood samples from a healthy patient aged around 60, and use flow cytometry to isolate 100 HSCs, 50 MEPs, and 50 GMPs. We grew these up into colonies, then whole genome sequenced each colony. Somatic mutations act as a unique barcode for each clone. We have designed a panel for targeted resequencing of the mutations that we find. We are now looking for these mutations in the peripheral blood, to see the dynamics of how HSCs contribute to the peripheral blood in health. This dataset contains all the data available for this study on 2018-04-19. Illumina HiSeq 2500 48
EGAD00001004124 CRISPR-Cas9 loss-of-function screens are instrumental to systematically identify genes important for cellular fitness in cancer cells. While structural rearrangements are a ubiquitous feature in cancer, their impact on CRISPR-Cas9 response has not yet been systematically assessed. Utilising data for 163 CRISPR-Cas9 screened cancer cell lines, we demonstrate that targeting tandem amplified regions is highly detrimental to cellular fitness, in stark contrast to amplifications arising from chromosomal duplications, which have little to no effect. In addition, high ploidy leads to decreased CRISPR-Cas9 loss of fitness effects in a gene-independent way. Using whole-genome sequencing and fluorescent in situ hybridisation we confirm that clustered Cas9 double-strand DNA cuts in a single chromosome, contrary to multiple chromosomes, are associated with a strong decrease in cell fitness. We propose this as a novel way to exploit collateral vulnerabilities introduced by structural rearrangements in cancer cells, by systematically identifying tissue non-expressed genes that are tandem amplified. 25% of the screened cell lines have at least one putative collateral essentiality, showing that this is a generalizable way to selectively kill tumour cells. Lastly, we present a flexible computational tool, Crispy, to perform association analysis of different types of genomic alterations in CRISPR-Cas9 screens. Our results demonstrate the importance of structural rearrangements in mediating the effect of CRISPR-Cas9-induced DNA damage on cell fitness, and how this could be harnessed to create selective cancer therapies, especially in tumours enriched for tandem duplications. Illumina HiSeq 2000 12
EGAD00001004152 Targeted pulldown of approx 60 ffpe normal samples to use as normal controls . This dataset contains all the data available for this study on 2018-06-06. Illumina HiSeq 2500 80
EGAD00001004158 The extent to which cells in normal tissues accumulate mutations during life is poorly understood. Some mutant cells expand into clones that can be detected by genome sequencing. We mapped mutant clones in normal esophageal epithelium from nine donors aged 20-75. Somatic mutations accumulate with age and are mainly caused by intrinsic mutational processes. We found strong Darwinian selection of clones carrying mutations in 14 cancer genes, with tens to hundreds of such clones per square centimeter. By middle age, clones with cancer-associated mutations cover most of the epithelium, with NOTCH1 and TP53 mutations affecting 40% and 10% of all cells, respectively. Remarkably, the prevalence of NOTCH1 mutations in normal esophagus is several times higher than in esophageal cancers. The esophagus emerges as an evolving patchwork of mutant clones that colonize the majority of the epithelium, with implications for our understanding of cancer and ageing. Illumina HiSeq 2500 866
EGAD00001004159 The extent to which cells in normal tissues accumulate mutations during life is poorly understood. Some mutant cells expand into clones that can be detected by genome sequencing. We mapped mutant clones in normal esophageal epithelium from nine donors aged 20-75. Somatic mutations accumulate with age and are mainly caused by intrinsic mutational processes. We found strong Darwinian selection of clones carrying mutations in 14 cancer genes, with tens to hundreds of such clones per square centimeter. By middle age, clones with cancer-associated mutations cover most of the epithelium, with NOTCH1 and TP53 mutations affecting 40% and 10% of all cells, respectively. Remarkably, the prevalence of NOTCH1 mutations in normal esophagus is several times higher than in esophageal cancers. The esophagus emerges as an evolving patchwork of mutant clones that colonize the majority of the epithelium, with implications for our understanding of cancer and ageing. HiSeq X Ten 25