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• Mayo Clinic and Illumina Collaborative Early Stage Ovarian Cancer (ESOC) Study

  Twenty five patients with early stage carcinoma (Stage I and II) of the ovary were consented for this study. As part of a collaborative agreement with Illumina Inc, Tumor-DNA and patient matched normal DNA from blood underwent whole genome sequencing and microarray genotyping and RNA underwent RNASeq. Tissue also underwent IHC staining for TP53 mutations. The aim of the study was to profile the genomic landscape of these early tumors to discover biomarkers for early detection or subgrouping into different genomic or outcome subgroups. Analyses performed include somatic mutation analysis, RNASeq mutation analysis, LOH analysis, structural variant detection. The current release of this study focusses on 17 patients with serous carcinoma and stage 1 or 2 and with high grade (3 or 4).

  Study phs000897

• NIDDK IBD Genetics Consortium Repository Exome Chip

  The Illumina Infinium HumanExome+ BeadChip contains putative functional exonic variants selected from individual exome and whole-genome sequences from diverse populations. It includes nonsynonymous variants, splice variants and stop-altering variants. It also includes tags for previous GWAS-identified loci, ancestry informative markers, markers designed for identity by descent analyses, synonymous variants, fingerprint SNPs common to major genotyping platforms, mitochondrial SNPs, chromosome Y SNPs, and HLA tag SNPs. For more information as well as a detailed description of the variant calling and QC procedures, see Li et al. (2016). Li, D., et al. (2016) A pleiotropic missense variant in SLC39A8 is associated with Crohn's disease and human gut microbiome composition. Gastroenterology, 151, 1-9. PMID: 27492617.

  Study phs001723

• VCRC Genetic Repository One Time DNA Protocol

  The purpose of this study is to identify genes that increase the risk of developing vasculitis, a group of severe diseases that feature inflammation of blood vessels. Better methods are needed to recruit patients with these rare diseases into cohorts of adequate size for high-quality genetics studies, and the existing infrastructure of the Vasculitis Clinical Research Consortium (VCRC) provides the means for such recruitment. Results of these studies will provide vasculitis researchers with insight into the causes of these diseases and generate new ideas for diagnostic tests and therapies, and will be of great interest to the larger communities of researchers investigating vasculitis and other autoimmune, inflammatory, and vascular diseases. This study will enhance the VCRC Data and Specimen Repository.

  Study phs001712

• Investigation of a method for generating cells for regenerative medicine using comprehensive nucleic acid analysis of iPS cell-derived cardiomyocytes.

  Regenerative medicine for heart failure is expected to restore cardiac function by using human iPS cells (hiPSCs). In our laboratory, it was shown that transplantation of cardiomyocytes (CMs) derived from hiPSCs into a pig model of myocardial infarction improves the disease condition. However, the instability of differentiation efficiency and tumorigenicity after transplantation are still issues to be resolved. We attempt to identify and analyze the genes and DNA methylation associated with the induction of differentiation of hiPSCs into CMs with the aim of achieving stable induction of CMs differentiation. Furthermore, we aim to analyze genes involved in tumorigenesis in CMs, and to develop a predictive marker for tumorigenesis to ensure the safety of cells before transplantation.

  Study JGAS000665

• Data Access Committee of CiRA Foundation

  The iPS Cell Stock Project promoted by the CiRA Foundation is intended to generate and distribute iPS cells for medical use so they can be effectively utilized for research and development of cell transplantation therapy and contribute to the advancement of regenerative medicine that may become a novel treatment for patients suffering from intractable diseases or trauma who are not expected to improve with conventional therapies. In order to achieve this objective, CiRA Foundation establish the DAC based on the basic policies and rules for handling analysis information including iPS cell stocks for the purpose of proper sharing of samples and analyzed data collected directly or indirectly from the donors of iPS cell stocks.

  Dac EGAC50000000128

• CCA WGS data (16 CCA with matched normal, 4 cell-line)

  Fastq files for WGS for 16 CCAs (with matched normal tissues), and 4 cell lines in an AA-treatment experiment (0, 10, 20, 40ug AA treatment after 180 days; 2 runs each for 10ug and 40ug experiments). Genomic DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen). Sequencing libraries were prepared from DNA extracted using the SureSelect XT2 Target Enrichment System for the Illumina Multiplexed Sequencing platform (Illumina) according to the manufacturer’s instructions. Whole genome sequencing was performed on Illumina HiSeq4000 sequencer with paired-end sequencing.

  Dataset EGAD00001012100

• CRC organoid RNA-seq data access committee

  This DAC is responsible for granting access to RNA-seq data (paired-end FASTQ files) from 10 patient-derived colorectal cancer organoid patients. The data was ad hoc generated as part of the development of NovumRNA, a non-canonical tumor-specific antigen prediction pipeline.

  Dac EGAC50000000406

• WGS dataset for malignant pleural and peritoneal mesothelioma

  This dataset contains Whole Genome sequencing data of pleural and peritoneal mesothelioma. The number of samples is 40. Sequencing was performed on Illumina NovaSeq 6000 and Illumina NovaSeqXPlus. The sequencing was always paired.

  Dataset EGAD50000001343

• Boyes Lab - DAC policy

  Access to this data is controlled. Upon request from a third party for access to the data, a separate Data Sharing Agreement would be put in place between the University of Leeds and the third party prior to EGA granting access to the data to the third party.

  Dac EGAC50000000283

• PETAL trial Whole Exome Sequencing (WES) from Tumor Samples

  Associated with Molecular profiling of DLBCL patients treated in the PETAL trial. Whole Exome Sequencing (WES) of 224 Tumor Samples. WES was used for Molecular Profiling by simultaneous screening of mutations. Data is Complementary to sWGS.

  Dataset EGAD50000001172