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• V4_Colorectal_panel_test

  Targeted gene screen of cell line tumours for testing the new V4 Colorectal gene panel.

  Study EGAS00001001807

• ChIP-Seq files for PCGP ATRX study

  ChIP-Seq files for PCGP ATRX study paper titled "MYCN Amplification and ATRX Mutations are Incompatible in Neuroblastoma"

  Dataset EGAD00001004429

• PACA-CA RNASeq fastq files

  Fastq files for PACA-CA RNA Seq analysis, for DCC release 27

  Dataset EGAD00001003972

• WGBS data for Glioblastoma (EGAS00001003953, H016)

  Whole Genome Bisulfite data for human glioblastoma patients, EGAS00001003953. 68 human samples

  Dataset EGAD00001006546

• A98269B

  Whole genome sequencing for single cells for library A98269B 1609 cells; filetype=bam

  Dataset EGAD00001006947

• A96217B

  Whole genome sequencing for single cells for library A96217B 1616 cells; filetype=bam

  Dataset EGAD00001006945

• Covacta RNAseq merged EGA metadata

  Sample metadata for the RNA-seq dataset. This dataset includes subject-level data and longitudinal visit day information for the corresponding samples.

  Dataset EGAD00001011162

• KiCS cancer panel academic only data

  This data set contains KiCS cancer panel data for academic and for-profit use.

  Dataset EGAD00001009733

• Mutation of FOXL2 in granulosa cell tumors of the ovary

  We generated paired-end RNA-Seq data using the Illumina Genome Analyzer II platform for four adult granulosa cell tumours (GCTs) of the ovary (1 primary, 3 recurrent). We screened this data for the presence of GCT specific sequence variants and detected a non-synonymous mutation in the FOXL2 gene that was found to be recurrent in 97% of 89 additional GCTs. To measure genomic stability of the four index cases, we generated Affmetrix SNP 6.0 data and analysed these data for copy number changes. Raw sequence reads as well as Affymetrix CEL files are available to applicants.

  Study EGAS00000000040

• Germline DNA Methylation Associated with Breast Cancer Predisposition

  Understanding and explaining hereditary predisposition to cancer has focused on the genetic etiology of the disease. However, mutations in known genes associated with breast cancer such as BRCA1 and BRCA2 account for less than 25% of familial cases of breast cancer. Heritable epigenetic modifications, in the form of hypermethylated MLH1 promoter alleles, have recently been shown to promote hereditary nonpolyposis colorectal cancer. We investigated the potential for an epigenetic basis for hereditary breast cancer by performing deep bisulfite sequencing of CpG islands and known promoter regions in germline DNA from 100 familial or early-onset breast or ovarian cancer patients.

  Study phs001699

• dbGaP Collection: Psychiatric Genomics Consortium (PGC) dbGaP Datasets

  This dbGaP Collection includes cases and controls used in the GWAS meta-analysis of neuropsychiatric phenotypes studied by investigators in the Psychiatric Genomics Consortium including major depression, bipolar disorder, attention deficit and hyperactivity disorder, schizophrenia, Tourette Syndrome, and obsessive-compulsive disorder. The consent type for data sets includes general research use as well as phenotype-specific restricted usage. This dbGaP collection was created to facilitate identification of datasets used in PGC analyses in order to expedite the application and ascertainment process for PGC members wishing to access data within the consortium. Non-PGC members may also apply for this dbGaP collection.

  Study phs001254

• Correction of the cytosine deamination artifacts in FFPE-based sequencing experiments

  Formalin-fixed paraffin-embedded (FFPE) samples are widely used in research and diagnostics, but cytosine deamination during fixation introduces sequencing artifacts, particularly C>T substitutions, which complicate reliable mutation detection. In this study, we systematically evaluated five computational methods and an enzymatic repair approach for FFPE artifact removal, as well as their combined application, using a custom dataset based on whole exome sequencing. Our results demonstrate that while computational strategies improve data quality, the enzymatic approach provides the most effective artifact correction. The study provides guidelines for both computational and enzymatic artifact correction strategies for reliable downstream analyses.

  Study EGAS50000001354

• The_Causes_of_Clonal_Blood_Cell_Disorders_Study___SCOR

  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.

  Study EGAS00001002132

• Comprehensive NGS Profiling to Enable Detection of ALK Gene Rearrangements and MET Amplifications in Non-Small Cell Lung Cancer

  We evaluate the analytical performance of the PGDx™ elio™ tissue complete assay, a 505 gene next-generation sequencing (NGS) tissue-based assay, that has now been FDA-cleared for use by physicians to help guide treatment decisions for cancer patients, using a NSCLC cohort of 38 patients.

  Study EGAS50000000010

• Single nuclei ATAC-Seq data from the human ganglionic eminences

  We performed the single nuclei Assay for Transposase-Accessible Chromatin with Sequencing (snATAC-Seq) to map potential regulatory genomic regions operating in individual cell populations of the human GE, using these to test for enrichment of schizophrenia common genetic variant liability and to functionally annotate non-coding variants associated with the disorder.

  Study EGAS50000000411

• Variables of diversity, clonality, V and J usage and main COVID-19-reactive GLIPH2 frequencies.

  Main results of the T cell repertorie analysis of a cohort of 61 patients. For each patient, repertorie diversity and clonality metrics, V an J alelle frequency and COVID-19-reactive sequencies have been calculated using open.source code. For more information about the study, please visit DOI: 10.1186/s40246-024-00654-0

  Study EGAS50000000587

• Clonal structure and oncogenic potential of liver cirrhosis tissues.

  Hepatocellular carcinoma (HCC) recurrently develops in cirrhotic liver composed of numbers of regenerative nodules (RNs). The biologic or genetic basis of RNs for hepatocarcinogenesis remains unclear at present. Thus, to uncover the basis of cirrhotic liver for multicentric tumorigenesis, we investigated the oncogenic potential of RNs in LC tissues using multi-omics analysis.

  Study JGAS000134

• An Organoid Biobank of Rare Human Neuroendocrine Neoplasms Enables Genotype-Phenotype Mapping

  We performed whole genome sequencing and RNA-sequencing of neuroendocrine neoplasm. The aim of this study was to provide genetic landscape of neuroendocrine neoplasm, to construct available animal models, and to engineer neuroendocrine neoplasm from normal colon epithelium. The reference genomes used are GRCh37 for whole genome sequencing and GRCh38 for RNA-sequencing.

  Study JGAS000237

• Mutator phenotype and specific mutational signature explain an increased risk of hematological malignancies in patients with Xeroderma Pigmentosum

  In this study we report for the first time the unique collection of 6 leukemias and two sarcomas from XP-C. Comprehensive WGS-based mutational analysis provides genetic explanation for the increased incidence of leukemia in XP-C and describes an unique mutational process in internal tumors associated with NER deficiency.

  Study EGAS00001004511

• Exome sequencing of patients with rare neurological disorders

  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.

  Study EGAS00001000159

• CRISPR_Screening_of_Brazilian_Acral_Melanoma_Cell_Lines

  Perform CRISPR Screening in acral melanoma cell lines, using a genome-wide gRNA library, aiming to identify genes essential for their survival and proliferation. The results will aid the identification of key genes and pathways implicated in acral melanoma progression, paving the way to understand the disease and offer potential targets for precision therapies to this subtype of melanoma.

  Study EGAS00001008230

• A somatic reference standard for cancer genome sequencing.

  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.

  Dataset EGAD00001002142

• Additional Methylation files for Roussel-ATRT-TM

  Additional Methylation files for Roussel-ATRT-TM paper titled "Atypical teratoid/ rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities"

  Dataset EGAD00010002495

• DAC for TFHL single-cell analysis project at Department of Hematology, University of Tsukuba

  DAC for study of tumor heterogeneity and immune-evasive microenvironment in T follicular helper cell lymphomas

  Dac EGAC50000000201

• COMPASS Next Generation Sequencing WGS data

  Whole genome sequencing data for Pancreatic Cancer Samples from the COMPASS clinical trial

  Study EGAS50000001091

• Data files for CONSERTING

  Data files for CONSERTING (WGS)

  Dataset EGAD00001001352

• RNA data for MMML (EGAS00001002422)

  RNA sequencing data for MMML (3 tumor samples and 1 gcbcell)

  Dataset EGAD00001003285

• Mucosal 16S metadata

  Metadata for 16S-V4 rRNA gene sequence data for intestinal biopsies from NCT02749630 trial participants.

  Dataset EGAD00001008823

• A95673A

  Whole genome sequencing for single cells for library A95673A 1446 cells; filetype=bam

  Dataset EGAD00001006941

• CUTRUN files for Klco-NUP98 data

  CUTRUN files for paper titled "Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia"

  Dataset EGAD00001015478

• WGS files for Mullighan_GL_reALL

  WGS files for Mullighan_GL_reALL paper titled "Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia"

  Dataset EGAD00001005506

• WXS files for Mullighan_GL_reALL

  WXS files for Mullighan_GL_reALL paper titled "Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia"

  Dataset EGAD00001005509

• WTCCC case-control study for Hypertension - Combined Controls

  WTCCC genome-wide case-control association study for Hypertension (HT) using six disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000010

• Development of a rapid and comprehensive genomic profiling test supporting diagnosis and research for gliomas

  Targeted sequencing dataset used for the paper entitled "Development of a rapid and comprehensive genomic profiling test supporting diagnosis and research for gliomas". The cohort includes 53 cases of targeted DNA squencing, 15 of them have matched control sequences. The capture panel was made by Agilent SureSelect and the sequence was performed using DNBSEQ or Illumina sequencer.

  Dataset EGAD50000000979

• Machine learning guided signal enrichment for ultrasensitive plasma tumor burden monitoring

  Development of a novel machine learning guided ctDNA detection platform for use in liquid biopsy detection and therapeutic monitoring of solid tumors in several clinical contexts. Included are WGS alignments from our study.

  Study EGAS00001007306

• Sequencing data for the Genomic Autopsy Study

  The .cram files of the Trio or Quad sequencing data used for generation of the genomic autopsy study. This contains a mix of genome sequencing and exome sequencing data for probands and their parents. A subset of families (n=32) did not provide consent to publicly sharing their data.

  Dataset EGAD00001009737

• Dataset of transcriptomic, whole genome and whole exome sequencing to identify predictive biomarkers in pediatric solid tumors

  This Dataset contains whole genome sequencing data for 148 sample, transcriptome sequencing for 66 samples and exome sequencing for 123 samples from pediatric solid tumors. Sequencing was performed on Illumina NovaSeq 6000 and Illumina HiSeq 4000. The sequencing was paired.

  Dataset EGAD00001015701

• Single-Cell Atlas of Common Variable Immunodeficiency shows germinal center-associated epigenetic dysregulation in B cell responses

  Common variable immunodeficiency (CVID) is the most prevalent primary immunodeficiency. Here the authors perform single cell omics analyses in CVID discordant monozygotic twins and show epigenetic and transcriptional alterations associated with activation in memory B cells.

  Dataset EGAD00001008575

• Genomic evolution and natural history of myeloproliferative neoplasms on therapy - MPN_bulk

  Philadelphia-negative myeloproliferative neoplasms are chronic blood neoplasms. Treatments control blood counts but disease can progress to myelofibrosis or acute myeloid leukaemia. We performed longitudinal whole-genome and targeted sequencing in 30 patients, integrating clonal dynamics with 7,986 blood counts and clinical histories. Distinct evolutionary patterns distinguished stable from progressive disease, with leukaemic transformation arising via TP53 loss, stepwise driver mutation acquisition within complex clones, or emergence of independent leukaemic clones. In contrast, stable disease showed long-term clonal equilibrium without new drivers. Phylogenetic analysis using 203 whole-genomes of haematopoietic colonies revealed age-appropriate polyclonal haematopoiesis in triple-negative essential thrombocythaemia and germline predisposition to thrombocytosis, supporting non-neoplastic origins. Therapy-associated mutagenesis was observed, including C>G mutations following azacitidine and characteristic T>A/T>G after hydroxycarbamide exposure in blood cells, although not in skin where UV damage predominated. These findings demonstrate progression is genomically encoded years in advance and support serial monitoring and further study of treatment-related mutagenesis.

  Dataset EGAD00001016067

• WES data for Heterogeneity of IKZF1 genomic alterations and risk of relapse in childhood BALL

  Whole exome sequencing data for 425 samples with B-cell acute lymphoblastic leukemia

  Dataset EGAD50000000150

• ASD WGS DAC

  This data access committee will oversee the request for applications to whole genome sequencing data (WGS) generated at The Centre for Applied Genomics (TCAG), as part of our Autism Genome Project.

  Dac EGAC50000000279

• Japanese population-specific reference panels (BioBank Japan genotype data)

  Develop Japanese population-specific reference panels to improve imputation quality for GWAS

  Study JGAS000738

• V2_Colorectal_panel_test

  Targeted gene screen of cell line tumour samples for testing the new V2 Colorectal gene panel.

  Study EGAS00001001806

• McGill EMC Release 4 for assay "smRNA-seq"

  McGill EMC Release 4 for assay "smRNA-seq": Transcriptome profiling by high-throughput sequencing

  Dataset EGAD00001001292

• McGill EMC Release 4 for cell type "induced pluripotent stem cell"

  McGill EMC Release 4 for cell type "induced pluripotent stem cell"

  Dataset EGAD00001001276

• McGill EMC Release 4 for assay "Bisulfite-seq"

  McGill EMC Release 4 for assay "Bisulfite-seq": Methylation profiling by high-throughput sequencing

  Dataset EGAD00001001289

• McGill EMC Release 4 for assay "RNA-seq"

  McGill EMC Release 4 for assay "RNA-seq": Transcriptome profiling by high-throughput sequencing

  Dataset EGAD00001001290

• McGill EMC Release 4 for assay "mRNA-seq"

  McGill EMC Release 4 for assay "mRNA-seq": Transcriptome profiling by high-throughput sequencing

  Dataset EGAD00001001291

• A96219B

  Whole genome sequencing for single cells for library A96219B 1743 cells; filetype=bam

  Dataset EGAD00001006946

• Additional data for 01_HepG2_LiHG_Ct1, H3K122ac

  Additional histone modification data, not yet released as part of IHEC, for cell line 01_HepG2_LiHG_Ct1, H3K122ac.

  Dataset EGAD00001005954