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• HIV exome pilot, exome data part 2 GRCh37_53

  exome sequence data for 25 HIV elite long term non-progressors and rapid progressors. Partial dataset (overlap with EGAD00001000047) of raw BAMs mapped to GRCh37_53.

  Dataset EGAD00001000087

• MiSeq-High Coverage

  Seven files of patients 3, 21, 29, 30, 31, 32 and 33 with WGS done on Illumina MiSeq with high coverage. For research purpose and authorised user only.

  Dataset EGAD00001003436

• Genome - MBD4-deficient AML

  Genome sequencing at diagnosis and post induction for WEHI-AML-1 and WEHI-AML-2. Whole genome sequencing was performed on an Illumina HiSeq X Ten.

  Dataset EGAD00001003568

• Colon cancer ctDNA

  Samples prepared using Safe-SeqS technology. All samples ran on an Illumina MiSeq instrument. Fastq files for read 1 and the index read present (R and I respectively).

  Dataset EGAD00001003579

• RNA-seq data of LMS tumors

  This dataset contains paired fastq files for LMS tumor samples

  Dataset EGAD00001003828

• BGI study for primary and metastatic Chinese lung adenocarcinomas

  We sequenced 292 patients who were suffering NSCLC with Whole genome sequencing or Exome sequencing method.

  Dataset EGAD00001001397

• FFPE Normal Panel V3 Cancer Panel

  FFPE normal panel generation for use with V3 cancer panel 0618521

  Dataset EGAD00001001122

• RNA-Seq Illumina GAII dataset

  RNA-Seq Illumina GAII dataset for the TraIT cell-line use case (added reverse and forward reads).

  Dataset EGAD00001001626

• ICGC Benchmark 2 (Medulloblastoma)

  Raw fastq files for sequence data generated at 5 sequencing centers from a Medulloblastoma sample and matching blood normal control.

  Dataset EGAD00001001859

• HIV exome pilot, exome data part 1 GRCh37_53

  exome sequence data for 49 HIV elite long term non-progressors and rapid progressors. Partial dataset (overlap with EGAD00001000087) of raw BAMs mapped to GRCh37_53.

  Dataset EGAD00001000047

• DNA sequencing for gastric cancer ascites

  Whole-exome sequencing (WES) was performed on a total of 34 PC specimens, with 15 cases having matched gDNAs extracted from blood.

  Dataset EGAD00001004364

• Melanoma exome profiling

  This dataset includes whole exome profiling of 65 early-passage metastatic melanoma cell lines. The data are provided as BAM files for tumor and normal samples.

  Dataset EGAD00001006271

• NICHE - DNA-seq of MMR proficient and MMR deficient early stage colon cancers

  The dataset includes 174 FASTQ files from paired-end WXS sequencing on Illumina HiSeq2500 for 39 patients.

  Dataset EGAD00001006041

• PacBio data of de novo assembly individual EGYPT

  This is the PacBio long read data used for performing de novo assembly of the EGYPT individual (mapped against GRCh38).

  Dataset EGAD00001006034

• RnaSeq samples for 25 UPS samples

  Whole Transcriptiome Rnaseq of 25 UPS samples - raw FastQ sequences, 125x2 nc Paired End Reads, min 30M PE, HiSEq technology

  Dataset EGAD00001006355

• Processed RNAseq data

  This dataset contains log2(TPM + 1) transformed counts for the 823 tumor samples profiled by RNAseq.

  Dataset EGAD00001006618

• RNA-seq data for de-methylation of FOXP3-TSDR study

  22 RNA-seq samples of ex-vivo (TN and Treg), cultured Treg, TET1 and untreated mCherry-MOCK

  Dataset EGAD00001006865

• FPKM expression values of the CUP/reference/validation cohort (H021)

  FPKM expression values of the CUP/reference/validation cohort used for tissue-of-origin prediction based on transcriptomic data

  Dataset EGAD00001008638

• 1_fibroblasts_HD_vs_Ctrl_DMSO_Branaplam

  n=4 Ctrl and n=4 HD fibroblasts lines were treated with DMSO or 10nM Branaplam for 72h and RNA-seq was performed.

  Dataset EGAD00001008807

• CBD-RAW-CLINVAR: Clinical metadata

  Anonymised patient metadata and associated data dictionary. For further information regarding this dataset, please contact Alexander Mentzer at contact@combat.ox.ac.uk.

  Dataset EGAD00001007931

• Tumor from individual with germline POLD1 L474P

  This dataset includes WXS sequencing for 1 tumor FFPE sample and adjacent normal tissue from the individual from one family member.

  Dataset EGAD00001009281

• Annotated germline variant calls from the lungNENomics project

  Annotated germline variant calls derived from WGS data for 72 individuals from the lungNENomics cohort. Variant calling was performed with Strelka2 and annotation with InterVar.

  Dataset EGAD00001015672

• Investigating Delayed-Onset Drug Hypersensitivity Reactions Prospectively

  Delayed-type drug hypersensitivity reactions (dtDHR) are significant causes of morbidity and mortality, but the origin, phenotype and function of pathogenic T cells across the spectrum of severity are unknown. Research has been hampered by several barriers. We leveraged recent technical advancements to study skin-resident memory T cells (TRM) versus recruited T cell subsets in the pathogenesis of severe systemic forms of disease, Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) and drug reaction with eosinophilia and systemic symptoms (DRESS), and skin-limited disease, morbilliform drug eruption (MDE). As part of the overarching study, we used single cell RNA sequencing (scRNA-seq) with CITE sequencing and TCR sequencing on prospectively collected skin and blood samples from patients with SJS/TEN and MDE patients. We compared this to healthy controls obtained from discarded skin from surgeries and discarded blood collars from a blood donation center. These data are included here in dbGaP database. The overarching study also performed bulk transcriptional profiling and microscopic analysis of clinical skin samples, as well as a mouse model of MDE (PMID: 39042477). Together, the data supported clonal expansion and recruitment of cytotoxic CD8+ T cells (identified using the mean normalized expression of NKG7, GNLY, GZMA, GZMB, and PRF1) from circulation into skin, along with both expanded and non-expanded cytotoxic CD8+ skin TRM in SJS/TEN whereas MDE displayed a cytotoxic T cell profile without expansion or recruitment of cytotoxic CD8+ T cells from circulation implicating TRM as the potential cause of disease. Concurrently, MDE displayed a pro-Treg signature, highlighted by CCR8 and TNFRSF4 (OX40), which promotes Treg survival compared to SJS/TEN.

  Study phs003344

• Inherited chromosomally-integrated human herpesvirus 6A/B (HHV-6A/B) genome sequences in the Japanese population

  The deposited sequences represent inherited chromosomally-integrated human herpesvirus 6 (iciHHV-6) genomes identified from 10 BioBank Japan (BBJ) subjects based on the analysis of the whole-genome sequencing (WGS) data. In brief, we re-aligned unmapped reads from the WGS to HHV-6A genome (Genbank accession number: KJ123690.1) using BWA-MEM algorithm. Ten out of 3,256 subjects were identified with high depth of coverage of HHV-6. We further distinguished subjects with integrated HHV-6A subtypes from those with integrated HHV-6B based on phylogenetic analysis of concatenated sequences of three viral genes (U27/U43/U83, which show high divergence between viral species). We reconstructed the HHV-6 viral genome of 10 subjects. First, reads that mapped to a reference HHV-6A genome (KJ123690.1) were further aligned against the integrated HHV-6A genome derived from a Japanese individual NA18999 (GenBank Accession number: KY316047.1) using BWA-MEM. Based on the alignment, variant calling was performed using freebayes (version: v1.2.0-2-g29c4002) with parameters ploidy = 1 and min-alternate-fraction = 0.8 {Garrison, 2012}. We generated subject-specific iciHHV-6 viral sequences by applying the resulting variants to the KY316047.1 reference genome using the FastaAlternateReferenceMaker function in the Genome Analysis Toolkit (GATK) v3.7. Please note that HHV-6B-specific variants are unlikely to be sensitively reconstructed using this method.

  Study JGAS000240

• Access to public datasets in the EGA

  Dac EGAC00001000514

• B and T Cell Determinants of Influenza Vaccine Responses in the Elderly

  The study sequenced antibody heavy chain gene rearrangements from human subjects receiving influenza vaccination.

  Study phs000666

• WGS sequencing of an ES tumor sample

  This Datasets contains whole genome sequencing data of one ES tumor sample. Sequencing was performed on Illumina NovaSeq 6000. The sequencing was paired in bulk.

  Dataset EGAD00001015607

• Nanopore targeted sequencing of the CFTR gene in Moroccan patients with suspected cystic fibrosis

  This dataset contains fastq files sequencing with Oxford Nanopore (MK1C)

  Dataset EGAD50000002062

• WES bam files associated with HNSCC patients in the LIONESS study

  This dataset contains 85 WES bam/bai files of HNSCC cancer patients as part of with the LIONESS study

  Dataset EGAD50000001487

• WGS

  Our cohort represents infants with ALL in whom KMT2Ar was not detected by FISH or by standard cytogenetics. Whole-genome sequencing (WGS) was performed using Illumina’s HiSeqX to a depth of >30X.

  Dataset EGAD50000000594

• Exome data from a high-density melanoma family

  This dataset contains whole-exome sequence data from four individuals in a high-density melanoma family. Sequences were aligned against human reference genome HG19 using BWA.

  Dataset EGAD50000002153

• HDAC inhibitor quisinostat in synovial sarcoma cell lines

  An RNA Seq study of the effects of HDAC inhibitor Quisinostat on six different synovial sarcoma cell lines

  Dataset EGAD00001003810

• Germline whole exome sequencing in testicular cancer

  This dataset contains variant call format files generated from whole exome sequencing of germline DNA from indiviudals with diagnosed with testicualr germ cell cancer.

  Dataset EGAD00001004345

• Germline variants in patients diagnosed with both uveal and cutaneous melanoma

  We sequenced the constitutional DNA from patients affected by both uveal and cutaneous melanoma.

  Study EGAS00001007584

• Whole exome sequencing dataset in follicular lymphoma without evidence of transformation

  Whole exome sequencing data of 5 patients diagnosed with FL that had undergone several relapse episodes without evidence of transformation

  Dataset EGAD00001001301

• Angiosarcoma follow-up 2 validation study

  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.

  Dataset EGAD00001000679

• DNMT3A MOPD patient ChIP-seq data

  ChIP-seq data from controls and patients with de novo DNMT3A mutations resulting in microcephalic primordial dwarfism.

  Dataset EGAD00001004473

• Targeted deep mtDNA amplicon sequencing MS discordant twins

  Single-end BAM files of the targeted deep sequencing analysis of several mtDNA candidate regions in blood and buccal-derived DNA of the corresponding twin pairs.

  Dataset EGAD00001002190

• BAP1 sequence of uveal melanoma and mesothelioma samples

  Detection of BAP1 mutations in DNA from uveal melanoma and mesothelioma samples.

  Dataset EGAD00001002229

• Neurodegenerative_TGS

  An investigation of clonal haematopoiesis in patients with neurodegenerative disease.

  Dataset EGAD00001006392

• Dataset of VCF files of three trio members

  This dataset contains whole genome sequencing data, based in VCF of three trio members.

  Dataset EGAD00001008097

• NiCOL Study Target-seq dataset

  10 samples sequenced in Target-sequencing of a panel of 571 genes (Illumina NovaSeq 6000) - Raw FASTQ data - Annotated VCF

  Dataset EGAD00001010911

• CHEWIE ctDNA in Rhabdomyosarcoma

  Targeted DNA based panel of multiple ctDNA samples from 10 patients througout clinical care to assess treatment response. The panel is custom-designed and property of UGS, IC.

  Dataset EGAD00001011127

• H3K27ac ChIPseq of cohesin-mutated and wildtype adult AMLs

  ChIP-seq targeting the H3K27ac histone modification in cohesin-mutated (STAG2 or RAD21 mutation) and cohesin wildtype (CTRL-AMLs) AMLs.

  Dataset EGAD00001011204

• Minority Health Genomics and Translational Research Bio-Repository Database

  The Minority Health Genomics and Translational Research Bio-repository Database (MHGRID) Network infrastructure facilitated the collection of biospecimens and related multidimensional data elements within a consortium of minority-serving clinics. This initiative expands the diversity of ancestral groups in national genomic medicine datasets and promises to accelerate the translation of personalized medicine into minority communities. MHGRID has an observational case-control design with severe hypertension as primary outcome.

  Study phs001815

• The MD Anderson Colorectal Cancer Case Control Study

  Colorectal cancer (CRC) is the second leading cause of cancer-related deaths in the US. Driven by common disease common variants hypothesis, genome-wide association studies only identified a number of common susceptibility loci that explained a small portion of CRC heritability. We conducted a case-control study using whole exome sequencing to identify rare genetic variants with intermediate effect size that predispose individuals to colorectal cancer.

  Study phs002691

• GUARDIAN: The Insulin Resistance Atherosclerosis Study (IRAS Classic)

  The Insulin Resistance Atherosclerosis Study (IRAS) was an epidemiologic cohort study designed to examine the relationship between insulin resistance and carotid atherosclerosis across a range of glucose tolerance. Individuals of self-reported Mexican-American ethnicity were recruited in San Antonio, TX and San Luis Valley, CO. Recruitment was balanced across age and glucose tolerance status. GUARDIAN includes 173 individuals from the IRAS. Insulin sensitivity was obtained by FSIGT.

  Study phs001014

• Pilot Sequencing Study: DNA Hydroxymethylation and Gene Expression in Peripheral Blood Mononuclear Cells in Healthy Human Aging

  This study was a pilot analysis of samples of human peripheral blood mononuclear cell (PBMCs) from 10 young (23-30 years) and 10 older (68-76 years) healthy Caucasian female volunteers. Whole genome sequencing was performed to assess multiple epigenetic mechanisms and gene expression, including 5hmC-capture sequencing and RNA-sequencing, followed by integrative analyses to identify regions and genes associated with age.

  Study phs001916

• Integrated Genetic and Pharmacologic Interrogation of Rare Cancers

  Due to the paucity of patient derived models in rare cancers, identification of therapeutic targets remains challenging. We developed a patient derived model, CLF-PED-015-T, from a patient with an undifferentiated sarcoma. From this model, we performed pooled RNAi and CRISPR-Cas9 negative selection screens and integrated that with a small molecule screen. Integration of these data identified CDK4 and XPO1 as potential therapeutic targets.

  Study phs001121

• Evolving Cell States and Oncogenic Drivers during the Progression of IDH-Mutant Gliomas

  The study aims to understand the changes in cell states during the progression of IDH mutant gliomas. We generated scATAC-seq data from tumor samples of patients with IDH mutant gliomas, ranging from grade 2 to grade 4, including both IDH mutant oligodendroglioma and IDH mutant astrocytoma samples. Additionally, we have generated scRNA-seq data from patient-derived organoids that were treated with a DNMT1 inhibitor.

  Study phs003697