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• GIST Comprehensive Cancer Panel

  DNA Sequencing of 864 genes from KiCS cancer panel. Multiple family members affected with multifocal GIST who underwent whole genome sequencing of the germline and tumor. Affected individuals with GIST harbored a germline variant found within exon 13 of the KIT gene, (c.1965T>G; p.Asn655Lys, p.N655K) and a variant in the MSR1 gene (c.877C>T; p.Arg293*, pR293X).

  Dataset EGAD50000000548

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10345i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003107

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10360i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003108

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10592i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003109

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10679iA

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003110

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10360i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003111

• Chromosomally integrated HHV6 data of parent-infant pairs

  Raw data used in the analysis of chromosomally integrated HHV6 genomes in parent-infant pairs, generated by means of full viral genome sequencing by SureSelect target enrichment, in the context of a larger study investigating the relationship between HHV6 and adverse pregnancy outcome.

  Dataset EGAD00001004592

• Single cell mRNA sequencing of primary GBM - SF 10282

  We collected fresh tissue from an untreated GBM (SF10282) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001002270

• Single cell mRNA sequencing of primary GBM - SF 10360

  We collected fresh tissue from an untreated GBM (SF10360) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001002272

• Single cell mRNA sequencing of primary GBM - SF 10345

  We collected fresh tissue from an untreated GBM (SF10345) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001002271

• Tumor evolutionary trajectories during the acquisition of invasiveness in early stage lung adenocarcinoma

  Genomic analysis between pre-invasive and invasive components of malignant pulmonary nodule (MPN) facilitates the description of lung adenocarcinoma (LUAD) evolutionary patterns. We conduct an analysis of gene-panel sequencing on 53 T1 stage LUAD cases, which extend the understanding of evolutionary trajectories during invasiveness acquisition in early LUAD.

  Dataset EGAD00001006457

• Tumor mutational burden (TMB) calculated on bladder tumor pre-treatment DNA sequencing data

  Data from NABUCCO cohort 1 (NCT03387761). This dataset includes Tumor mutational burden (TMB) calculated on bladder tumor pre-treatment DNA sequencing data (n=24). Details about the Tumor Mutational Burden calculation can be found on the Methods section from the Nature Medicine paper (https://doi.org/10.1038/s41591-020-1085-z)

  Dataset EGAD00001006851

• LBC1921 fastq files

  297 members of the LBC1921 were sequenced using the Illumina HiSeq X platform. This dataset contains the fastq files.

  Dataset EGAD00001008775

• Exome sequencing in a consanguineous family with hypoaldosteronism identtifying LGR4 mutations

  The dataset contains whole exome sequencing of a family revealing a homozygous splice variant LGR4 gene rresponsible of salt wasting and adrenal zonation alteration. The members sequences were the proband with hypoaldosteronism , her parents and her two healthy brother in a consanguineous family.

  Dataset EGAD00001009761

• 340 human whole genome sequences from Angola and Mozambique

  CRAM files of 340 human genomes from Angola and Mozambique. Paired-end reads were generated in an Illumina-X Ten and were mapped against the human reference genome build hg19/GRCh37. More details about the sequencing and the samples in Tallman et al. 2023. Nature Communications.

  Dataset EGAD00001011992

• Brazilian GWAS Axiom850K Cancer Study

  Genome-wide genotyping data generated using the Affymetrix Axiom 850K PMDA Array from 2,844 Brazilian individuals enrolled in a cancer-focused biorepository. The dataset includes colorectal, breast, and cervical cancer cases as well as cancer-free controls. The data support genome-wide association studies (GWAS), replication analyses, and polygenic risk score evaluation in an admixed Brazilian population.

  Dataset EGAD00010002841

• Genetics of Eating Disorders

  This genetic study examines Anorexia Nervosa, Bulimia Nervosa, and Binge Eating Disorder. We performed whole exome sequencing (WES) on 93 unrelated individuals with eating disorders (38 restricted-eating, 55 binge-eating) to identify novel damaging variants. Using an unbiased, data-driven approach, we prioritized candidate genes with an excessive burden of predicted damaging variants. We then empirically tested one top candidate pathway in a mouse model of binge-like eating. We identified an excess of novel damaging variants in 186 genes in the restricted-eating group and 245 genes in the binge-eating group. The list of genes significantly enriched (OR = 4.6, p

  Study phs001414

• Disease recurrence after pathologic response (Recurrence DNAseq)

  In this study we aim to gain insight into the mechanisms of immune evasion after initial pathologic response to neoadjuvant immune checkpoint inhibition in macroscopic stage III melanoma by pooling data of the neoadjuvant OpACIN, OpACIN-neo and PRADO trials(EGAD00001012116, EGAS00001004832, EGAD00001006730, EGAS50000000268). Therefore we analyzed in-depth paired baseline(n=10) and recurrent tumor samples of the lymph nodes(n=10) and brain metastasis (n=2) through Whole Exome Sequencing (WES) analyses. Additionally we incorporated transcriptome sequencing data from 22 patients (21 paired-end samples and one single end sample)

  Study EGAS50000000488

• 463 newly diagnosed patients with Multiple Myeloma underwent whole exome sequencing of tumour and peripheral blood DNA.

  463 newly diagnosed patients from the UK Myeloma XI clinical trial (NCT01554852) underwent whole exome sequencing plus targeted capture of the IGH/K/L and MYC loci. 200 ng of DNA were processed using NEBNext DNA library prepartion kit and hybridised to the SureSelect Human All Exon V5 Plus. Four samples were pooled and run on one lane of a HiSeq 2000 using 76-bp paired end reads. DNA from CD138+ selected bone marrow cells (myeloma tumour) as well as peripheral white blood cells were analysed and somatic mutations detected.

  Study EGAS00001001147

• CEHM

  Study of the genetic and epigenetic clonal evolution of blood cancers.

  Study EGAS00001002366

• Immune deconvolution output

  Results of comprehensive immune deconvolution analysis through the TIMER2 web portal with algorithms specified in the publication.

  Dataset EGAD00001008789

• Whole genomes from Sahel

  The dataset includes 43 high coverge (30x) whole genome samples mostly from the Sahelian belt.

  Dataset EGAD00001011812

• Single-cell RNA-sequencing for peripheral blood mononuclear cells and plasma proteomics data from COVID-19 patients and healthy controls of Japanese

  We performed single-cell RNA-sequencing of peripheral blood mononuclear cells and measured plasma protein expression from COVID-19 patients and healthy controls.

  Study JGAS000783

• Targeted capture sequencing from High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Targeted capture sequencing for 366 newly added samples in High-grade B-cell lymphoma, not otherwise specified: an LLMPP study and 29 samples from a previously uploaded dataset.

  Dataset EGAD50000001364

• Whole genome sequencing from High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Whole genome sequencing for 10 newly added samples in High-grade B-cell lymphoma, not otherwise specified: an LLMPP study, and 6 samples from a previously uploaded dataset.

  Dataset EGAD50000001366

• BIOMIROX

  This dataset regroups RNAseq of paired primary colorectal cancers and liver metastases extracted from 113 patients In Paris and Besançon University Hospitals. 216 FASTQ files from single-end 3' PolyA (QuantSeq 3′mRNA-Seq Kit FWD for Illumina (Lexogen)) RNAseq samples were generated On NOVASEQ 6000 (ILLUMINA).

  Dataset EGAD50000000443

• IMpower133 (GO30081) clinical data and biomarker data

  Relevant clinical data for IMpower133 (GO30081) including treatment arm, overall survival, progression-free survival, best overall response, PD-L1 IHC, molecular subtype, and baseline clinical features.

  Dataset EGAD50000000195

• Exome Sequencing for brazilian patients with Idiopathic Collapsing Glomerulopathy

  This dataset contains 2 BAM files sequenced with Illumina NextSeq 500 e NovaSeq 600 and 20 files with variant calling sequenced with Illumina NextSeq 500 e NovaSeq 600.

  Dataset EGAD50000000091

• T and NK cell PBMC metadata

  Cell annotation for single T and NK cells of PBMC collected from 113 patients, including UMAP coordinates and annotation.

  Dataset EGAD50000000140

• Whole genome sequencing data to study therapeutic targeting of ependymoma

  This dataset contains whole genome sequencing data from 24 patients. For each patient a tumour and control sample has been sequenced on a Illumina HiSeq2000 instrument in paired-end mode. Up to three lanes per sample have been sequenced resulting in 112 Fastq files.

  Dataset EGAD00001003940

• Single cell characterization of arrested B-lymphoid differentiation and leukemic cell states in ETV6-RUNX1-positive pediatric leukemia

  Leukemic bone marrow in primary ETV6-RUNX1 positive acute lymphoblastic leukemia samples (Six diagnostic and two 15 days after treatment) using Chromium 3' single cell RNA-seq. Samples sequenced on 1-3 lanes and raw fastq files provided for each sample.

  Dataset EGAD00001006074

• Sequencing data for oesophageal and related samples - Katz-Summercorn, Jammula et al (RNA)

  Data supporting: “Multi-omic cross-sectional cohort study of pre-malignant Barrett’s esophagus reveals structural variation and retrotransposon activity occur early in cancer evolution.” Katz-Summercorn, Jammula et al. RNAseq (BAM files)

  Dataset EGAD00001006353

• CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function

  Single cell sequencing analysis for Dengue patients using Smart-seq2 and 10X platforms

  Dataset EGAD00001007656

• Novel method for efficient establishment, expansion and drug response profiling of high-grade serous ovarian cancer organoids

  HGSOC patient-derived organoids and their tissue of origin

  Dataset EGAD00001008753

• Combined Metabolic Activators Reduces Liver Fat in Nonalcoholic Fatty Liver Disease Patients

  Metagenomics data for "Combined Metabolic Activators Reduces Liver Fat in Nonalcoholic Fatty Liver Disease Patients". Samples were sequenced on NovaSeq6000(NovaSeq Control Software 1.7.0/RTA v3.4.4) with a 151nt (Read1)-10nt(Index1)-10nt(Index2)-151nt(Read2) setup using ‘NovaSeqXp’ workflow in ‘S4’ mode flow cell.

  Dataset EGAD00001008142

• S:CORT Stratification in COloRecTal cancer

  Colorectal cancer samples will be submitted for Illumina sequencing using a custom capture of 116 genes implicated in colorectal tumourigenesis. Driver mutations will be detected and ultimately correlated with phenotypic data.

  Dataset EGAD00001009760

• ChIP-seq ERa and H3K27ac in endometrial healthy and tumor tissues

  ChIP-seq has been perfomed on 4 healthy and 5 tumor fresh-frozen endometrial tissues from post-menopausal patients. Immunoprecipitation has been performed for H3K27ac and ERa. Raw single-end fastq data have been aligned using bwa-mem using Hg19 genome assebly as reference. Aligment bam files are provided.

  Dataset EGAD00001010896

• Infant_Spindle_Tumour_Study

  We aim to describe the transcriptomic landscape of infant spindle cell tumours.

  Study EGAS00001002935

• Methylome profiling of epithelioid sarcoma

  Explore the methylome landscape of epithelioid sarcoma using array data.

  Study EGAS00001007257

• Settlement of Polynesia

  Genotypes used to reconstruct the settlement timings and paths of Polynesia.

  Study EGAS00001005362

• HCA_Muscle_Adult_Wellcome_RNA_Managed_Access

  Transcriptomic analysis of skeletal muscle, to understand the mechanisms of muscle ageing.

  Study EGAS00001007495

• The transcriptomic response of skeletal muscle in life-long high-level trained and untrained men and women after acute exercise

  To investigate the influence of lifelong exercise training on the response of skeletal muscle to a bout of acute exercise we generated global transcriptomic data from long-term endurance (8 men, 8 women) and strength (8 men, 8 women) trained individuals and healthy age-matched untrained controls (8 men, 8 women). Skeletal muscle biopsies were taken from M. vastus lateralis before, directly after, and after 1h and 3hrs following acute exercise. All subjects completed one bout of acute endurance exercise and one bout of acute resistance exercise, separated by 4-8 weeks. All 384 samples were multiplexed in 4 lanes and sequenced (2x250bp paired end) on the Illumina NovaSeq 6000.

  Study EGAS00001006139

• Genomics from LCCC1525: A Priming Dose of Cyclophosphamide Prior to Pembrolizumab to Treat mTNBC

  This phase II, single-arm, multicenter study will evaluate pembrolizumab therapy, 200 mg IV, given every 3 weeks (Q3W), following a single priming dose of cyclophosphamide, 300 mg/m2 IV, in patients with advanced triple-negative breast cancer (TNBC) who have received at least one prior line of therapy. Data uploaded consists of FASTQ sequencing data from tumor RNASeq (pre-pembrolizumab), tumor and normal tissue WES, and sequencing for targeted T and B cell chains (TRB, IGK, IGL, IGH) from peripheral blood at various timepoints: pre-, post-, and during pembrolizumab therapy.

  Study phs002659

• Epigenomics of Prostate Cancer from Cell Free Plasma

  We sought to perform epigenomic characterization of prostate cancers by profiling circulating nucleosomes isolated from patient plasma using cell free chromatin immunoprecipitation followed by sequencing (cfChIP-seq). Our major findings include identification of prostate-cancer specific regulatory elements using a novel statistical method accounting for variable tumor DNA fraction in plasma, inferring transcription factor activity based on binding motif enrichment within regulatory elements, and epigenetically phenotyping patients based on clinical and genomic features. Data available in dbGaP will include cfChIP-seq and targeted sequencing from approximately 50 patients with a known diagnosis of cancer and healthy patient controls.

  Study phs003482

• Sequencing data for oesophageal and related samples - Xiaodun Li et al (WGS, RNA)

  Data supporting: "Esophageal adenocarcinoma organoid cultures recapitulate human disease heterogeneity and provide a model for clonality studies and precision therapeutics." Li et al. WGS (BAM files) RNAseq (BAM files) Tumours, organoids, normals

  Dataset EGAD00001004007

• Raw DNA and RNA data from breast cancer organoids, control samples and biopsies

  Whole genome sequencing data for primary tumors, matching control material from blood and their corresponding organoid. Whole transcriptome data for organoids.

  Dataset EGAD00001003751

• A108735A

  Whole genome sequencing for single cells for library A108735A 714 cells; filetype=bam

  Dataset EGAD00001007593

• WGS data for manuscript titled: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

  WGS data for manuscript titled: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

  Dataset EGAD00001008646

• 10x Genomics Single Cell Gene Expression for SA1188

  10x Genomics Single Cell Gene Expression for Telomerase immortalized breast epithelium cell line 184-hTert L9 116.66

  Dataset EGAD00001009114

• 10x Genomics Single Cell Gene Expression for SA604X7XB02089

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA604 passage 7

  Dataset EGAD00001009119