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• Meniere Disease Genomic Data Access Committee

  This Data Access Committee is responsible for reviewing and managing data access requests related to genomic variant files from whole exome sequencing of patients diagnosed with Meniere disease. This includes data from both familial and sporadic forms of the disease.

  Dac EGAC50000000708

• Transcriptome Analysis of Treg and Tfh cells

  Treg and Tfh cells (8 Samples)from the same donors was subject to RNA-seq (TruSeq Stranded Total RNA) processing. Single end fastq-files are supplied.

  Dataset EGAD00001007662

• Comprehensive genetic analysis of chronic active Epstein-Barr virus infection

  Comprehensive genetic analyses including whole-exome sequencing, targeted sequencing, and whole-genome sequencing were performed to reveal the molecular pathogenesis of chronic active Epstein-Barr virus infection.

  Dataset EGAD00001004299

• BRIDGE Bleeding and Platelet Disorders

  Whole exome sequencing BAM files for samples from the BRIDGE Consortium with pathogenic or likely pathogenic variants on genes linked to bleeding or platelet disorders.

  Dataset EGAD00001001333

• ICGC Benchmark 1 (CLL)

  Raw fastq files from WGS sequencing of CLL and matching blood normal for the ICGC Techval Benchmark1 study. Sequence data was provided to multiple centers for independent analysis and comparison.

  Dataset EGAD00001001858

• Targeted Sequencing of Tumor-Normal pairs from advanced Melanoma

  Aligned BAM files from NextSeq500 tageted panel sequencing of 84 samples from matched tumour-normal pairs of 42 melanoma patients. The dataset consists of 30 non-responders and 12 responders to ICB.

  Dataset EGAD00001005778

• Clinical phenotype data

  Clinical data corresponding to the patients with ovarian cancer studied using scRNA-seq and bulk RNA-seq. Variables include molecular subtype, predicted immune phenotype, reviewing pathologist comment, final immune phenotype, histology characterization, and tumor stage.

  Dataset EGAD00001006973

• EGAD00010000516

  Samples from the Pomak Villages in Greece, Pomak isolate

  Dataset EGAD00010000516

• Baka_saliva_450K

  Epigenome of 36 rainforest hunther-gathering Baka of Cameroon by Illumina HumanMethylation450 array, used in the EGAS00001002226 study

  Dataset EGAD00010001251

• SEAsia.Oceania.Australia

  the tar archive contains unflitered genotype data from Reich et al AJHG 2011 study in plink format

  Dataset EGAD00010002302

• SolomonIslands.Dataset

  The tar archive contains unflitered genotype data from Pugach et al 2018 in plink format

  Dataset EGAD00010002306

• The BAF chromatin remodeling complex is a novel target of spliceosome dysregulation in SF3B1-mutated chronic lymphocytic leukemia

  Study EGAS00001006771

• Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer

  Study EGAS00001007291

• Small Intestine Adenocarcinoma Subtyping Data Access Committee

  DAC created for the Molecular classification of small intestinal adenocarcinomas Study in Amsterdam UMC.

  Dac EGAC50000000663

• Swedish schizophrenia patients

  The genomic sequence of brain expressed miRNA genes was sequenced in Swedish schizophrenia patients

  Dataset EGAD00001001849

• Belgian epilepsy patients

  The genomic sequence of brain expressed miRNA genes was sequenced in Belgian epilepsy patients.

  Dataset EGAD00001001851

• DAC for "Cancer-associated fibroblasts promote drug resistance in ALK-driven lung adenocarcinoma cells by upregulating lipid biosynthesis"

  DAC for the data of "Cancer-associated fibroblasts promote drug resistance in ALK-driven lung adenocarcinoma cells by upregulating lipid biosynthesis" with: • Holger Sültmann • h.sueltmann@dkfz.de • German Cancer Research Center (DKFZ) • Ann-Kathrin Daum • a.daum@dkfz.de • German Cancer Research Center (DKFZ)

  Dac EGAC50000000076

• Tumor Profiler Project - AML scRNA data

  The dataset contains single-cell RNA seq data from 23 patients with Acute Myeloid Leukemia (AML). Samples were collected from bone marrow or blood. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format.

  Dataset EGAD50000000823

• Detection of Cancer Mutations by Urine Liquid Biopsy in 12 Bladder Cancer Patients

  Set of FASTQ sequences generated from Urine Liquid Biopsy in 12 Bladder Cancer Patients using the IDT PanCancer Panel, Illumina Nextera Flex for Enrichment libraries (aka DNA Prep libraries) and Illumina NovaSeq 2x150bp sequencing.

  Dataset EGAD00001008429

• FACS-based purification and paired-end RNA sequencing

  We performed a prospective investigation in Sézary syndrome by the application of a standardized multiparameter flow cytometry, FACS-cell sorting, and RNA-sequencing for an in-depth immunophenotypic and transcriptional profiling of Sézary cells.

  Dataset EGAD00001007687

• ASPSCR1-TFE3 gene fusion panel deep amplicon sequencing data

  Dataset contains compressed, paired-end Fastq files of deep amplicon sequencing data from a custom ASPSCR1-TFE3 gene fusion panel for three alveolar soft part sarcoma cases described in "Development and first-in-human CAR T therapy targeting the pathognomonic MiT-fusion driven protein GPNMB".

  Dataset EGAD50000002438

• MutWP5: CRUK Mutographs of Cancer: Cancer Mastectomy (WG)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 40 women who underwent mastecomies due to breast cancer. LCM and sequencing will be conducted on both normal, unaffected breast, and, where possible, tumour tissue. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue, and compare findings between the normal and associated cancer tissues. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this poriton of the study will be compared to women who had cosmetic breast reduction surgeries and those who are BRCA carriers. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010114

• AML Proteogenomic Landscape Whole-transcriptome RNA-Sequencing

  Whole transcriptome RNA-sequencing of purified bone marrow blasts of 136 de novo, treatment naive AML patients. For further details, we refer to the manuscript "The Proteogenomic Landscape of AML" by Jayavelu, Wolf, Buettner et al. mRNA extraction and whole transcriptome sequencing For transcriptome analysis the TruSeq Total Stranded RNA kit was used, starting with 250ng of total RNA, to generate RNA libraries following the manufacturer’s recommendations (Illumina, San Diego, CA, USA). 100bp paired-end reads were sequenced on the NovaSeq 6000 (Illumina) with a median of 57 mio. reads per sample. RNA Data Analysis Data quality control was performed with FastQC v0.11.9. Reads were aligned to the human reference genome (Ensembl GRCh38 release 82) using STAR v2.6.1. Gene count tables were generated while mapping, using Gencode v31 annotations. All downstream analyses were carried out using R v4.0 and BioConductor v3.12 (Huber et al., 2015; R Core Team, 2020). Size-factor based normalization was performed using DESeq2 v1.28.1(Love et al., 2014).

  Dataset EGAD00001008484

• Whole-genome sequencing of normal Singaporean volunteers

  Sleep is associated with various health outcomes. Despite their growing adoption, the potential for consumer wearables to contribute sleep metrics to sleep-related biomedical research remains largely uncharacterized. Here we analyzed sleep tracking data, along with questionnaire responses and multi-modal phenotypic data generated from 482 normal volunteers. First, we compared wearable-derived and self-reported sleep metrics, particularly total sleep time (TST) and sleep efficiency (SE). We then identified demographic, socioeconomic and lifestyle factors associated with wearable-derived TST. Among others, male gender (β = -15.539, 95% confidence interval [CI] = -26.245 - -4.832, p = 0.005), older age (β = -0.493, CI = -0.941 - -0.044, p = 0.032) and manual labor (β = -26.856, CI = -49.715 - -3.997, p = 0.022) were associated with reduced TST, whereas alcohol consumption (β = 19.247, CI = 8.008 - 30.486, p = 8.54x10-04) was associated with increased TST. Multi-modal phenotypic data analysis showed that wearable-derived TST and SE were associated with various cardiovascular disease risk markers such as body mass index (β = -0.006, CI = -0.00 - -0.000, p = 0.040) and waist circumference (β = 0.001, CI = -0.015-0.017, p = 0.893), whereas self-reported measures were not. We then showed that insufficient sleep was associated with premature telomere attrition, using telomere length estimated using whole-genome sequencing (β = 1.275, CI = 0.187 - 2.363, p = 0.023) and quantitative PCR (β = 0.001, CI = 8.318x10-05 - 0.001, p = 0.028). Our study highlights the potential for sleep metrics from consumer wearables to provide novel insights into data generated from population cohort studies.

  Study EGAS00001004007

• African American Breast Cancer GWAS

  The GWAS includes African American participants from 9 epidemiological studies of breast cancer, comprising a total of 3,153 cases and 2,831 controls (cases/controls: The Multiethnic Cohort Study (MEC), 734/1,003; The Los Angeles component of The Women's Contraceptive and Reproductive Experiences (CARE) Study, 380/224; The Women's Circle of Health Study (WCHS), 272/240; The San Francisco Bay Area Breast Cancer Study (SFBCS), 172/231; The Northern California Breast Cancer Family Registry (NC-BCFR), 440/53;The Carolina Breast Cancer Study (CBCS), 656/608; The Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) Cohort, 64/133; The Nashville Breast Health Study (NBHS), 310/186; and, The Wake Forest University Breast Cancer Study (WFBC), 125/153). Quality control of the GWAS data and additional details can be found in Chen et al. Hum Genet. 2013 (PMID: 22923054)

  Study phs000851

• Single-cell RNA-sequencing of peritoneal fluid from patients with achalasia

  The data published here contains single-cell RNA-sequencing (scRNAseq) data as obtained using the 3' scRNAseq using Chromium Single Cell 3’ Reagent from 10X Genomics on peritoneal fluid (PF) from patients with achalasia. Sequencing was performed in a paired-ended fashion on the NovaSeq6000.

  Dataset EGAD50000000251

• Targeted DNA sequence

  Targeted DNA sequencing files that were used in our study. The cohort was composed of 36 cases of tumor-only targeted DNA sequencing data. All files are UMI processed. The panel is designed with Agilent Sure Select and the sequence was performed using DNBSEQ sequencer.

  Dataset EGAD50000000972

• Understanding the multicellular dynamics of clear cell renal cell carcinoma - spatial transcriptomics

  The dataset comprises of transcriptomes of tissue sections derived from either the tumour normal interface or tumour core from clear cell renal cell carcinomas. 16 sections are sampled in total using 10x Genomics' Visium technology.

  Dataset EGAD00001008781

• Exome sequencing of tumor DNA samples from patients with Waldenstrom macroglobulinemia

  DNA extracted from sorted CD19+ tumor cells (18 samples - 16 patients) was used for exome capture with the SureSelect All Exon Kit following the standard protocols. Paired-end sequencing (2 x 100 bp) was performed using HiSeq2000 sequencing instruments. The files are in FASTQ format.

  Dataset EGAD00001005322

• RNAseq data for 6 samples from the DEV cell line

  - Six samples from the DEV cell line: 2 controls, 2 transduced with IL4R WT and 2 transduced with IL4R mutant (I242N) - This DEV cell line is not commercially available and was acquired from a colleague in the Netherlands

  Dataset EGAD00001003908

• The South Asia Rheumatic Heart Disease Genetics Network Data

  This dataset comprises over 850 individuals recruited in Uttar Pradesh, India, including cases of rheumatic heart disease based on echocardiographic diagnosis and controls recruited on the basis of normal echocardiograms. For this analysis all available samples were genotyped using the Illumina HumanCore-24 BeadChip platform.

  Dataset EGAD00001004882

• The acute effects of morning bright light on the human white adipose tissue transcriptome: exploratory post hoc analysis

  The circadian rhythm of the central brain clock in the suprachiasmatic nucleus (SCN) is synchronized by light. White adipose tissue (WAT) is one of the metabolic endocrine organs containing a molecular clock, and it is synchronized by the SCN; excess WAT is a risk factor for health issues including type 2 diabetes mellitus (DM2). We hypothesized that bright-light exposure would affect the human WAT transcriptome. Therefore, we analyzed WAT biopsies from two previously performed randomized cross-over trials (trial 1: lean healthy men, and trial 2: men with obesity and DM2). RNA sequencing results showed major group differences between men with obesity and DM2 and lean healthy men, as well as a differential effect of bright light exposure.

  Study EGAS50000001206

• H3Africa Consortium WGS VCF

  Joint called VCF for whole genome sequence data from 410 samples described in the paper: PMID:33116287. It includes 314 high coverage (average 30X) samples sequenced on the Illumina X-Ten, also available as individual datasets under the H3Africa Chip study (EGAS00001002976) and 112 medium coverage (average 10X) samples from the TrypanGen study (EGAS00001002602) sequenced on Illumina HiSeq 2500. Supplementary table 3 of the paper describes the geographic breakdown of the samples. 16 samples from the Southern African Human Genome project have been removed from this VCF.

  Dataset EGAD00001008577

• RNASeq from PC12 cell lines (derived from PPGL) cultivated under 21% (normoxia) and 1% (hypoxia) oxygen conditions.

  RNASeq fastq files from PC12 cells (derived from rat PPGL) were cultivated in normoxia conditions (37˚C, 5% CO2 and 21% O2 balanced with N2) or in hypoxia conditions in a hypoxic incubator (37˚C, 5% CO2 and 1% O2 balanced with N2), for short time (12h, 24h, and 48h) or prolonged time (36 days). Samples at each timepoint were cultured in triplicate (total 24 paired end fastq files). Sequencing was performed with the Illumina NovaSeq6000.

  Dataset EGAD50000001200

• Gene Expression Signatures in CATHGEN

  Case control cohort: The details have been previously published: American Heart Journal. 2010;160:371-379 e372. Briefly, a nested case:control cohort of CATHGEN participants who had experienced death or MI (n = 250) after their index catheterization and age-, sex-, and race-matched controls (n = 250) who were free of death/MI > 2 years after cardiac catheterization was identified as part of the MURDOCK Horizon 1 Cardiovascular Disease Study.21 Sufficient RNA for microarray analysis was available in 447 members of this cohort. Observational cohort: 224 sequential CATHGEN samples were selected for whole blood RNA analysis, of which, 191 had sufficient RNA for microarray analysis.

  Study phs000551

• Data access committee (DAC) in the Graduate School of Medical Science and Engineering (GSMSE) at Korea Advanced Institute of Science and Technology (KAIST)

  Dac EGAC00001001643

• Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths

  Study EGAS00001007402

• Exome sequencing Parkinson's disease patients

  In this project we will sequence the exomes of 250 patients with Parkinson's disease

  Dataset EGAD00001000405

• A new beta-globin mutation responsible of a beta-thalassemia (HbVar database ID 2928) was observed in 8 unrelated French families. The mutation carriers originated from Nord-Pas-de-Calais, a Northern French region where the chief town is Lille.5 unrelated mutation carriers were genotyped for a set of 12 microsatellites from chromosome 11, around the beta-globin gene. Among the 5 mutation carriers, 4 were genotyped for 97 European Ancestry Informative SNPs (EAIMs). 32 controls from Nord-Pas-de-Calais were genotyped for the microsatellites and SNPs.

  Dac EGAC00001000245

• BCR sequences and metadata for cultured single B-cell clones from blood

  The dataset contains VDJ sequences in FASTA format, the same sequences run through IMGT/HighV-QUEST (tsv file) and accompanying metadata (csv file) including antigen specificity (transglutaminase 2-specific or other). The data was generated from cultured single B-cell clones from the peripheral blood of four untreated celiac disease patients. Sequences were obtained by a nested RT-PCR approach targeting the immunoglobulin chains followed by Sanger sequencing.

  Dataset EGAD50000000343

• GenomeDenmark Phase 2 - whole genome variants called using BayesTyper

  Variants and genotypes called in 50 danish parent-offspring trios from 80x Illumina sequencing data using BayesTyper. Data was produced using different insert size libraries of the sizes 180, 500, 800, 2000, 5000, 10000 and 20000 bp. The sample IDs for the fathers and mothers are TrioID-01 and TrioID-02, respectively, and the IDs for the children are TrioID-0x, where x is a number between 3 and 7

  Dataset EGAD00001003188

• The somatic mutation landscape of normal gastric epithelium - TGS

  The landscapes of somatic mutation in normal cells inform on the processes of mutation and selection operative throughout life, permitting insight into embryogenesis, normal ageing and the earliest stages of cancer development. Here, by whole-genome sequencing and targeted panel sequencing of microdissections from 30 individuals, including 18 with gastric cancer, we elucidate the developmental trajectories of normal and malignant gastric epithelium.

  Dataset EGAD00001015352

• The somatic mutation landscape of normal gastric epithelium - WGS

  The landscapes of somatic mutation in normal cells inform on the processes of mutation and selection operative throughout life, permitting insight into embryogenesis, normal ageing and the earliest stages of cancer development. Here, by whole-genome sequencing and targeted panel sequencing of microdissections from 30 individuals, including 18 with gastric cancer, we elucidate the developmental trajectories of normal and malignant gastric epithelium.

  Dataset EGAD00001015351

• BLUEPRINT Hematopoietic Stem/Progenitor Cell Methylomes

  An optimized whole genome bisulfite sequencing protocol (µWGBS, Farlik et al. 2015 Cell Reports) was used to establish DNA methylation profiles of FACS-purified stem and progenitor cells types of the human blood lineage. Most cell types were sorted from the peripheral blood of three donors with eight pools of ten cells, two pools of 50 cells, and one pool of 1000 cells. HSCs and MPPs were also sorted from fetal liver (HSCs only), cord blood, and bone marrow. Single-cell methylomes using the scWGBS protocol (Farlik et al. 2015 Cell Reports) were established for six cell types (HSC, MPP, CMP, GMP, CLP, MLP0). Gene expression profiling using the Smart-seq2 protocol (Picelli et al. 2013 Nature Methods) was done for nine stem/progenitor cell types (HSC, MPP, CMP, GMP, CLP, MLP0, MLP1, MLP2, MLP3).

  Study EGAS00001002070

• EGAD00010000624

  A new beta-globin mutation responsible of a beta-thalassemia (HbVar database ID 2928) was observed in 8 unrelated French families. The mutation carriers originated from Nord-Pas-de-Calais, a Northern French region where the chief town is Lille. 5 unrelated mutation carriers were genotyped for a set of 12 microsatellites from chromosome 11, around the beta-globin gene. Among the 5 mutation carriers, 4 were genotyped for 97 European Ancestry Informative SNPs (EAIMs).

  Dataset EGAD00010000624

• EGAD00010000626

  A new beta-globin mutation responsible of a beta-thalassemia (HbVar database ID 2928) was observed in 8 unrelated French families. The mutation carriers originated from Nord-Pas-de-Calais, a Northern French region where the chief town is Lille. 5 unrelated mutation carriers were genotyped for a set of 12 microsatellites from chromosome 11, around the beta-globin gene. Among the 5 mutation carriers, 4 were genotyped for 97 European Ancestry Informative SNPs (EAIMs).

  Dataset EGAD00010000626

• Targeted amplicon sequencing on 218 samples from Stage 1 epithelial ovarian cancer biopises

  BAM files (aligned against the hg38 genome) from a targeted amplicon sequencing (139 genes) experiment (median depth 1000X) on 218 samples from Stage 1 epithelial ovarian cancer biopises. Samples labeled "bis" or "tris" with the same ID are relapses; "left" or "right" samples indicate, in the case of bilateral tumor, from which ovary the sample was taken.

  Dataset EGAD00001006873

• Evaluation of triple negative breast cancer with heterogeneous immune infiltration

  This dataset contains the raw RNA-seq data (FASTQ files) of the samples used in the study title: "Evaluation of triple negative breast cancer with heterogeneous immune infiltration". The dataset is composed of 3 patients with 6 samples per patient (3 with high TILs and 3 with low TILs).

  Dataset EGAD00001010280

• Ex vivo modeling of precision immuno-oncology responses in lung cancer

  Single-cell RNA-sequencing (scRNA-seq) data from paired lung cancer organoids and immune cells. The experiment was performed using the Single Cell 5' solution of 10X Genomics. The dataset includes 15 samples from 4 multiplexed experiments. The multiplexing was performed using the Feature Barcoding technology of 10X Genomics.

  Study EGAS50000000593

• 4 - transcriptome (.bam) files, 2 -called somatic mutations (.vcf) files and 2 coverage (.csv) files

  The dataset contains 4 .bam whole transcriptome files that were generated from 2 tumor samples (one .bam file per sample was created using exome-capture (hybrid capture) and the other .bam file was created using ribo-repletion (inverse mRNA selection) library preparation technology). The dataset also contains 2 somatic mutations (.vcf - sample) files (one per sample) which serve as input for Vardetector package (vardetector/vardetector at main · julijselb/vardetector) to produce somatic coverage over those mutations from the .bam file. Therefore, the dataset also contains 4- .csv files (number of reads per somatic mutation that contain the somatic mutation variant and the ones that do not contain the somatic mutation variant) that serve as outputs of the Vardetector package.

  Dataset EGAD50000002055