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• Mexican_Biobank_Genotypes

  Samples from the Mexican Biobank

  Dataset EGAD00010002361

• EGAD00010000518

  Samples from the Greek island of Crete, MANOLIS cohort

  Dataset EGAD00010000518

• Datasets 929/938

  Datasets Galaxy 929/938 describe the amplified single chromosome sequencing data.

  Dataset EGAD00001004457

• qDNAseq CLUC dataset

  qDNAseq shallow sequencing dataset of the cell line use case.

  Dataset EGAD00001002071

• Cell Line Dataset

  Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

  Dataset EGAD00001001349

• Capture Hi-C

  Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci.

  Dataset EGAD00001001243

• The UCSF Low Grade Glioma Genome Project #1

  Dataset EGAD00001000714

• Single-nuclei multiomic analysis of KOLF2.1J human induced pluripotent stem cells-derived differentiated dopaminergic neurons

  Datasets consists of 12 samples of nuclei from hIPSCs differentiated optimized protocols for generating dopaminergic neurons. 6 single nuclei (RNA-ATAC) samples of XMAS protocol with cells collected at days 0,11,16,28,42 and 56 after differentiation. 3 snRNA-seq samples from AMS protocol of cells collected at days 14,16 and 28 after differentiation and 3 snRNA-seq samples with AMS protocol until day 14 grafted and grafts processed after 5 months grafting.

  Dataset EGAD50000002054

• Leukemia WGS data

  Whole-genome sequencing data from 38 leukemia patients and 12 leukemia cell lines; Containing 100 fastq files; Two files for each sample.

  Dataset EGAD00001008659

• CITEseq data

  CITEseq data of CLL patients receiving VEN treatment for resistance study

  Dataset EGAD00001008366

• Sequencing data for oesophageal and related samples - OACs release 4 (RNA)

  Dataset EGAD00001004021

• Prostate WGS data (late onset)

  Whole genome sequencing for 12 late onset prostate cancer tumor/control pairs (ICGC)

  Dataset EGAD00001003290

• Prostate WGS data (early onset)

  Whole genome sequencing for 131 early onset prostate tumor/control pairs (ICGC)

  Dataset EGAD00001003256

• GCAT| WGS FASTQ V1

  This dataset include FASTQ files of 808 samples from GCAT cohort. Technology used HiSeq 4000, read length 150 bp, inner mate distance 300 bp. For each sample the paired -ends are generated in separated files. Each FASTQ is splitted in multiple LANEs and grouped by the Multiplex index.

  Dataset EGAD00001008201

• DAC monitoring the usage of ultra-low-coverage MinION nanopore sequencing results of NA12877 and NA12878 from NIGMS Human Genetic Cell Repository.

  Dac EGAC00001000876

• Azienda Ospedaliero-Universitaria di Parma Data Accessibility

  Regulation on the sharing and accessibility of data belonging to Azienda Ospedaliero-Universitaria di Parma

  Dac EGAC50000000239

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Cambridge, UK

  Study EGAS00001005854

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Dublin, Ireland.

  Study EGAS00001005844

• Whole Exome Sequencing of Bipolar cases and controls performed at the Broad Institute on a cohort from Cardiff, UK (Craddock)

  Study EGAS00001005845

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from London, UK

  Study EGAS00001005851

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Umea, Sweden.

  Study EGAS00001005842

• Integration of metabolomics, genomics and immune phenotypes reveals the causal roles of metabolites in disease

  Study EGAS00001005348

• PEVOsq WES data

  Raw paired FASTQ data of patients at baseline from the PEVOsq cohort

  Dataset EGAD50000001013

• preQC Genotypes

  preQC genotype data from the Affymetrix AxiomTM HGCoV2 1 array in plink ped/map format

  Dataset EGAD00010002437

• Gentoypes_SouthAfrica

  Individuals genotyped on the Illumina Omni2.5. Autosome and X chromosome.

  Dataset EGAD00010002467

• GLASS-NL DNA-Methylation

  DNA-methylation data of samples included in the GLASS-NL cohort

  Dataset EGAD00010002647

• EGA_PBC_phased

  A cohort of 2886 participants of the Japan PBC-GWAS Study

  Dataset EGAD00010001533

• Biomarker data

  Biomarker data including the time point of sample collection, tumor content and ERBB2 gene expression.

  Dataset EGAD00001009415

• BC WGS Dataset 4

  Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

  Dataset EGAD00001001353

• BC WGS Dataset 3

  Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

  Dataset EGAD00001001351

• Determining the quality and complexity of NGS data without a reference genome

  Dataset EGAD00001000759

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Cardiff, UK (Owen)

  Study EGAS00001005855

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Edinburgh, Scotland, UK.

  Study EGAS00001005843

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Cardiff, UK (O'Donovan)

  Study EGAS00001005852

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Landen, Stockholm, Sweden.

  Study EGAS00001005838

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Stockholm, Sweden (Pedersen)

  Study EGAS00001005856

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

  Study EGAS00001007291

• Kinomics data

  To ellucidate protein activity in mRCC, Kinomics data was generated as part of the EuroTarget study

  Dataset EGAD50000002293

• Study2OrangeFiber

  SOMAscan plasma proteome datasets generated from participants consuming the orange fiber snack prototype (study 2)

  Dataset EGAD00010002191

• Study1PeaFiber

  SOMAscan plasma proteome datasets generated from participants consuming the pea fiber snack prototype (study 1)

  Dataset EGAD00010002192

• SolomonIslands.Dataset

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

  Dataset EGAD00010002306

• SEAsia.Oceania.Australia

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

  Dataset EGAD00010002302

• Present-day genomics from the Eurasian steppe

  502 genotypes obtained from Illumina DNA-arrays. Available as plink formatted files

  Dataset EGAD00010001538

• Hessequa-descendants mitogenomes

  Complete sequence of the mitochondrial DNA of 87 Hessequa-descendant individuals

  Dataset EGAD00001007676

• Bacteria Lateral sclerosis

  The study aims to find bacteria in neural tissue from patients with amyotrophic lateral sclerosis

  Dataset EGAD00001004458

• Belgian epilepsy patients

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

  Dataset EGAD00001001851

• Swedish schizophrenia patients

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

  Dataset EGAD00001001849

• Structural variant analysis of homologous recombination-deficient genomes

  Homologous recombination (HR) deficiency causes DNA breaks and cytogenetic aberrations. Paradoxically, the types of DNA rearrangements specifically associated with HR-deficient cancers only minimally impact chromosomal structure. Addressing this, we combined a genome graph analysis of short-read whole genome sequencing (WGS) profiles across thousands of tumors with deep linked-read (LR) WGS of 46 BRCA1 or BRCA2 mutant breast cancers to discover a distinct class of HR deficiency-enriched rearrangements called reciprocal pairs. LR WGS showed that reciprocal pairs with identical rearrangement orientations gave rise to one of two distinct chromosomal outcomes, distinguishable only with long molecule data. While one (cis) outcome corresponded to the copy and pasting of a small segment to a distant site, a second (trans) outcome was a quasi-balanced translocation or multi-megabase inversion with substantial (10kb) duplications at each junction. The full spectrum of reciprocal pair outcomes could be explained by an HR-independent replication restart repair mechanism. LR WGS additionally identified single-strand annealing (SSA) as a BRCA2-deficiency specific repair pathway in human cancers. Replication restart- and SSA-associated SVs improved BRCA1- vs. BRCA2- deficiency classification and identified metastatic cancer cases with favorable chemotherapy responses. Our data reveal classes of BRCA1- and BRCA2-deficiency specific rearrangements as drivers of cytogenetic aberrations in HR deficient cells.

  Study EGAS00001007186

• 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

• DAC of The polarity and specificity of antiviral T lymphocyte responses determine susceptibility to SARS-CoV-2 infection in cancer patients and healthy individuals

  Dac EGAC00001002517