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• BLUEPRINT ChIP-seq data for cells in the haematopoietic lineages, from adult and cord blood samples.

  ChIP-seq data for cells in the haematopoietic lineages, from adult and cord blood samples.

  Study EGAS00001000326

• Rare Diseases Clinical Research Network (RDCRN) Vasculitis Clinical Research Consortium (VCRC) Longitudinal Protocol for Polyarteritis Nodosa

  The development and validation of accurate biological markers and predictors of disease activity and outcome in Polyarteritis Nodosa (PAN), a form a idiopathic vasculitis, would have a major positive impact on the clinical care of patients with this rare disease, be an important advance in the design of clinical trials and feasibility of new drug development, and provide important insight into the pathogenesis of this condition. Current measures of disease activity, including erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP), while helpful in selected settings, are mostly considered highly flawed and markers whose poor correlation with disease flares makes them inadequate to help guide therapy. Similarly, ESR and CRP are clearly unhelpful as diagnostic tests for vasculitis. The current state of clinical investigation for vasculitis relies heavily upon determination of disease status solely by clinical presentation and investigator opinion. Thus, discovery and validation of more precise markers that quantifiably measure activity, predict disease course, and correlate with an important biological process, would be of great importance. Knowledge to be gained from this study could potentially be highly important. Discovery of effective biomarkers of vasculitis and assessment of long term disease course and complications by the collection of clinical and diagnostic imaging studies proposed could lead to better care and less toxic treatment regimens. Furthermore, insight into the pathophysiology of vasculitis could be gained and this might lead to better treatments and improved outcomes in terms of reduction of vascular and treatment related complications. Ideally, excellent biomarkers reflect a sophisticated understanding of the pathophysiology of a disease.

  Study phs000590

• Non-Coding Autoimmune Risk Variant Defines Role for ICOS in T Peripheral Helper Cell Development

  Our fine-mapping of 76 non-MHC loci associated with risk for rheumatoid arthritis (RA, 11,475 cases, 15,870 controls) has recently identified rs117701653, a non-coding single nucleotide polymorphism (SNP) in the CTLA4/CD28/ICOS locus, as the variant most likely to modulate RA risk within this region, with the minor allele C showing disease protection compared to the major allele A. We found that this SNP exhibits allele-specific protein binding and transcriptional modulation, further supporting its regulatory nature. Here, we aimed to determine whether the functional non-coding variant rs117701653 modulates the expression of genes within the CD28/CTLA4/ICOS locus. To address this question, we employed low-input RNA sequencing using the Illumina SmartSeq2 platform on resting total CD4+ T cells from the blood of 24 healthy subjects (8 AA, 8 AC, 8 CC) recruited based on genotype from the Mass General Brigham biobank. We performed a targeted cis-eQTL mapping analysis for protein coding genes with transcription start sites (TSS) within a 1MB window of SNP rs117701653. These genes included WDR12, NBEAL1, CYP20A1, ABI2, RAPH1, CD28, CTLA4, ICOS, and PARD3B. Surprisingly, allelic variation at rs117701653 correlated strongly with expression of ICOS. This suggests that individuals carrying the protective allele C at rs117701653 express lower levels of ICOS, implicating ICOS as a plausible target gene influenced by this protective allele. The raw sequence data from the 24 healthy individuals are available through dbGAP. Gene expression matrices have been deposited to GEO accession GSE235868.

  Study phs003448

• Dataset for Sarcoma RNA sequencing linked from study EGAS00001004813

  Sequencing data of 410 sarcoma tumor runs, which were uploaded to EGAS00001004813. The sequencing was always paired.

  Dataset EGAD00001010276

• RFMix

  This dataset contains the per-chromosome RFMix input and output files for the local ancestry inference of 59 Aboriginal Australian genomes as reported in Malaspinas et al., 2016. Local ancestry was inferred assuming four mixing ancestral populations represented by: Europeans (27 individuals), Asians (29 individuals), Papuans (13 individuals) and Native Australians (7 individuals from the WCD region).

  Dataset EGAD00010001575

• Hepatitis B virus integrations promote local and distant oncogenic driver alterations in hepatocarcinogenesis

  This study contain the WGS and WEX aligned bam files and RNA-seq fastq files for human liver tumors.

  Dataset EGAD00001006426

• SARS-CoV2 mRNA-vaccination-induced Immunological Memory in Human Non-Lymphoid and Lymphoid Tissues

  This dataset includes combined single-cell RNA-Seq and T cell receptor profiling data for SARS-CoV-2 spike protein-reactive CD4+ T cells and NK cells from blood, liver, lungs, and bone marrow of human donors.

  Dataset EGAD50000000062

• Age-dependent association of clonal hematopoiesis with COVID-19 mortality in patients over 60 years

  Targeted sequencing with the Myeloid Solutions™ Panel (MYS) of SOPHiA Genetics for COVID-19 patientds (n=241 deceased, n=239 survivors).

  Dataset EGAD50000000001

• scRNA-seq of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19 to assess dexamethasone response in the lungs

  Single-cell RNA-sequencing of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19 with or without Dexamethasone treatment and for responders and non-responders was performed using 10x Genomics technology.

  Dataset EGAD50000000292

• Clones derived from early passage tumoroids of colorectal cancer

  We obtained different clones from early passage CRC tumoroids to study mutational signatures specific for truncal or private somatic alterations. These whole genome sequences are part of a larger study on the heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer.

  Dataset EGAD50000000152

• Strand-seq data of six CK-AML patient samples and three matching PDXs

  We performed strand-specific single-cell sequencing of six primary leukemia samples from four CK-AML patients. We also performed strand-specific single-cell sequencing of three matching patient-derived xenografts (PDXs). The dataset contains BAM files for each cell.

  Dataset EGAD50000000634

• SMPaeds PanelSeq of tumour tissue

  Deep sequencing of a targeted panel of 92 paediatric cancer related genes or 233 pan-cancer related genes for both relapse/archival disgnostic tumour tissue and germline DNA from whole blood cell pellet. Tumour tissue was sequenced to approximately 400X coverage and germline DNA was sequences to aproximately 100X coverage.

  Dataset EGAD50000000783

• McQuillin_Global_London_SCZ_Bipolar_WES

  "McQuillin_Global_London_SCZ_Bipolar_WES. This research project was a collaboration between University College London, UK and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 1,623 Schizophrenia and Bipolar case/control samples from collaborators in UK. Genomic DNA from each sample was sequenced to a mean depth of 20x. For EGA Study ID: 1128"

  Dac EGAC50000000311

• Dataset for Multiple Myeloma WGS data, part 2

  This dataset contains 518 case and control WGS sequencing samples of patients with multiple myeloma. Sequencing was performed on Illumina NovaSeq 6000 and HiSeq X using TruSeq Nano DNA Kits. The sequencing was always paired.

  Dataset EGAD50000000681

• Dataset for Multiple Myeloma WGS samples

  This dataset contains 221 case and control WGS sequencing samples of patients with multiple myeloma. Sequencing was performed on Illumina NovaSeq 6000 and HiSeq X using TruSeq Nano DNA Kits. The sequencing was always paired.

  Dataset EGAD50000000682

• 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

• Shallow Whole Genome Sequencing (sWGS) of pancreatic ductal adenocarcinoma

  Associated with CNA differences between RNA-based subtypes of PDAC. Shallow Whole Genome Sequencing (sWGS) generated 47 .bam files from 37 patients. sWGS was used for Copy number aberrations (CNA) determination.

  Dataset EGAD50000001732

• cfDNA sWGS BAM — NSCLC stage I–III

  Plasma cfDNA sWGS for NSCLC patients (stage I–III), blood drawn pre-operatively, CHU Montpellier/LUNGDOC study. Libraries: DSP as recorded. Sequencing provider IntegraGen (2022–2024). Alignment to GRCh38 (hg38 canonical), BWA-MEM; BAMs sorted/indexed; only primary mapped reads retained (analysis pages list -F/MAPQ). Controlled access.

  Dataset EGAD50000001878

• Bulk RNAseq dataset for "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

  This dataset contains 84 paired fastq files of Bulk RNAseq collected from 14 patients with Extramedullary multiple myeloma, 14 patients with newly diagnosed multiple myeloma and 14 patients with Relapsed/refractory multiple myeloma

  Dataset EGAD50000000051

• 10X snMultiome (ATAC+GEX) sequencing of 5 human reactive tonsil samples

  10X snMultiome (ATAC+GEX) sequencing of 5 human reactive tonsil samples for the study of Non-canonical NF-κB signaling skews B cells away from germinal center to low-affinity effector fate.

  Dataset EGAD50000002366

• SNP array data for 140 individuals from 5 populations in Pakistan

  We have genotyped 140 individuals from 5 populations in Pakistan, using the OmniExpressExome-8 array, which includes approximately one million autosomal SNP markers.

  Study EGAS00001002965

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90560A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 585 samples; filetype=bam

  Dataset EGAD00001004733

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A95660A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1522 samples; filetype=bam

  Dataset EGAD00001004750

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A95632B

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 626 samples; filetype=bam

  Dataset EGAD00001004748

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A95670B

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 636 samples; filetype=bam

  Dataset EGAD00001004754