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• Normal sample for patient SA679

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA679

  Dataset EGAD00001009379

• WES files for Newman MAP3K8 melanoma

  WES files for Newman MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas"

  Dataset EGAD00001004566

• Thymic epithelial transplantation for complete DiGeorge syndrome: RNA (2025-10-02)

  Single cell transcriptomics study of thymic transplant biopsies . This dataset contains all the data available for this study on 2025-10-02.

  Dataset EGAD00001015721

• Tumour sample for patient SA1026

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1026

  Dataset EGAD00001009607

• WGS files for Newman MAP3K8 melanoma

  WGS files for Newman MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas"

  Dataset EGAD00001004579

• Dataset for "Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability"

  Dataset for "Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability"

  Dataset EGAD00001000691

• DATA FILES FOR MULLIGHAN MEF2D RNASEQ UNSTRANDED

  DATA FILES FOR MULLIGHAN MEF2D RNASEQ UNSTRANDED

  Dataset EGAD00001002704

• ChIP-seq for AR, FOXA1 and HOXB13 on 8 prostectomy samples

  ChIP-seq for AR, FOXA1 and HOXB13 on 8 prostectomy samples, both regions with/-out tumor cells, Fastq files.

  Dataset EGAD00001005374

• Illumina Reads for patient with ataxia-pancytopenia syndrome.

  Illumina BAMs for a patient with ataxia-pancytopenia syndrome and both of their parents.

  Dataset EGAD00001005034

• Whole Genome Sequencing data for epigenetic subgroups of meningioma

  Bam files for 124 samples (62 tumor vs blood pairs); Whole Genome Sequencing performed on Illumina HiSeq X Ten

  Dataset EGAD00001005061

• TENX069

  Transcriptome profiling by high-throughput sequencing for single cells for library TENX069 1 samples; filetype=fastq

  Dataset EGAD00001006483

• SCRNA10X_SA_CHIP0141_004

  Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0141_004 1 samples; filetype=fastq

  Dataset EGAD00001006463

• TENX068

  Transcriptome profiling by high-throughput sequencing for single cells for library TENX068 1 samples; filetype=fastq

  Dataset EGAD00001006482

• IMpower133 processed RNA-seq data whole transcriptome

  This dataset contains log2(TPM + 1) for 271 tumor samples profiled by RNA-seq for the entire transcriptome.

  Dataset EGAD00001006927

• Normal sample for patient SA533

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA533

  Dataset EGAD00001009571

• Normal sample for patient SA597

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA597

  Dataset EGAD00001009572

• Normal sample for patient SA997

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA997

  Dataset EGAD00001009573

• Normal sample for patient SA1027

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1027

  Dataset EGAD00001009588

• Normal sample for patient SA1028

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1028

  Dataset EGAD00001009589

• Normal sample for patient SA1040

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1040

  Dataset EGAD00001009590

• Normal sample for patient SA1058

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1058

  Dataset EGAD00001009672

• single cell RNA sequencing for healthy controls and patients having NFATc1 deficiency

  single cell RNA sequencing for 4 healthy controls and 2 patients having NFATc1 deficiency

  Dataset EGAD00001011044

• Genotype-Tissue Expression (GTEx) (2025-07-28)

  Dual snRNAseq and ATACseq of replicate PBMC samples for 10X beta testing. . This dataset contains all the data available for this study on 2025-07-28.

  Dataset EGAD00001015663

• Assessment of Health-related Quality of Life in Rare Kidney Stones

  The purpose of this study is to learn about Health-related Quality Of Life (HRQoL) in patients enrolled in the Rare Kidney Stone Consortium (RKSC) registries. Quality of life studies look at different aspects of both physical and mental components of people's lives. HRQoL data for people affected by kidney stones are not currently available for people followed over time. All participants enrolled in the RKSC registries will be invited, via email or postal mail, to participate in this study. Health-related quality of life in people with rare kidney stones enrolled in the RKSC registries will be measured. Instruments used in this study are the SF-10 for pediatric participants and SF-36v2 for adult participants. The surveys will be completed online. Participants without a computer or internet access will participate using a paper version of the survey. These surveys will be done at enrollment and annually thereafter. The SF-36v2 includes 36 questions and is estimated to take 15 minutes for its completion, while the SF-10 includes 10 questions and could be completed in 5 minutes. The research questions are: Assessment of HRQoL in patients with rare kidney stones. Comparison of HRQoL results between rare kidney stone formers, general population and other populations with relevant chronic diseases. Comparison of HRQoL results in the same populations affected by different stones and analyzed with attention to the effects of various factors included in the disease registry, such as stone activity, burden of urologic interventions, medication and other treatments. Evaluation of HRQoL and its trends over time in patients undergoing treatment for rare kidney stones. About this study: The plan is to have 400 participants from all four registries take part in this multi-center study. The assessment of your HRQoL will be done annually for 5 years.

  Study phs001770

• Uncovering RNA Signatures of C9orf72-Linked ALS and Related Disorders

  Substantial clinical and pathological variability has been reported in patients carrying an expanded repeat in C9orf72, who are generally diagnosed with amyotrophic lateral sclerosis (ALS) and/or frontotemporal dementia (FTD). Emerging evidence suggests that C9orf72 expression, RNA foci, and dipeptide-repeat proteins contribute to C9orf72-related diseases; however, the majority of the clinicopathological variability remains unexplained. We hypothesize that RNA sequencing (RNA-Seq) might reveal individual genes or groups of highly correlated genes (modules) that could account for this variability, which may help to identify much-needed druggable targets and/or biomarkers. Our preliminary studies performed in the frontal cortex, where we compared C9orf72 expansion carriers to (disease) controls, demonstrated that the top differentially expressed gene was C9orf72 itself. We also noticed that differentially expressed genes were enriched for the endocytosis pathway, which is consistent with the reported function of the C9orf72 protein in vesicle trafficking. Furthermore, we detected a module enriched for vesicular pathways, and additionally, we discovered an association with survival after onset for several promising candidates involved in vesicular transport. To find new therapeutic targets and biomarkers, here we have completed RNA-Seq on an increased number of samples to examine another relevant region: the cerebellum. As such, we performed RNA-Seq on a well-characterized cohort of C9orf72 expansion carriers, patients without this expansion, and control subjects without neurological diseases. We used multivariable linear regression models for gene-level analysis, weighted correlation network analysis for module-level analysis, and leafcutter for splicing analysis. Using the cerebellar RNA-Seq data, we found a large number (>6,000) of differentially expressed genes, with a notable increase in expression of homeobox genes in C9orf72 expansion carriers, as well as many gene modules that were associated with C9orf72 expansion status. Additionally, using leafcutter, we detected over 1,000 differential splicing events and an increase in the number of cryptic splicing events in C9orf72 expansion carriers.

  Study phs003065

• The Sea Islands Genetic Network (SIGNET): Identifying genetic contributors to diabetes and dyslipidemia in African Americans

  Recent genome-wide association studies (GWAS) have successfully identified genetic variants that influence diabetes risk in European populations, however most do not have a major impact on diabetes risk in populations of African descent. The African American (AA) population from the Sea Islands of coastal South Carolina and Georgia has high rates of type 2 diabetes, low levels of admixture, and in general, consume a diet rich in saturated fats. We postulate that this unique combination of ancestral and environmental factors results in a more consistent penetrance of diabetes risk alleles, as well as enrichment of risk alleles of African origin. The existing DNA samples and rich phenotypic data from the Sea Island Families Project comprise a unique resource for genetic studies of type 2 diabetes and related metabolic traits such as dyslipidemia. Our central hypothesis is that the increased risk for T2DM in AA compared with European American (EA) is due, in part, to susceptibility alleles of African origin, and that these alleles can be identified using a GWAS. The Specific Aims are to: 1) Identify genetic risk factors for type 2 diabetes utilizing DNA samples and data from the Sea Island Families Project, Reasons for Geographic and Racial Differences in Stroke (REGARDS) Study recruited from SC, GA, NC, and AL; and a GWAS approach; 2) Identify genetic contributors to lipoprotein subclasses in African Americans using the lipoprotein subclass profile (particle size and concentration for multiple subclasses of VLDL, LDL, and HDL) assessed by NMR at LipoScience, Inc., and the GWAS data from Aim 1. The rationale for this project is that identification and validation of novel pathophysiological pathways and informed selection of candidate genes for diabetes risk will inform development of new, targeted prevention and treatment strategies in this underserved, high risk population.

  Study phs000433

• A Phase 2 Study of Tipifarnib in Large Granular Lymphocyte (LGL) Leukemia

  LGL leukemia can be divided into three subsets including the following: αβ or γδT-LGL and NK-LGL leukemia. All three subtypes will be enrolled using a two-stage design. The primary endpoint of the study is assessment of overall clinical response. Correlative laboratory studies will be performed aimed at determining the mechanism of response to treatment. Thirteen participants will be accrued in the first stage at a dose of 300 mg BID administered intermittently every other week (i.e., 7 days on and 7 days off). If there are two or more responders, the protocol will be extended to a second stage of the study and accrual will be extended to 25 evaluable participants. Allowing for 10% rate of ineligibility due to unexpected events and dropout, we will accrue 14 patients in the first stage and 27 patients in total. Participants that withdraw from the study for reason unrelated to toxicity, will be replaced. There are two potential stopping rules for toxicity. If 3 or more participants out of the 13 enrolled in the first stage experiences grade IV neurotoxicity, the study will be stopped due to excessive toxicity. Dose reductions have been incorporated for hematologic toxicity. Treatment of T and NK LGL leukemia with immunosuppressive agents such as low-dose methotrexate generally require from four to six months for a clinical response and sometimes much longer. Therefore, in participants who show clinical improvement with less than grade three toxicity, tipifarnib treatment will be continued for as many as four additional months (12 months total). After the first 8 months, response will be assessed. The protocol treatment will be discontinued in participants with progression of disease. A long-term follow up will be performed for five years in patients that receive a complete clinical response. The long-term follow up will consist of vital signs, weight, CBCs, serum chemistries, and physical examination at six month intervals.

  Study phs000594

• Genome-wide Association Study of Myasthenia Gravis

  The purpose of this project was to conduct a genome-wide associate study to search for the genetic factors that predispose to myasthenia gravis. The rationale for this study lies in the fact that, although the immunological and physiological processes affecting the neuromuscular junctions of myasthenia gravis patients are well understood, the spectrum of genetic factors that predispose to myasthenia gravis and influence its disease manifestations are not well known. Identification of the myasthenia gravis-related genes will shed light on the fundamental cellular events underlying myasthenia gravis, and will provide focus for research aimed at developing therapies that alter the natural course of the disease. A consortium of fourteen institutions in North America collected DNA samples from 1028 people diagnosed with autoimmune myasthenia gravis. Relevant clinical data have been collected for each patient, including age of onset, severity of disease, response to drug therapy, personal and family history of other autoimmune diseases. Genotyping of the case cohort was performed in the Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD. Genotyping of the case cohort was performed using the HumanOmniExpress-12v1_C SNP array manufactured by Illumina Inc. For the control cohort, we downloaded genotype data from dbGAP (accession phs000196.v2.p1) for 1,998 US neurologically normal individuals. The control cohort had been previously genotyped at the Center for Inherited Disease Research at Johns Hopkins University on HumanOmni1-Quad version 1.0B beadchips (Illumina) as part of the NeuroGenetics Research Consortium GWAS of Parkinson's disease. Analyses were confined to the 677,673 autosomal SNPs that were common to both chips. Of the 1028 samples which were genotyped, 21 samples were excluded due to mismatched genders, 9 were excluded due to low genotype call rate, 5 samples were excluded as duplicates, and 25 samples were excluded as ethnic outliers. The remaining 972 samples were used in analysis.

  Study phs000726

• Structure and Diversity of Urinary Cell-Free DNA Informative of Host-Pathogen Interactions in Human Urinary Tract Infection

  The risk of acquiring urinary tract infection (UTI) is very high for patients who have received kidney transplants; nearly half will develop bacteriuria and an eighth viruria via BK polyomavirus in the first three years following transplantation. Current methodology for diagnosing viral and bacterial infections, while well practiced, is often limited in scope. The advent of next generation sequencing of cell-free DNA has shown promise in its ability to capture multiple perspectives of human health from discovering the origin of cell-free DNA in plasma; such a diagnostic has not been readily applied to urinary cell-free DNA. In this study, we selected 141 urine samples from a cohort of kidney transplant patients, which were collected and stored at Weill Cornell Medical College - New York Presbyterian Hospital. Of these samples, 43 samples were determined to be culture positive (> 10,000 CFU) for one or more bacterial species, including E. coli, Enterococcus, Klebsiella, Haemophilus, and Raoultella. A separate 23 samples were confirmed for BK virus nephropathy, with presence of BK polyomavirus confirmed via qPCR. We also included 29 samples from 14 patients who did not develop UTIs in the first three months following transplantation, and 11 samples that were negative for BK virus nephropathy. For a full description of samples, please see the Supplementary Data 1 in https://pubmed.ncbi.nlm.nih.gov/29925834/. From these urine samples, we aimed to capture and sequence urinary cell-free DNA using a single-stranded library preparation. In addition, we performed whole-genome bisulfite sequencing to 170 plasma samples collected from 27 hematopoietic cell transplant patients who developed graft-versus host disease and BK polyomavirus infection. We also performed Sample-Intrinsic microbial DNA Found by Tagging and sequencing (SIFT-seq) on 196 cell-free DNA (cfDNA) samples (154 plasma and 42 urine) collected from five groups of subjects. For a full description of samples, please see publications in PMID: 35864089 and PMID: 35058359.

  Study phs001564

• OurHealth - Cardiovascular Disease in South Asians

  The OurHealth Study aims to build a biobank comprised of South Asian samples from participants residing in the United States. Primary objectives are to (1) identify genetic and non-genetic drivers of cardiometabolic disease in South Asians, (2) engage participants and researchers in scientific advances and research opportunities to accelerate discovery, and (3) assess the impact of returning polygenic risk scores for cardiovascular-related health conditions. Participants use a web-based platform to complete electronic informed consent, and contribute data via (1) online health surveys, (2) mailed saliva biospecimens for sequencing, and (3) optional electronic health record sharing. Surveys capture medical history, medication data, lifestyle factors, family history, mental health history, and detailed information about cultural and ancestral background. Biospecimens, procured via saliva self-collection kits, undergo DNA isolation and are sequenced using the "blended genome exome" (BGE) method, which consists of sequencing on the NovaSeqX 10B Flowcell followed by Dynamic Read Analysis for GENomics (DRAGEN) analysis for alignment to GRCh38, mapping, and variant calling. BGE uses low-coverage whole genome sequencing (lcWGS) (2-3x) combined with deep-coverage exome sequencing (30-40x), improving on SNP arrays for common variant imputation across European and non-European populations while also capturing rare coding variants. Relative to array genotyping, coverage, genotyping breadth, imputation generalizability, and cost are more optimal.BGE requires imputation for which the NHLBI TOPMed reference panel was used, and GLIMPSE2 was used for imputation emitting genotyping dosages (i.e., 0-2 multimodal continuous). Quality control (QC) included the following procedures. Sample QC excluded those with mean coverage 3% contamination from FREEMIX/VerifyBamID, sex aneuploidy and genotype/phenotype sex-mismatch due to potential phenotyping errors, fingerprinting discordance, and sample metric-level outliers were ancestry-aware, given expected distribution differences. Variant QC metrics including allele frequencies, imputation INFO scores, and Hardy-Weinberg Equilibrium (HWE) p-values are provided with the data; the genotype files provided are not filtered.

  Study phs003821

• Utlizing the RA signature to predict response to TNFi

  This study involves bulk RNA-seq analyses of blood cells from patients with rheumatoid arthritis who have had an inadequate response to methotrexate, collected before and 12 weeks after effective treatment with either etanercept or adalimumab. Peripheral blood mononuclear cells were stimulated with anti-CD3 for 24 hours and sorted into CD4+, CD19+, and CD4-CD19- (DN) populations for bulk RNA-seq.

  Study phs002562

• Investigating Human Placentation and Pregnancy Using First Trimester Chorionic Villi

  Chorionic villus sampling (CVS) is routinely used for prenatal diagnosis of cytogenetic disorders, but also possesses great potential for studying placentation. To better understand villi biology, human placentation, and how these relate to pregnancy outcomes, we examined the morphology and transcriptomes of villi obtained via CVS from 10-14 weeks of pregnancy and correlated these with pregnancy attributes and clinical outcomes.

  Study phs001320

• ICARUS-LUNG01 dataset

  A total of 46 frozen tumor biopsies underwent WES analysis, while 41 blood samples were used as germline controls.Tumor samples qualified for whole exome sequencing (WES) if they contained ≥10% tumor cells. For bulk RNA-seq, 20 paired baseline and on-treatment frozen tumor biopsies were analyzed. Tumor samples qualified if they contained ≥30% tumor cells. For GeoMx spatial transcriptomic study we used 7 patients from the ICARUS LUNG01 trial focusing on tumour and immune cell compartments. We selected 7 paired baseline and on-treatment patient samples for analysis. We selected up to 4 regions of interest (ROI) per sample tissue. We identified tumour and immune cell areas of illumination (AOI) using CK and CD45 antibodies respectively

  Dataset EGAD50000001014

• The landscape of somatic mutations in epigenetic regulators across 1000 pediatric cancer genomes

  To define the frequency and pattern of somatic mutations in epigenetic regulators in pediatric cancer, we sequenced 633 genes, encoding the majority of proteins involved in patterning the epigenome, in 1000 pediatric tumors spanning 21 different cancer subtypes. This analysis establishes an epigenetic landscape of pediatric cancer, which expands the knowledge for potential therapeutic targets and for developing personalized therapy.

  Study EGAS00001000449

• Genetic_screening__of_GPI_anchor_protein_synthesis__

  This study will analyse the guide sequence which were used for making mutations in the Cas9-expressing cells. We used GeCKO v2 library which were released by Feng Zhang, 2014. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001256

• Genomic and transcriptomic profiling of signalling networks in follicular lymphoma

  This dataset is composed of sequencing data from 16 patients diagnosed with follicular lymphoma, who developed transformed disease and for whom representative frozen tumor biopsy samples were available. For 14 patients there is paired material from both disease stages. DNA and RNA libraries were constructed and captured with a kinome bait library (Agilent Technologies), before sequencing on an Illumina platform.

  Study EGAS00001002175

• Subclonal evolution of four ER+ breast cancers determined by WGS and scRNA-Seq

  We analyzed the subclonal evolution of four ER+ breast cancers over 2-15 years using whole-genome sequencing (WGS) and single-cell RNA-Seq (scRNA-Seq). For each patient we analyzed 2-6 cancer samples, generally metastatic pleural effusions or ascites, by WGS, along with germline DNA. Two of the samples per patient were selected for single-cell RNA-Seq.

  Study EGAS00001002436

• Ancient nuclear genomes enable repatriation of Indigenous human remains

  For many decades Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return of their ancient people. By sequencing ten ancient nuclear genomes of Aboriginal Australians and 27 mitogenomes from ancient pre-European Aboriginal Australians (up to 1,540 yr BP) of known provenance we demonstrate the feasibility of successfully identifying the geographic origins of unprovenanced ancestral remains using genomic methods.

  Study EGAS00001003359

• Test_of_PCR_library_method_on_whole_genmoe_samples

  We will sequence 2 whole genome pairs which have had the libraries prepared with a PCR step. The resulting sequence will be compared to teh same samples which have had sequence obtain using a no_PCR library method. the sequence obtained in this experiment may or may not be used in conjunction with the other sequence obtain for these samples in the search for novel cancer mutations.

  Study EGAS00001000214

• Genome_Diversity_in_Africa_Project___GemCode_libraries_

  High depth whole genome sequencing from GemCode (10x Genomics) DNA libraries containing long range linkage information for one Baganda trio and one Baganda child (parent already sequenced at high depth). This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001828

• Mapping_genetic_variants_underlying_gene_regulation_in_inflammed_intestinal_cell_types_to_identify_novel_IBD_drug_targets

  Biopsies from the terminal ileum and rectum of individuals with Crohn's disease are digested on ice to single cells and processed for single-cell RNA-sequencing (10X Genomics and Illumina) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001003770

• Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence (RNA-seq)

  Understanding how prostate cancer cells adapt to AR-targeted interventions is critical for identifying novel drug targets to improve the clinical management of treatment-resistant disease. Our study revealed an enzalutamide-induced epigenetic plasticity towards pro-survival signaling, and uncovered circadian regulator ARNTL as an acquired vulnerability after AR inhibition, presenting a novel clinical lead for therapeutic development.

  Study EGAS00001006016

• Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence (ChIP-seq)

  Understanding how prostate cancer cells adapt to AR-targeted interventions is critical for identifying novel drug targets to improve the clinical management of treatment-resistant disease. Our study revealed an enzalutamide-induced epigenetic plasticity towards pro-survival signaling, and uncovered circadian regulator ARNTL as an acquired vulnerability after AR inhibition, presenting a novel clinical lead for therapeutic development.

  Study EGAS00001006017

• November 2020 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  November 2020 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001007529

• HV31 - Read identifier list for local CCS, CLR, ONT and MGI reads

  This file contains read identifiers for local CCS, CLR, ONT and MGI reads for each of the eight selected genomic regions (HLA, KIR, IGH, IGK, IGL, TRA, TRD, andTRG). We extracted these reads by aligning whole-genome sequencing data to a draft whole-genome de novo assembly, and selecting reads that map to contigs representing each region. These reads were involved in the polishing and validation of the HV31 assembly. Please refer to the relevant manuscript (https://doi.org/10.1101/2021.02.03.429586) for additional details. Read identifiers are stored in JSON format. Along with the full FASTQ files, this file enables convenient re-analysis of the HV31 sequencing data in the eight selected regions.

  Dataset EGAD00001007761

• A standardised framework for robust fragmentomic feature extraction from cell-free DNA sequencing data

  Fragmentomic features of cell-free DNA represent promising non-invasive biomarkers for cancer diagnosis. However, a lack of systematic evaluation of biases in feature quantification has hindered the adoption of such applications. We compared features derived from whole-genome sequencing of ten healthy donors using nine library kits and ten data-processing routes, and validated them in 1,182 plasma samples from published studies. Our results clarify the variations resulting from library preparation and feature quantification methods. We designed the Trim Align Pipeline and the cfDNAPro R package as unified interfaces for data pre-processing, feature extraction, and visualisation, aiming to standardise multimodal feature engineering and integration for machine learning.

  Dataset EGAD00001015535

• Chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) data from immune cells for healthy young and healthy old subjects

  Dataset consisting of: (1) N=234 genome-wide chromatin accessibility (ATAC-seq) profiles for distinct N=21 healthy old and N=28 healthy young subjects. ATAC-seq biological samples provided for the following tissues: PBMC (N=24), CD14+ monocytes (N=18), CD8+ memory T cells (N=7), CD8+ naive T cells (N=7), CD4+ memory T cells (N=7), CD4+ naive T cells (N=7), and naive B cells (N=7). (2) N=39 genome-wide transcription (RNA-seq) data for distinct N=15 healthy old and N=24 healthy young subjects' PBMCs.

  Dataset EGAD00001003602

• Prevention and Early Treatment of Acute Lung Injury (PETAL) - Low Tidal Volume Universal Support Feasibility of Recruitment for Interventional Trial (LOTUS FRUIT) (PETAL-LOTUS FRUIT-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. Objectives: The two main goals of PETAL-LOTUS FRUIT were to conduct a prospective, observational study within all PETAL Network sites to determine the frequency of and outcomes from acute respiratory failure and the current usual care for tidal volume ventilation in patients with and without acute respiratory distress syndrome (ARDS), and to simulate the design and power of the proposed LOTUS trial. Background: A previous study demonstrated improved survival among patients with ARDS receiving tidal volume (Vt) targeted to 6 ml/kg of predicted body weight (PBW). As a result, low–tidal volume ventilation (LTVV) is now recommended for all patients with ARDS, although penetration of this evidence-based practice has been limited, especially early in mechanical ventilation. LTVV may also benefit patients without ARDS. Consequently, there has been increasing call to apply LTVV for all patients with acute respiratory failure upon initiation of mechanical ventilation. The PETAL Network considered performing a pragmatic stepped-wedge, cluster-randomized, controlled, hybrid implementation trial to examine systematic implementation of a default 6 ml/kg PBW LTVV strategy in patients with acute respiratory failure requiring intubation to improve adherence to LTVV and decrease mortality in acute respiratory failure. Trial planning may be better estimated by simulation than routine, simplistic calculations, but such simulations require detailed data of initial parameters. Participants: 2848 patients from 49 hospitals were enrolled. Enrollment varied by hospital, ranging from 4 to 100 patients, the maximum enrollment allowed per site. Design: PETAL-LOTUS FRUIT was a multicenter, prospective, observational cohort study of patients with acute respiratory failure on mechanical ventilation in the PETAL Network hospitals. For all patients, baseline demographic data, the hospital location, indication for intubation (hypoxemic or hypercapnic respiratory failure or both, altered level of consciousness, or surgery), type of intensive care unit (ICU), and Sequential Organ Failure Assessment score in the first 24 hours after intubation were collected. Baseline ventilator data immediately after intubation, arterial blood gas results and oxygen saturation as measured by pulse oximetry, and presence of ARDS was also collected for all patients. ARDS was defined as a ratio of arterial oxygen tension to fraction of inspired oxygen (FiO2) less than or equal to 300 with a chest radiograph within 24 hours of the qualifying ratio of arterial oxygen tension to FiO2 that had bilateral infiltrates unexplained by mass, collapse, or effusion. For the first 50 patients enrolled at each hospital, daily data on ventilator mode, Vt, and presence of ARDS for the first 3 days after intubation was collected. Vt indexed to PBW was calculated from the set Vt for patients on ventilator mode with volume settings. For patients on pressure ventilation modes, Vt was calculated from the ratio of minute ventilation (in ml/min) to the respiratory rate. Enrolled patients were followed until hospital discharge or 28 days for clinical outcomes including mortality, ventilator-free days, and length of stay. To determine the possible improvement in mortality that could be observed with a reduction in Vt from current usual care in the PETAL-LOTUS FRUIT cohort to 6 ml/kg PBW, mortality was estimated as a function of initial Vt. Five models based on data from three distinct patient populations were used. 500 simulations of a stepped-wedge, cluster-randomized clinical trial using the model with greatest predicted benefit for lowering the Vt to 6 ml/kg PBW in PETAL-LOTUS FRUIT sites were performed. Conclusions: Use of initial tidal volumes less than 8 ml/kg predicted body weight was common at hospitals participating in the PETAL Network. After considering the size and budgetary requirement for a cluster-randomized trial of LTVV versus usual care in acute respiratory failure, the PETAL Network deemed the proposed trial infeasible (PMID: 30407869).

  Study phs003791

• NHLBI TOPMed - NHGRI CCDG: The Johns Hopkins University School of Medicine Atrial Fibrillation Genetics Study

  Atrial fibrillation (AF), the most common sustained cardiac arrhythmia, is the primary cause of many hospital admissions, and is associated with significant secondary morbidity by increasing the risk of stroke, heart failure, and all-cause mortality. The incidence of AF is on the rise, and it is projected that by the year 2050 more than 10 million patients will be affected by AF in the United States alone. Anti-arrhythmic medications have limited success in maintaining sinus rhythm, are associated with side effects, and appear ineffective at reducing mortality compared to a strategy of rate control and anticoagulation. Given the significant morbidity associated with this common arrhythmia, surgical and catheter ablation techniques have been developed to treat AF. However, despite the incorporation of various strategies for ablation, long-term recurrence rates of AF remain higher than 25 percent after ablation. Current techniques for catheter ablation of AF include pulmonary vein isolation and complex fractionated atrial electrogram (CFAE) ablation. However, the contribution of each strategy to long-term procedural success and the relative importance of each strategy for different patients remain unknown. Recent advances in cardiac imaging have allowed detailed analysis of left atrial myocardial anatomy. Parallel advances in molecular genetics have identified several candidate genes involved in familial and non-familial AF. However, the pathophysiology of AF generation and maintenance, and the potential contribution of such genetic or anatomic substrates for patient selection, and for target identification during catheter ablation have not yet been examined. Advances in molecular genetics and imaging, coupled with techniques for endocardial and epicardial mapping in the electrophysiology laboratory present an opportunity to significantly improve our understanding of (1) The relation of paroxysmal versus persistent AF with (a) structural left atrial changes (left/right atrial scar, wall thinning, pulmonary vein anomalies, and coronary sinus dilation) and with (b) candidate genetic variants. (2) The relation of candidate genetic variants with (a) structural left atrial changes and with (b) electrophysiologic properties (atrial effective refractory period (AERP) inhomogeneity, voltage abnormalities, trigger burden and location, C FAE extent and location), (3) The relation of structural left atrial changes with (a) CFAE location as targets for catheter ablation and with (b) reversible conduction block/myocardial injury after pulmonary vein isolation, and (4) Individualized endocardial targets for AF ablation based on candidate genes and anatomic substrates. The proposed study will improve our understanding of the underlying pathophysiology of AF, and may improve current techniques for treatment of this important arrhythmia.

  Study phs001598

• Genetic Analysis of Normal Human Facial Variation

  The purpose of this project is to identify genes associated with normal human quantitative facial variation. The motivation for this project stems from the fact that very little is known about how variation in specific genes relates to the diversity of facial forms commonly observed in humans. Viable candidates for these morphogenes originate from a number of sources: tissue expression studies, animal models with targeted or spontaneous mutations, and genetic syndromes with craniofacial manifestations. Importantly, understanding the genetic basis for normal facial variation also has important implications for health-related research. For example, this work has the potential to shed light on the factors influencing liability to common craniofacial anomalies such as orofacial clefts. There is now ample evidence that certain facial features (e.g., increased midfacial retrusion) characterize individuals genetically at-risk for orofacial clefts (e.g., biological relatives of affected cases). While these predisposing facial features are statistically over-represented in at-risk groups, they are also common in the general population. Since many of the current candidate genes for clefting are thought to play a critical role in facial morphogenesis, variation in these genes may also underlie normal variation in these facial features. These candidate genes, however, probably represent only a small fraction of the total number of loci influencing normal human facial variation. Phenotypes for this project were obtained from over 3000 healthy Caucasian subjects recruited through three separate studies. The majority of the subjects were recruited as part of the 3D Facial Norms Project, which is described in extensive detail here: (https://www.facebase.org/facial_norms/notes). The provided dbGaP phenotypes include a series of anthropometric craniofacial measurements (linear distances) primarily derived from 3D photographic facial surface scans (see previous hyperlink). The specific genotyping requested is described elsewhere in this document. Our analysis team is pursuing a variety of different analytic approaches to derive genetically informative phenotypes, including various shape-based morphometric methods. For those interested in pursuing more advanced phenotypic approaches, the original 3D surface scans and additional phenotypic traits are available to researchers through the FaceBase Consortium. This dataset has the potential to facilitate the discovery of new genetic loci with an important role in both normal and abnormal facial development. It may also serve as a dataset to test hypotheses regarding specific SNP associations (e.g. as a replication dataset) or as part of a larger meta-analysis.

  Study phs000949

• Caregiving as a Natural Stressor in Studies of the Role of Genes That Affect Serotonin Function in Regulating Risk Factors for Coronary Heart Disease (CAREGIVER)

  The burden of caregiving for an ill relative has been shown to interact with existing comorbidities to increase risk of several health outcomes including metabolic syndrome and blood pressure reactivity. The CAREGIVER study was developed to compare cardiometabolic risk factors in caregivers and controls. These risk factors include physiologic measures, psychologic measures, neighborhood characteristics, and genetic and genomic factors. DNA and plasma were collected and used for examination of cardiometabolic and stress biomarkers, genotyping and methylation analysis.

  Study phs001747

• cfDNA Methylomes for HCC Detection and Postoperative Monitoring

  To overcome the limitations of current ctDNA-based HCC detection, specifically mutational profiling, we propose quantifying cfDNA methylation levels using cfMeDIP-seq and evaluating its capacity for HCC detection and post-surgery recurrence monitoring. This approach aims to reveal the clonal dynamics of HCC during surgery and upon relapse. Our preliminary data and analyzed results demonstrate that tumor-agnostic cfDNA methylomes can accurately detect HCC and predict recurrence after liver resection or transplantation. This method could have significant implications for the diagnosis, treatment, and monitoring of HCC.

  Study EGAS50000000450

• Gene signature for predicting homologous recombination deficiency in triple-negative breast cancer

  We developed a gene expression-based classifier for homologous recombination deficiency (HRD) in breast cancer patients using WES and RNA-seq data obtained from 94 TNBC samples from a Malaysian hospital-based cohort (MyBrCa). This classifier was able to predict for high levels of a mutational signature associated with HRD in an additional MyBrCa TNBC validation cohort (this EGA study) as well as in TNBCs from TCGA. We also validated the classifier on a NanoString platform with both fresh frozen and FFPE tissue.

  Study EGAS00001006518

• Myeloid-specific KDM6B inhibition sensitizes Glioblastoma to PD1 blockade

  This data set include FASTQ files for five experiments: Human scRNA-Seq data (6 samples), Human Visium spatial transcriptomic data (3 samples), Mouse scRNA-seq data (4 samples), Mouse scATAC-seq data (2 samples), Mouse ChIP-seq data (8 samples). For the mouse scATAC-seq data (2 samples), there are originally three FASTQ files, R1, R2 and R3 files. The R1 and R2 FASTQ files were merged into one larger file ("R1R2") per sample for submission as paired-end sequencing setting to follow the EGA guidelines. They can be split into individual R1 and R2 files in order to be processed by Cell Ranger software. The files with IC1 suffix are CHIP-seq Input control for anti-KDM6B antibody pull down experiments and the files with IC2 suffix are CHIP-seq Input control for anti-H3K27ME3 antibody pull down experiments in murine model.

  Dataset EGAD00001010073

• Next gen seq of eye cancers (2019-08-14)

  Retinoblastoma (RB), the commonest eye cancer in children was the first cancer for which a genetic cause was identified: the Rb1 gene is a tumour suppressor gene that is mutated in RB. The Rb1 gene defect alone does not predict the clinical outcome. We propose to study other possible mechanisms: 1. Stepwise further mutations occur in RB, increasing its carcinogenesis. We will sequence the whole genome in RB tissue, and relate the different genes expressed to the treatments used. 2. Extracellular matric proteins contribute to a tumour permissive environment for RB to continue to grow. This includes Samll Leucine Rich Proteoglycans (SLRP), a family of 15 secreted extracellular matrix proteins involved in eye development. 3. Cancer stem cells (CSC), a subpopulation of treatment resistant cells, drive RB tumours, and whether these stem cells can be manipulated for new therapies. The aim of this study is to assist finding targeted diagnostic techniques and treatments for RB. . This dataset contains all the data available for this study on 2019-08-14.

  Dataset EGAD00001005251

• Whole-genome sequence data for The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer

  Each tumor sample was cut into three pieces, yielding two end-pieces for cryovials and a middle portion placed in 10% buffered formalin. End pieces were homogenized manually and with a paddle blender (Stomacher). All paraffin-embedded blocks, including formalin-fixed tumor samples and molecular-fixed fallopian tubes, were sectioned and stained with hematoxylin and eosin prior to expert histopathological review to confirm the presence of high grade serous carcinoma. Homogenized end pieces were then flash frozen and later used for WGS. For all tumor and matched normal (peripheral blood) samples, DNA was extracted with the Qiagen AllPrep DNA/RNA kit (tumor samples from patients 25,26,28-32) or the Qiagen Blood and Tissue Extraction Kit (tumor samples from patients 1-4,7,9-17, and all blood samples). For all tumor and normal samples, DNA extraction was followed by library construction and sequencing using Illumina HiSeq2500 whole genome shotgun v4 chemistry with paired-end 125bp reads.

  Dataset EGAD00001003984

• Alcohol Dependence: Sequencing from Multiplex Families

  Two multiplex for alcohol dependence family studies were initiated based on the gender of a pair of probands. Ascertainment of a pair of AD probands was used to increase the density of alcohol dependence within the family. Identification of male (Cognitive and Personality Factors in Relatives of Alcoholics Family Study) and female (Biological Risk Factors in Female Alcoholics Family Study) alcohol dependent probands was accomplished by identifying an alcohol dependent proband while in treatment in a substance abuse treatment facility in Pittsburgh and surrounding communities who provided contact information for a sibling whom he/she thought might be interested in participating. The studies had identical ascertainment requirements. DNA was banked for all willing participants.

  Study phs001775

• National Cancer Institute (NCI) Head and Neck Cancer Study

  Head and neck cancers have well-documented associations with tobacco and alcohol exposure, but the disease develops in only a small fraction of users, which implies an important role for genetic susceptibility. Therefore, head and neck cancers are an excellent model for studying genetic susceptibility to environmental carcinogens. The primary goal of this study is to perform a comprehensive two-stage, high-density, genome-wide single-nucleotide polymorphism (SNP) analysis of head and neck cancer cases and corresponding frequency matched controls to identify novel genetic risk factors for head and neck cancer. In the study, we genotyped 2242 head and neck cancer cases and 1198 controls using Illumina HumanOmniExpress-12v1 BeadChip.

  Study phs001173

• Immune Profiles Study

  This study assesses glioma patient blood methylation longitudinally beginning pre-surgery through other clinically important timepoints. Progression and survival are studied in relation to methylation derived immunologic profiles and other characteristics. For this study, patients scheduled for surgery at University of California San Francisco (UCSF) for a possible newly diagnosed glioma (grades 2-4) or recurrent grade 2/3 glioma were consented and enrolled. Patients had blood collected pre-surgery and, if the pathology results confirm a glioma, every few weeks or months during their treatment (up to 30 total timepoints). Blood immunomethylomic profiles were measured at these timepoints to assess associations with glioma patient outcomes, clinical measures, other known prognostic markers, and imaging characteristics.

  Study phs002998

• Coenzyme Q10 (CoQ) in Huntington's Disease (HD) (2CARE)

  This is a multi-center, randomized, double-blind, placebo-controlled trial of CoQ involving 609 ambulatory subjects with HD who are not requiring skilled care or institutionalization. Eligible subjects were randomized to receive either CoQ 2400 mg/day or matching placebo. Subjects were followed prospectively and systematically for 60 months of double-blind observation. The primary outcome variable is a combination of time to death (for subjects who die) and the change from baseline to Month 60 in Total Functional Capacity (TFC) score (for subjects who survive). The primary hypothesis of the study is that chronic treatment of early-stage HD subjects with high-dosage CoQ will slow the progressive functional decline of HD.

  Study phs001065

• Development and Validation of Patient-Derived Xenografts from Fibrolamellar Carcinoma Human Tissue

  We developed and validated Patient-Derived Xenografts (PDX) of Fibrolamellar Carcinoma human tissue from surgical resections. Human tissues from primary liver tumor, recurrent liver, and liver metastases were implanted into NOD-SCID-Gamma (NSG) mice (Jackson laboratories) and monitored for tumor growth. Some of the original tissues were frozen for further analysis including RNA sequencing. Tumors that grew were then harvested and passaged into additional mice. Some tumor tissues from the PDX samples were frozen for RNA-Seq analysis. The PDX was validated by histologic, transcriptomic and proteomic analysis. The RNA-Seq analysis was performed on original tissue samples including primary liver tumor, recurrent liver, liver metastases, normal liver, and the derived PDX.

  Study phs002435

• Division of Cancer Epidemiology and Genetics (DCEG) Imputation Reference Dataset

  We have built a new resource for imputation of SNPs for existing and future genome-wide association studies (GWAS), known as the Division of Cancer Epidemiology and Genetics (DCEG) Reference Set. The first build of the data set includes 728 cancer-free individuals of European descent from three large prospectively sampled studies, 98 African-American individuals from the Prostate, Lung, Colon, and Ovary Cancer Screening Trial (PLCO), 74 Chinese individuals from a Chinese clinical trial in Shanxi, China (SHNX), and 349 unrelated individuals from the HapMap Project (see Molecular Data Section for details on arrays used). The final harmonized dataset includes 2.8 million autosomal polymorphic SNPs on 1,249 subjects after rigorous quality control metrics were applied.

  Study phs000396

• PGRN-Leducq: Identification of the KCNE1 D85N Polymorphism as a Possible Modulator of Drug-Induced Torsades de Pointes

  The goal of this study was to search for genetic variants that could be responsible for modifying the risk of drug-induced long QT syndrome (diLQTS). diLQTS is a relatively common adverse drug event and has been a leading cause for drug relabeling and withdrawal from the market. Our hypothesis, that variants in genes which regulate electrical properties in the heart modify the risk of diLQTS, was tested by genotyping patients of European descent at 1424 single nucleotide polymorphisms (SNPs) in 18 candidate genes. We found that the SNP KCNE1 D85N was highly predictive of diLQTS with an odds ratio of 9.0 (95% confidence interval: 3.5-22.9).

  Study phs000617

• Genetics of Lymphatic Anomalies from Center of Applied Genomics (CAG) at CHOP

  Lymphatic anomaly, a rare and devastating disease spectrum of mostly unknown etiologies, is characterized by diffuse or multicentric proliferation of dilated lymphatic vessels, and includes a variety of diagnoses: lymphangiectasia, central conducting lymphatic anomaly, generalized lymphatic anomaly, kaposiform lymphangiomatosis, and Gorham Stout disease. Currently, most treatments are considered palliative; lymphatic anomalies are often chronic debilitating conditions that require multiple yearly outpatient visits and hospital admissions for procedures that ameliorate symptoms, but do not correct the underlying cause. Identifying the causal genes will be hugely informative for our understanding of diseases. This will also allow for the development of affordable and successful diagnostic tests and therapies in keeping with "precision medicine" implementation.

  Study phs001802

• Longitudinal Study of the Porphyrias

  This is an observational, longitudinal study of approximately 800 individuals with various types of porphyria. Those participants will be evaluated annually for 5 years, or longer if they agree. Participation in this project will include: Participating in annual visits or contacts. Providing samples, including blood, buccal cells (cells from inside of the mouth), saliva, and urine. The type of samples and amounts may vary from person to person, depending on the type of porphyria. Giving permission for samples to be stored and used for porphyrias research. Granting permission to obtain your medical records. Providing information about your medical history and family history. Completing a questionnaire about your porphyria symptoms and quality of life.

  Study phs001278

• The Diabetes Heart Study (DHS)

  The Diabetes Heart Study is a family based study enriched for type 2 diabetes (T2D). The cohort included 1220 self-reported European Americans from 475 families (Bowden et al 2010 Review of Diabetic Studies 7:188-201: PMID: 21409311; Bowden et al 2008 Annals of Human Genetics 72:598-601 PMID: 18460048) and included siblings concordant for T2D; where possible unaffected siblings were also recruited. The cohort was recruited between 1998 and 2006. Participants were extensively phenotyped for measures of subclinical CVD and other known CVD risk factors. Primary outcomes were quantified burden of vascular calcified plaque in the coronary artery, carotid artery and abdominal aorta all determined from non-contrast computed tomography scans.

  Study phs001012

• Sequencing data of tumor tissue obtained from GANNET53 study patients

  The GANNET53 clinical trial evaulated novel treatment options for ovarian cancer patients with platinum-resistant relapse. Archival fresh-frozen paraffin embedded tissue was available from 131 of the 133 enrolled patients. NGS sequencing aimed at assessing the mutational spectrum of key ovarian cancer genes (with a focus on TP53), and their relevance for therapy resistance. From available FFPE samples, DNA was extracted and NGS sequenced using the SureSeq™ Ovarian Cancer Panel and the NGS Library Preparation kit covering all exons of 7 key ovarian cancer genes BRCA1, BRCA2,TP53, PTEN, ATM, ATR, NF1 for single nucleotide variants (SNV) and indels. Finally, sequence data from 118 individual FFPE tumor tissue samples were generated.

  Study EGAS50000000935

• Comparison of WGBS, EPIC array, EM-seq, and Nanopore sequencing in assessing DNA methylation marks

  Bisulfite sequencing has long been the default method for analyzing methylation marks due to its single base resolution. However, the associated DNA degradation poses a concern for fragmented samples. Although several methods have been proposed to circumvent this issue, there has yet to be a clear consensus on which method is best suited for detecting methylation. We present an overview of the two mostly used and two alternative approaches: whole-genome bisulfite sequencing (WGBS), Illumina methylation microarray (EPIC), Enzymatic Methyl-sequencing (EM-seq) and third-generation sequencing by Oxford Nanopore Technologies (ONT). We evaluated DNA methylation levels in three human genomes derived from tissue, cell line, and whole blood.

  Study EGAS00001008014

• bulk RNAseq analysis of tumor from 3 non-muscle-invasive bladder cancer patients

  We performed screenings of patient-specific neo-epitopes by tumor-infiltrating CD8+ T lymphocytes of 4 non-muscle invasive bladder cancer patients. After the tumor resection, these patients went on to receive BCG treatment as they had high-risk disease. In order to select the neo-epitopes, we performed bulk RNAseq of the bladder tumor to select the mutated genes that were expressed in the tumor (TPM >1). For patient UC2, 3 different tumors were resected at the same time and RNA from these 3 tumors were sent separately for RNAseq. For patient UC4, no RNA was available, so this patient is not included in this study.

  Study EGAS50000001383

• The European Bank for Induced Pluripotent stem cells (EBiSC) is designed to address the increasing demand by iPSC researchers for quality-controlled, disease-relevant research grade iPSC lines, data and cell services.In this study Whole Genome Sequencing was performed on a selection of lines from the project.

  Induced pluripotent stem (iPS) cells have the potential to significantly advance drug development and health research, yet collections of stem cells are scattered across the world, their quality cannot always be guaranteed, and accessing them is often difficult. The goal of EBiSC is to establish a European iPS cell bank that will be the ‘go-to’ resource for the characterisation, storage and distribution of high quality iPS cells. Ultimately, EBiSC will become an independent organisation, distributing high quality iPS cells on a not-for-profit basis to scientists worldwide.

  Study EGAS00001002755

• TRACERx 100: RRBS data from a subset of the first 100 TRACERx tumours

  TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC). This study looks at multi-region RRBS data from the TRACERx100 cohort selected for quantity of material available and high tumour purity. RRBS data was collected for 122 tumour regions across 36 patients each with matched normal. A subset of this cohort was used in a sister study looking at tumour neo-antigen promoter methylation status in NSCLC (71 tumour regions across 28 patients for a total of 99 samples).

  Study EGAS00001003484

• Whole_exome_sequencing_for_clarification_of_rare_causes_of_axonal_Charcot_Marie_Tooth_disease_

  The project is focused on the axonal forms of Charcot-Marie-Tooth (CMT) disease. We have selected 13 families (7 from Spain and 6 from Czech Republic) that have been indepth clinically assessed and previously tested for mutations in known CMT genes without causal variants characterised. In these patients we expect to discover several CMT2 genes. Thus, we requested for exome sequencing of 45 DNAs:27 exomes in families from Spain and 18 exomes in the families from Czech Republic. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002067

• MYOSEQ project

  The MYOSEQ project focuses on the application of next generation sequencing, in particular whole exome sequencing (WES), in a large cohort of patients with unexplained limb‐girdle weakness (LGW). Focusing on undiagnosed patients with a clearly defined clinical phenotype enables increased diagnostic rates for known genes (in particular Pompe disease, GNE related pathologies and other known LGMD subtypes) in this cohort, while the use of WES provides scope both for new gene discovery and for additional research into disease modifiers and genotype‐phenotype correlation with substantial cost effectiveness. The LGW patient cohort was collated by Newcastle University in collaboration with clinical centers across Europe. The sequencing was performed at the Broad Institute and jointly analyzed with Newcastle University.

  Study EGAS00001002069

• Heart Failure: A Controlled Trial Investigating Outcomes of Exercise Training (HF-ACTION-BioLINCC)

  Accessing Data Please refer to “Authorized Access” below regarding accessing data through the BioData Catalyst ecosystem. The data from this accession is not available for download through dbGaP.ObjectivesThe HF-ACTION study examined whether exercise training reduces a composite endpoint of all-cause mortality or all-cause hospitalization for patients with left ventricular systolic dysfunction and heart failure symptoms. Background Heart failure (HF) is a major and growing cardiovascular syndrome that is the end result of many cardiovascular disorders. Although evidence-based drug and device therapies decrease mortality, hospitalizations, and HF symptoms and improve quality of life, many patients treated with these regimens often remain burdened by dyspnea and fatigue, diminished exercise tolerance, reduced quality of life, recurrent hospitalizations, and early mortality. Whereas rest was traditionally recommended for HF patients, there has been evidence that physical deconditioning may play a key role in the progression of symptoms and poor outcomes. Previous studies have shown positive effects of exercise training on exercise capacity, quality of life, and biomarkers and suggest that exercise training might improve survival and decrease HF hospitalizations. Nonetheless, there remains a safety concern regarding exercise training in HF and a large scale, multicenter, controlled clinical trial was needed to provide definitive clinical outcome data. Participants A total of 2,331 participants were randomized. 2,130 consented to share data with non-commercial entities, and 1,753 consented to share for commercial purposes. Design All participants underwent baseline cardiopulmonary exercise testing. Test results were reviewed by investigators to identify significant arrhythmias or ischemia that would prevent safe exercise training, to determine appropriate levels of exercise training, and to establish training heart rate ranges. Demographics, socioeconomic status, past medical history, current medications, physical exam, and the most recent laboratory tests were obtained prior to randomization. All participants received detailed self-management educational materials which included information on medications, fluid management, symptom exacerbation, sodium intake, and physical activity. Participants randomized to the exercise training arm first participated in a structured, group-based, supervised exercise program, with a goal of 3 sessions per week for a total of 36 sessions in 3 months. The primary exercises were walking, treadmill, or stationary cycling. Exercise was initiated at 15 to 30 minutes per session at a heart rate corresponding to 60% of heart rate reserve, and was increased after 6 sessions to 30 to 35 minutes duration and 70% of heart rate reserve. Participants began home-based exercise after completing 18 supervised sessions and were to fully transition to home exercise after 36 supervised sessions. The target training regimen for home exercise was 5 times per week for 40 minutes at a heart rate of 60% to 70% of heart rate reserve. Participants randomized to the usual care group were not provided with a formal exercise prescription. To provide comparable levels of attention from study personnel, all participants were called every 2 weeks for the first 9 months, monthly until 24 months of follow-up, and quarterly thereafter. Participants returned for clinic visits every 3 months for the first 2 years of participation and yearly thereafter for up to 4 years. Follow-up assessments included cardiopulmonary exercise testing, a 6-minute walk test, and a physical activity questionnaire. The primary end point was a composite of all-cause mortality or all-cause hospitalization. Secondary end points included all-cause mortality, the composite of cardiovascular mortality or cardiovascular hospitalization, and the composite of cardiovascular mortality or HF hospitalization. Conclusions After adjustment for highly prognostic predictors of the primary end point, exercise training was associated with modestly significant reductions for both all-cause mortality or hospitalization and cardiovascular mortality or heart failure hospitalization.

  Study phs003599

• Polygenic Risk Score for the Prediction of Breast Cancer Is Related to Lesser Terminal Duct Lobular Unit Involution of the Breast

  The Susan G. Komen Tissue Bank (KTB) at the Indiana University Simon Cancer Center is an annotated biobank, which has recruited healthy women who provided demographic, lifestyle, and cancer-related information via self-administered questionnaire, blood samples and normal breast tissues. H&E slides of the normal breast tissues were scanned for image analysis and a pathologist measured the number of terminal duct lobular units (TDLUs) ("TDLU count"). The acini count per TDLU was quantified using the TDLU analyzer software. In this analysis, we computed the recently developed polygenic risk score (PRS) based on 313 common variants for the prediction of breast cancer and related this PRS to TDLU count and acini count per TDLU. We did this for the overall PRS, the ER-positive PRS and the ER-negative PRS.

  Study phs002062

• Identification of four new susceptibility loci for testicular germ cell tumour, including variants near GAB2, GSPT1 and ZFPM1

  Genome wide association studies (GWAS) have identified multiple risk loci for testicular germ cell tumour (TGCT), revealing a polygenic model of disease susceptibility strongly influenced by common variation. To identify further SNPs associated with TGCT we conducted a multistage GWAS with a combined dataset of >25,000 individuals (6,059 cases and 19,094 controls). We identified new risk loci for TGCT at 3q23 (rs11705932, TFDP2, P = 1.5 x 10-9), 11q14.1 (rs7107174, GAB2, P = 9.7 x 10-11), 16p13.13 (rs4561483, GSPT1, P = 1.6 x 10-8) and 16q24.2 (rs55637647, ZFPM1, P = 3.4 x 10-9). We additionally present detailed functional analysis of these loci, identifying a statistically significant relationship between rs4561483 risk genotype and increased GSPT1 expression in TGCT patient samples. These findings provide additional support for a polygenic model of TGCT risk and further insight into the biological basis of disease development.

  Study EGAS00001001302

• An exome sequencing approach to defining the genetic risk factors for Achilles tendinopathy

  Musculoskeletal soft tissue injuries are complex phenotypes. Case control association studies using the candidate gene approach have predominantly been used to identify risk loci for these injuries. However, the ability to identify all risk conferring variants using this approach alone is unlikely. Therefore, this study aimed to define the genetic profile of these injuries using whole exome sequencing and a customized analysis pipeline. The exomes of ten exemplar asymptomatic controls and ten exemplar cases with Achilles tendinopathy were individually sequenced using a platform that included the coverage of the untranslated regions and miRBase miRNA genes. These results provide a proof of concept for the use of a customized pipeline for the exploration of a larger genomic dataset. This approach, using previous research to guide a targeted analysis of the data has generated new genetic signatures in the biology of musculoskeletal soft tissue injuries.

  Study EGAS00001003234

• ENOC WGS for the study Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

  For ENOC cohorts, OvCaRe cases were reviewed, including frozen material, by at least two expert gynecopathologists prior to inclusion in the sequencing cohort who provided the confirmation on final selected cohort. Frozen H&E from Tokyo were also used for evaluation along with representative H&E photos and review done at the Jikei School of Medicine. For ENOC, DAH985 and DG1288 are recurrent and both were treated with chemotherapy after their first surgery. DAH123 is a untreated sample, metastasis from an primary endometrial tumour. All HGSC, GCT, CCOC and the rest ENOC tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome.

  Dataset EGAD00001003266

• Dataset for CD8-Positive lymphocyte samples

  This dataset contains scRNA sequencing data for CD8-Positive lymphocytes samples. Sequencing was performed on a Illumina NextSeq 550. The sequencing was always paired.

  Dataset EGAD50000000092

• WES data from patient samples at the stage of NDMM and EMM and normal samples

  This contains the raw Whole Exome sequencing data used for the publication

  Study EGAS50000000036

• RNA-seq dataset for gamma delta (γδ) T-ALL patients

  RNA-seq data for 85 patients with acute lymphoblastic leukemia expressing the gamma delta T cell receptor (γδ T-ALL)

  Dataset EGAD50000000027

• Bulk RNAseq of patient samlpes at the stage of NDMM, RRMM without EMM and EMM

  This study contains the raw bulk RNAseq data used for the publication

  Study EGAS50000000035

• Array data for oesophageal and related samples – Ganguli et al (methylation array)

  Array data for oesophageal and related samples – Ganguli et al (methylation array)

  Dataset EGAD00010002682

• EARLY DIAgnosis of PAncreatic Cancer (EARLY DIAPAC) study

  Whole genome sequencing of pancreatic cyst fluid for early detection and diagnosis of pancreatic cancer.

  Study EGAS50000000611

• Helse Bergen HF Data Access Committee for the MetBreCS trial dataset submitted to Federated EGA Norway

  This Data Access Committee is appointed by Helse Bergen HF to administer access requests for the MetBreCS trial dataset submitted to Federated EGA Norway.

  Dac EGAC50000000523

• DAC for Single cell RNA sequencing of peripheral blood HSPC from patients with sickle cell anemia and healthy donors.

  Data access comittee for Single cell RNA sequencing of peripheral blood HSPC from patients with sickle cell anemia and healthy donors.

  Dac EGAC50000000650

• Genomic sequencing data for PNG15 and PNG16

  This data set contains genomic sequencing data and variant calls for PNG15 and PNG16.

  Dataset EGAD50000001598

• shallow Whole-Genome sequencing of 14 TNBC tumor in the MATADOR trial - for in silico spike-in experiment

  14 TNBC tumors with tumor percentage ~90% were selected for in silico spike-in experiment

  Dataset EGAD50000001863

• scRNAseq dataset of vitligo dermis and epidermis

  scRNAseq dataset of vitligo dermis and epidermis for 6 patients. For each patient nonlesional and perilesional skin were sampled and processed separately.

  Dataset EGAD50000001874

• NAR-GAB 2025 deposit data

  Human exome gVCFs: rare-disease cohort for the NAR-GAB 2025 study on splicing-SNV prioritization.

  Study EGAS50000001456

• HICHIP_TALL_t_14_16_translocation

  For patient P01, HiChIP experiment for was performed using the Arima-HiC+ kit (A510008, Arima genomics) according to the manufacturer’s protocols.

  Dataset EGAD50000002167

• Primary Neuroblastoma Circle-seq

  We generated Circle-seq data for primary neuroblastoma to describe the landscape of extrachromosomal circular DNA in neuroblastoma.

  Study EGAS00001004797

• Res1_PC9_exp2_MC_01_04_22

  8 cell pellet samples for genomic DNA extraction. CRISPR PCR1 and PCR2 indexing - Please use standard Kosuke primers.

  Study EGAS00001006170

• V4_panel_bait_design_test

  Targeted gene screen of FFPEs, cell lines and primary tumours for testing the new V4 Cancer gene panel.

  Study EGAS00001001808

• Myeloma_Follow_up_Pilot

  Targeted capture of exonic and intronic regions of interest for the study of genomic alterations in multiple myeloma.

  Study EGAS00001000743

• Res1_PC9_exp1_MC_29_03_22

  8 cell pellet samples for genomic DNA extraction. CRISPR PCR1 and PCR2 indexing - Please use standard Kosuke primers.

  Study EGAS00001006169

• Res1_H23_exp2_MC_13_07_22

  8 samples are cell pellets for genomic DNA extraction. CRISPR PCR1 and PCR2 indexing - Please use standard Kosuke primers.

  Study EGAS00001006683

• WXS files for Mullighan BiTE WXS

  WXS files for Mullighan BiTE WXS paper titled "Tumor intrinsic and extrinsic mechanisms of response and resistance to blinatumomab in relapsed/refractory acute lymphoblastic leukemia"

  Dataset EGAD00001005730

• Whole-genome sequencing data for 449 Nigerian individuals

  Whole-genome sequencing data in the form of multi-sample, per-chromosome VCFs for n=449 individuals across 47 unique ethnolinguistic groups.

  Dataset EGAD00001010095

• RNASeq files for Mullighan Leventaki ALCL Project

  RNASeq files for Mullighan Leventaki ALCL Project paper titled "Integrative molecular analysis of pediatric Anaplastic large cell lymphoma reveals subtypes with distinct immune suppression signatures."

  Dataset EGAD00001005951