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• NHLBI TOPMed: Whole Genome Sequencing of Venous Thromboembolism (WGS of VTE)

  This study consists of 338 VTE cases from an inception cohort of Olmsted County, MN residents (OC) with a first lifetime objectively-diagnosed idiopathic VTE during the 40-year study period, 1966-2005. All living study subjects were invited to provide a whole blood sample at the Mayo Clinical Research Unit for leukocyte genomic DNA and plasma collection. For living study subjects who did not provide a blood sample, we retrieved any leftover blood ("waste" blood) from samples collected as part of routine clinical diagnostic testing and used this to extract DNA after obtaining patient consent. For deceased cases, with IRB approval, we extracted DNA from any available stored tissue within the Mayo Tissue Archive. This "tissue" DNA has been successfully genotyped in prior studies. Three trained and experienced study nurse abstractors reviewed the complete medical records in the community of all potential cases. Note: WGS sample IDs for the previous GENEVA study cases (phs000289) are included in this dataset. The phenotypes for the GENEVA study are located under the above phs number.

  Study phs001402

• Coronary Artery Risk Development in Young Adults (CARDIA-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.Related Studies: Other CARDIA data available include:phs000236.v2.p2 PAGE: CALiCo: Coronary Artery Risk Development in Young Adults(CARDIA) phs000309.v3.p2 The CARDIA-GENEVA Study phs000399.v1.p2 NHLBI GO-ESP: Heart Cohorts Exome Sequencing Project (CARDIA) phs000613.v1.p2 NHLBI CARDIA Candidate Gene Association Resource (CARe) phs003675.v1.p1 CARDIA Multi-omics Obesity & CVD Substudy – Year 20 Untargeted Metabolomics Data phs001612.v3.p2 NHLBI TOPMed: CARDIA (Coronary Artery Risk Development in Young Adults) phs003045.v1.p1 Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Coronary Artery Risk Development in Young Adults Study (CARDIA) phs000285.v4.p3 CARDIA_Cohort Available Data: Available data for request include exam data through Year 30 and outcomes and death data through 2022. Additionally, data from 28 ancillary studies are available for request.Objectives: The original objectives of CARDIA were to document levels of risk factors for coronary artery disease and potential determinants of these risk factors in young adults; to study the interrelationships of risk factors and lifestyles and to document behavioral and environmental changes during the transition from young adulthood to middle age; to compare cross-sectional and longitudinal data on age-related trends in cardiovascular disease risk factors; and to compare levels and evolution of risk factors between men and women, blacks and whites, and in groups of differing socioeconomic status. Goals of the study have evolved to emphasize understanding determinants of left ventricular mass, emerging obesity and hypertension, and sequelae of hypertension in pregnancy.Background: CARDIA is designed to increase understanding of contributors to changes in cardiovascular disease (CVD) risk factors during the critical years of transition from young adulthood to middle age. CARDIA was funded initially in 1983 for a five-year cycle that included two rounds of examinations. Contract renewals have allowed for subsequent re-examinations.Participants: Black and white men and women; ages 18-30 years at entry with a range of attained education; original sample size: 5,115.Design: CARDIA is a population-based observational study of 5,115 participants aged 18-30 years recruited in 1985-1986. The sample was designed to achieve approximately balanced subgroups of race, gender, education (high school or less and more than high school) and age (18-24 and 25-30). Forty percent of the cohort had no more than a high school education. A total of nine examinations have been completed in the cohort with examination cycles at year 2 of the project and years 5, 7, 10 , 15, 20, 25, and 30.In addition to standard measurements of blood pressure, anthropometry, blood lipids, smoking behavior, physical activity, diet, pulmonary function, and many psychological factors, CARDIA has other included measurements (in subsets or in the full cohort) to obtain unique information on other aspects of risk factor development and early morbidity. These have included: graded exercise treadmill testing; echocardiography, particularly for measurement of left ventricular mass; cardiovascular reactivity; serum cotinine; Lp(a), apoE phenotype, apolipoprotein A1 and B; homocysteine; skin reflectance; body composition by dual X-ray absorptiometry; glucose tolerance testing; vascular resistance and compliance; and plasma renin activity and sympathetic nervous system activity.

  Study phs003739

• LRS - episignature samples

  This dataset contains 22 long-read WGS fastq.gz files sequenced ONT PromethION. In total the dataset includes 20 individuals, for all of them sequencing starting from blood was performed, and for one of the samples sequencing from urine and from the buccal swab was also included. In all the samples methylation calls are included in the fastq file.

  Dataset EGAD50000001000

• Spatial Transcriptomics of Pulmonary Vascular Remodelling in IPAH

  In compliance with the research ethics and governance under which these data and samples have been collected, the transcriptomic data are available through restricted access for approved researchers who agree to the conditions of use, i.e. keeping it secure and only using it for approved purposes. To apply for access please contact either a.lawrie@imperial.ac.uk, m.keles@imperial.ac.uk, b.wojciak-stothard@imperial.ac.uk.

  Dac EGAC50000001023

• Genomic Analysis of Follicular Lymphoma

  We included tumors from newly diagnosed or untreated follicular lymphoma in this study. Samples consented to the University of Iowa and Mayo Clinic Lymphoma Specialized Program of Research Excellence (SPORE) were included for data sharing. RNA was extracted from 1) CD19 sorted B cells from tumor cell suspension frozen in dimethyl sulfoxide (DMSO; RNA Tumor B Cell, n=77), 2) tumor cell suspensions frozen in DMSO (RNA Tumor DMSO, n=78), and 3) tumor tissue sections frozen in optimal cutting temperature compound (OCT; RNA Tumor OCT, n=53). For RNA sequencing, library preparation was done using the Illumina TruSeq RNA Exome Kit and sequenced with 100 nucleotide paired-end reads using the HiSeq 4000. DNA was extracted from 1) tumor cell suspensions frozen in DMSO (DNA Tumor DMSO, n=78), 2) tumor tissue sections frozen in OCT (DNA Tumor OCT, n=33), and 3) germline DNA from peripheral blood (n=102) and from normal tissue adjacent tumor (n=9). For whole exome sequencing (WES), library preparation was done using the Agilent SureSelect XT kit and sequenced with 100 nucleotide paired-end reads using the Illumina HiSeq 4000.

  Study phs002989

• Identification of 19 novel loci reveals gene regulatory mechanisms determining susceptibility to testicular germ cell tumour

  Testicular germ cell tumour (TGCT) is the most common cancer in young men1,2, and is characterised by strong inherited genetic risk factors3. Here we have undertaken large-scale genome wide association study (GWAS) for TGCT, encompassing ~7,500 cases and ~23,000 controls, through the Oncoarray consortium. We identified 19 novel loci, approximately doubling the number of known TGCT risk loci to 44 (P<5x10-8)4-14 and conduct deep, high-throughput functional annotation of all risk loci. We establish a network of physical interactions for all risk SNPs to candidate casual genes in 3D space, using high-throughput chromosome conformation capture techniques (HiC) in TGCT cells. Firstly, functional evidence reveals widespread disruption of developmental transcriptional regulators, consistent with failed primordial germ cell differentiation as an initiating step in TGCT oncogenesis15. We secondly observe multiple risk loci associated with defective microtubule assembly, compatible with the high level of aneuploidy observed in TGCTs, suggesting gross chromosomal instability. Finally KIT-MAPK signalling features as a recurrently dysregulated pathway. In summary our findings substantially increase the number of known TGCT risk alleles, and provides a functional basis for disease susceptibility.

  Study EGAS00001001836

• Indexing Genes Impacted by Copy Number Variation in Developmental Disorders

  A challenge in clinical genomics is to predict whether copy number variation (CNV) affecting a gene or multiple genes will manifest as disease. Increasing recognition of gene dosage effects in neurodevelopmental disorders prompted us to develop a computational approach based on critical-exon (highly expressed in brain, highly conserved) examination for potential etiologic effects. Using a large CNV dataset, our updated analyses revealed significant (P < 1.64 x 10-15) enrichment of critical-exons within rare CNVs in cases compared to controls. Separately, we used a weighted gene co-expression network analysis (WGCNA) to construct an unbiased protein module from prenatal and adult tissues and found it significantly enriched for critical exons in prenatal (P < 1.15 x 10-50, OR = 2.11) and adult (P < 6.03 x 10-18, OR = 1.55) development. WGCNA yielded 1,206 proteins for which we prioritized the corresponding genes as likely to have a role in neurodevelopmental disorders. We compared the gene lists obtained from critical-exon and WGCNA analysis and found 438 candidate genes associated with CNVs annotated as pathogenic, or variants of uncertain significance (VOUS), from among 10,619 developmental delay cases. We identified genes containing CNVs previously considered to be VOUS, to be new candidate genes for neurodevelopmental disorders (GIT1, MVB12B and PPP1R9A) demonstrating the utility of this strategy to index the clinical effects of CNVs. Reprinted from Uddin et al, 2016, with permission from Scientific Reports.

  Study phs001154

• A Combined Omics and Tissue Biobank for Paediatric Cancers

  The Swedish Childhood Tumour Biobank (BTB) is a nonprofit national infrastructure for samples and genomic data collection from pediatric patients diagnosed with central nervous system and other solid tumours in Sweden. Fresh frozen tumour tissue and patient’s matched blood are collected from affected patients and genomic data is continuously generated and made available for approved medical research projects. We expect that the accessibility of biological samples and/or data to the research community will contribute to further advances in the understanding of tumour biology, which in turn will impact many aspects of clinical care of children with cancer, by refining diagnosis and/or identifying oncogenic drivers and therapeutic targets.

  Study EGAS50000000209

• Correction of the cytosine deamination artifacts in FFPE-based sequencing experiments

  Formalin-fixed paraffin-embedded (FFPE) samples are widely used in research and diagnostics, but cytosine deamination during fixation introduces sequencing artifacts, particularly C>T substitutions, which complicate reliable mutation detection. In this study, we systematically evaluated five computational methods and an enzymatic repair approach for FFPE artifact removal, as well as their combined application, using a custom dataset based on whole exome sequencing. Our results demonstrate that while computational strategies improve data quality, the enzymatic approach provides the most effective artifact correction. The study provides guidelines for both computational and enzymatic artifact correction strategies for reliable downstream analyses. This project was funded by the Polish National Science Centre, grant no. 2021/41/B/NZ2/04134.

  Study EGAS50000001354

• DAC for "Pyjacker identifies enhancer hijacking events in acute myeloid leukemia including MNX1 activation via deletion 7q"

  This is the DAC for the study "Pyjacker identifies enhancer hijacking events in acute myeloid leukemia including MNX1 activation via deletion 7q" of Christoph Plass (c.plass@dkfz.de).

  Dac EGAC50000000472