4078 results for "*geneti*"

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• LifeChange Data Access Committee

  The LifeChange study aimed at tracking the biological consequences of the societal changes undergone by the Yakut people of Far Eastern Siberia, after the colonization of the region by Russians in the 17th century. This study builds upon more than 15 years of archaeological research conducted in Yakutia, Sakha Republic, an autonomous region of the Russian Federation located in northeastern Siberia. The fieldwork was conducted under the MAFSO program (“Mission Archéologique Française en Sibérie Orientale”, or “French Archaeological Mission in Eastern Siberia”), a collaboration between French researchers and local Yakut experts, including scholars from North-Eastern Federal University in Yakutsk. The program was supported by several inter-university collaborative research agreements, notably between Université Paul Sabatier, Krasnoyarsk State Medical University, and North-Eastern Federal University in Yakutsk. It also received endorsement from the Institute of Ecology and Evolution at CNRS through the International Associated Laboratory “Co-evolution Human-Environment in Eastern Siberia”. The LifeChange Data Access Committee, composed of French and Russian archaeogeneticists, geneticists and archaeologists, reviews any access request to LifeChange data, consisting of genomes of ancient and modern Yakut, Eveni and Evenki individuals sampled in Eastern Siberia for the LifeChange study. The DAC grants access to any academic researcher aiming to study the population history of autochthonous peoples from Siberia. When reviewing data access requests, the DAC members ensure that the applicant will not re-use the data to trace present-day descendants of studied ancient individuals. They also ensure that secondary use of the modern genomic data is conducted in full respect of the conditions stipulated in living participants’ informed consent. Specifically, the applicant is not authorised to (i) use the data for diagnostic purposes, (ii) store the data outside of secure servers, (iii) reidentify research participants, and (iv) share the data with a third party.

  Dac EGAC50000000713

• UMCG Immunogenetics DAC

  DAC for the data generated in the Immunogenetics group in the genetics department of the University Medical Center Groningen

  Dac EGAC50000000785

• ATACseq in blood-derived monocytes from CGD patients

  Study EGAS00001005915

• Idiopathic Scoliosis (SNP-array & WES study)

  This study aimed to investigate the genetic basis of severe idiopathic scoliosis (IS) using whole exome sequencing (WES) and SNP array methods. We intended to identify structural and point genetic variations contributing to the development of IS. By analyzing intraoperatively collected articular processes (AP) and blood (BL) samples from 70 unrelated individuals with IS, we sought to uncover pathogenic copy number variants (CNVs), regions of homozygosity (ROH), and single-nucleotide variants (SNVs) linked to the condition. EGAD00001015758

  Study EGAS00001008152

• NHLBI TOPMed: San Antonio Family Heart Study (SAFHS)

  The San Antonio Family Heart Study (SAFHS) is a complex pedigree-based mixed longitudinal study designed to identify low frequency or rare variants influencing susceptibility to cardiovascular disease, using whole genome sequence (WGS) information from 2,590 individuals in large Mexican American pedigrees from San Antonio, Texas. The major objectives of this study are to identify low frequency or rare variants in and around known common variant signals for CVD, as well as to find novel low frequency or rare variants influencing susceptibility to CVD. WGS of the SAFHS cohort has been obtained through three efforts. Approximately 540 WGS were performed commercially at 50X by Complete Genomics, Inc (CGI) as part of the large T2D-GENES Project. The phenotype and genotype data for this group is available at dbGaP under accession number phs000462. An additional ~900 WGS at 30X were obtained through Illumina as part of the R01HL113322 "Whole Genome Sequencing to Identify Causal Genetic Variants Influencing CVD Risk" project. Finally, ~1,150 WGS at 30X WGS were obtained through Illumina funded by a supplement as part of the NHLBI's TOPMed program. Extensive phenotype data are provided for sequenced individuals primarily obtained from the P01HL45522 "Genetics of Atherosclerosis in Mexican Americans" for adults and R01HD049051 for children in these same families. Phenotype information was collected between 1991 and 2016. For this dataset, the SAFHS appellation represents an amalgamation of the original SAFHS participants and an expansion that reexamined families previously recruited for the San Antonio Family Diabetes Study (R01DK042273) and the San Antonio Family Gall Bladder Study (R01DK053889). Due to this substantial examination history, participants may have information from up to five visits. The clinical variables reported are coordinated with TOPMed and include major adverse cardiac events (MACE), T2D status and age at diagnosis, glycemic traits (fasting glucose and insulin), blood pressure, blood lipids (total cholesterol, HDL cholesterol, calculated LDL cholesterol and triglycerides). Additional phenotype data include the medication status at each visit, classified in four categories as any current use of diabetes, hypertension or lipid-lowering medications, and, for females, current use of female hormones. Anthropometric measurements include age, sex, height, weight, hip circumference, waist circumference and derived ratios. PBMC derived gene expression assays for a subset of ~1,060 individuals obtained using the Illumina Sentrix-6 chip is also available from the baseline examination. The WGS data have been jointly called and are available in the current TOPMed accession (phs001215).

  Study phs001215

• NHGRI GREGoR Consortium: Genomics Research to Elucidate the Genetics of Rare Disease

  The NHGRI GREGoR (Genomics Research to Elucidate the Genetics of Rare Disease) Consortium was established in June 2021 with the goal of developing novel tools and approaches to advance the discovery of the genetic basis of rare conditions. Numerous types of molecular data are generated in GREGoR and available on the AnVIL cloud platform via dbGaP application, including short- and long-read genome and exome sequencing, transcriptomics, metabolomics, methylomics, and proteomics. De-identified clinical and demographic data is obtained, with a focus on standardized ontologies.Visit the GREGoR Consortium data webpage for summary information about the GREGoR Dataset, including numbers of participants and data types, methods documentation, and Release Notes. The Consortium comprises five Research Centers (RCs - see below), a Data Coordinating Center (DCC), and various partner members and external collaborators.Baylor College of Medicine Research Center (BCM-GREGoR) The Baylor College of Medicine GREGoR program, which is part of the GREGoR consortium, enrolls individuals, families, and cohorts with suspected rare disease across a range of syndromic and non-syndromic phenotypes. Subjects are enrolled from national and international collaborating physician referrals. Subjects provide written informed consent for future re-contact. Data generated and shared include family structure, detailed phenotypes, exome or short-read genome data, and in some cases long-read genome or RNA-sequencing, and these are shared upon completion of standard quality control checks and annotation. Broad Institute (Broad) The Broad Center for Mendelian Genomics, part of the GREGoR consortium uses next-generation sequencing (exome, genome, transcriptome, and long read sequencing), computational approaches, and functional studies to discover the variants and genes that underlie Mendelian conditions with a particularly focus on neuromuscular, neurodevelopmental, and syndromic phenotypes. Samples come from collaborators and direct enrollment through the Rare Genomes Project and we are committed to rapid data sharing without an embargo period. University of California, Irvine (UCI-GREGoR) To accelerate the pace of Mendelian disease gene discovery and clinical implementation, we propose a Mendelian Genomics Research Center, part of the GREGoR Consortium, leveraging the broad pediatric and adult clinical and research expertise at Children's National Hospital and University of California, Irvine. Our goal is to develop best practices to increase the diagnostic yield of rare diseases, engage the community to reduce health disparities for complex diagnoses, while creating a dataset accessible to all. Our Center will unite world class experts combining basic and translational research with innovative approaches to phenotyping, variant identification and functional investigation of both coding and non-coding sequence changes with the goals of discovering novel Mendelian gene variations and identifying variants not detected on current sequencing pipelines, disambiguating uncertain variants into disease-causing versus benign categorizations, and sharing information by working collaboratively with the GREGoR community.GREGoR Stanford Site (GSS) The goal of the GREGoR Stanford Site (GSS) is to provide a platform for functional genomics research and validation to improve diagnosis in Mendelian disease. Participants included individuals with undiagnosed suspected Mendelian disease who had non-diagnostic exome sequencing and their immediate family members. Participants and their family members provided written, informed consent and biological samples from which DNA, RNA, plasma, fibroblasts, PBMCs and other cell types were generated and stored. Samples from research participants and their immediate family members may have undergone short and long-read genome sequencing, transcriptome sequencing, metabolomics and/or lipidomics profiling, methyl-capture-sequencing and ATAC-sequencing. De-identified clinical data extracted from participant medical records are linked to the samples. University of Washington Center for Rare Disease Research (UW-CRDR) The goals of the University of Washington Center for Rare Disease Research are to: (1) maximize novel gene discovery for Mendelian conditions by recruitment, short- and long-read whole genome sequencing, transcriptome sequencing and analysis of families with rare conditions for which the gene is either unknown or the gene is known but no pathogenic variant can be identified via clinical testing; (2) develop new strategies for gene discovery for Mendelian conditions caused by variants that are difficult to detect using conventional testing strategies, variants of unknown function effect (e.g., regulatory, structural variants) or have unusual modes of inheritance; and (3) implement high-throughput screening and targeted follow-up functional studies to prioritize and validate candidate non-coding variants. De-identified data and phenotypic information are shared via MyGene2, ClinVar, and AnVIL.

  Study phs003047

• Genome-wide methylation profiling by high-throughput sequencing of tissue (resident) versus blood circulating memory T lymphocyte populations

  This study contains RRBS data generated from 54 ex vivo samples, including CD4+ Trm (2x intestine, 2x lung, and 3x skin), CD4+CD69- tissue cells (2x bone marrow, 2x spleen, 2x intestine, 2x lung, and 3x skin), CD8+ Trm (2x bone marrow, 2x spleen, 2x intestine, 2x lung, and 3x skin), CD8+CD69- tissue cells (2x bone marrow, 2x spleen, 2x intestine, 2x lung, and 2x skin), blood CD4+ (7x) and CD8+ (8x) memory T cells.

  Study EGAS50000000085

• Khoe-San genome Project (KSGP)

  The Khoe-San Genome Project (KSGP) includes whole genome data generated for 190 study participants from Southern Africa (Namibia and South Africa) representing people speaking a Namibian Khoe-San language (n=150, 12 groups) or regional non-Khoe-San groups (n=40), specifically defined here as Namibian Himba (n=10), South African Southern Bantu (n=12 and representing the Ubuntu Genome Project led by the University of Limpopo) or South African Coloured/European (n=18). Deep whole genome data has been generated for the purposes of cataloguing the extent of regional genetic diversity, creating population specific references and evolutionary trajectories, while creating a population-matched panel of normal (PoN) genetic diversity required for disease associated studies across the region.

  Dac EGAC50000000798

• 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

• A Case Controlled Etiologic Study of Sarcoidosis (ACCESS-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. Access to Biospecimens is through the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biospecimens from (ACCESS) include Bronchial Lavage, DNA, Peripheral Blood Mononuclear Cells, and Plasma. Please note that use of biospecimens in genetic research is subject to a tiered consent. Objectives: To determine the etiology of sarcoidosis by establishing a case control, multi-center study. In addition to etiology, this study also sought to examine socioeconomic variables and the clinical course of patients with sarcoidosis, including quality of life.Background: Sarcoidosis is a chronic granulomatous disorder of unknown cause that is characterized by activation of T-lymphocytes and macrophages. For many years, sarcoidosis was presumed to be an atypical manifestation of tuberculosis because of the similarity between the inflammatory responses of the two diseases. However, as culture techniques became more widely employed to diagnose tuberculosis and it became less common, it became clear that sarcoidosis was not simply a variation of tuberculosis. Data on the etiology of sarcoidosis have come from diverse sources: in clinical investigations, alveolitis has been found to precede granulomatous inflammation; in case control studies, familial aggregation has been identified; and in case reports, recurrence of granulomatous inflammation has been observed after lung transplantation. The cause may not prove to be a single, known exposure. Interactions of exposures with genetic dispositions could have important implications for our understanding of immune responses as well as the pathogenesis of sarcoidosis.Participants: 736 participants with sarcoidosis enrolled within 6 months of diagnosis from 10 clinical centers in the U.S. Using the ACCESS sarcoidosis assessment system, organ involvement was determined for the whole group and for subgroups differentiated by sex, race, and age (Conclusions: The initial presentation of sarcoidosis is related to sex, race and age, and it tends to remain stable over two years in the majority of patients. The etiology is probably multifactoral with both genetic and environmental factors contributing.Specimen Details: The PBMC for this study are pelleted and suspended in guanidinium-based solution and are nonviable.

  Study phs004276