3613 results for "*geneti*"

in 43.98 milliseconds.

• Long-Term Isolation and Archaic Introgression Shape Functional Genetic Variation in Near Oceania

  We generated 175 whole-genome sequences (WGS) from 12 populations across the Bismarck Archipelago and Bougainville (Papua New Guinea). We used these data to infer the evolutionary history of these populations, quantify levels of Neandertal and Denisovan ancestry, detect signatures of positive selection, and functionally characterize genetic variants introgressed from Neandertals and Denisovans. FASTQ files for 175 individuals and variant calls jointly genotyped with a larger dataset of worldwide humans are made available. These genotype calls include samples from the Human Genome Diversity Project (HGDP, PRJEB6463), HGDP samples sequenced by the Simons Genome Diversity Project (SGDP, PRJEB9586), as well as samples from Vernot et al. 2016 (phs001085.v1.p1) and Tucci et al. 2018 (phs001633.v1.p1).

  Study phs004464

• Childhood Cancer Data Initiative (CCDI): Texas Pediatric Patient Derived Xenograft 

  The DNA/RNA samples of patients for which PDX models were developed were from a population of children, adolescents, and young adults from South Texas. Consent was obtained for collection of malignant and non-malignant tissue samples for genetic analysis and for the development of models to study new ways to treat cancer. For additional details, please refer to these publications: PMID: 37915590; PMID: 37990009.

  Study phs003215

• Lipid Research Clinics - Prevalence Study (LRC-PS-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 LRC Program began in 1971 under the sponsorship of the National Heart, Lung, and Blood Institute, National Institutes of Health. Part of this program was the Lipid Research Clinics Prevalence Study, a standardized series of cross-sectional surveys of various North American populations designed to determine the prevalence of dyslipidemias and to describe the distributions of lipids and lipoproteins in major ethnic and social groups. In addition to contributing to the aggregate analysis, each independent population-based study was designed with capabilities for separate analyses of lipid and lipoprotein distributions. The participating populations were not selected to be a probability sample representative of the North American population per se, but by virtue of their size and economic and geographical diversity, they provide a useful cross-sectional group. The Family Study was the third phase of the Lipids Research Clinics North American Population Studies. The Family Study was designed to obtain knowledge of the distribution of lipids and lipoproteins among family members and of the association of familial and genetic attributes to dyslipoproteinemias. Background: An association between serum cholesterol and coronary heart disease is well established. A system was developed for classifying hyperlipoproteinemias into six types of patterns, as a basis for characterizing lipoprotein disorders. The Lipid Research Clinics was thus created to improve the detection of and clinical management of hyperlipoproteinemias. The three primary objectives were: 1) to acquire data on the prevalence of different types of hyperlipoproteinemia in various age and ethnic groups, with special emphasis on the nature and frequency of genetic forms; 2) to collect reliable data on the prevalence and incidence of atherosclerosis in different types of hyperlipoproteinemia; and 3) to conduct an intervention trial to determine if lowering plasma lipid levels would reduce the risk of CHD. Participants: There were 60,495 participants. Conclusions: Data from this study confirm findings from earlier studies in developed countries, showing age-related differences in plasma lipid levels. However, for overall distributions, the LRC data showed slightly lower cholesterol and markedly higher trigylceride values than those previously reported for North America. Some variation in plasma lipid values was evident among the clinic populations. The large number of participants within most subgroups permitted a variety of analytic and comparative studies. For example, data from the large pediatric population revealed a drop in plasma cholesterol levels in adolescent males and females. Males aged 20-50 years had higher cholesterol levels than females in the same age group, and higher trigylceride levels between ages 20-70 years. Numbers were also significient for meaningful comparisons between lipid distributions of females who were taking sex hormones and those who were not; in females taking sex hormones, cholesterol and triglyceride levels were higher for subjects younger than 45 years, but slightly lower after age 45, than lipid levels in females not taking hormones (Circulation 1979; 60(2):427-439).

  Study phs003995

• Veterans Administration (VA) Million Veteran Program (MVP) Summary Results from Omics Studies

  MVP is an ongoing prospective cohort study and mega-biobank in the Department of Veterans Affairs Healthcare System designed to study genetic influences on health and disease among veterans.

  Study phs001672

• KOLF2.1J iPSC and Differentiated Cell Types

  KOLF2.1J is a human induced pluripotent stem cell (iPSC) line that was selected and characterized by the iPSC Neurodegenerative Disease Initiative (iNDI) as a community reference line to support large-scale, collaborative research, with particular emphasis on neurodegenerative disease modeling. The line was generated as a sub-clone of the parental KOLF2-C1 iPSC line, which was originally reprogrammed from fibroblasts obtained from a male donor of European ancestry under informed consent and appropriate ethical approvals. During sub-cloning, a heterozygous 19-bp deletion in ARID2 present in the parental line was corrected, yielding a clonally derived line with a low burden of deleterious variants and no known high-risk alleles for neurodegenerative disease, making it well suited as a neutral genetic background for disease modeling.KOLF2.1J demonstrates robust and reproducible pluripotency, high genomic stability in culture and after gene editing, efficient CRISPR editing, and reliable tri-lineage differentiation potential, with performance validated across multiple independent laboratories. The KOLF2.1J has been chosen as a high-quality, broadly applicable reference iPSC line suitable for adoption as a common cellular substrate to reduce inter-line variability and facilitate cross-laboratory data integration. To enable widespread use, KOLF2.1J and a growing collection of gene-edited isogenic derivative clones have been made openly available to the research community. More details can be found in Pantazis et al., "A reference human induced pluripotent stem cell line for large-scale collaborative studies", Cell Stem Cell (2022); doi: https://doi.org/10.1016/j.stem.2022.11.004.Building on this foundation, the present study extends the genomic characterization of KOLF2.1J using long-read and long-range sequencing to generate a complete, telomere-to-telomere reference assembly, together with matched long-read genomic, epigenetic and long- and short-read based expression data from differentiated derivative cell types. This work is described in the accompanying preprint Alvarez Jerez et al., "The complete genome of the KOLF2.1J reference iPSC line", bioRxiv (2026); doi: https://doi.org/10.64898/2026.03.06.710144. Data available through this dbGaP study include newly generated long-read sequencing data of the parental KOLF2.1J iPSC line and the differentiated cell lines (astrocytes, cortical neurons, NGN2-derived neurons, microglia, and oligodendrocytes) derived from the parental KOLF2.1J, along with corresponding expression data, and the assembled Y chromosome sequence. The assembled Y chromosome will be shared under controlled access for research use only, given the heightened re-identification risk associated with Y chromosome sequence data. The full diploid assembly, excluding the Y chromosome, is available through GenBank under BioProject PRJNA1478016.

  Study phs004798

• Cutaneous Squamous Cell Carcinoma: Integrating Germline and Somatic Alterations that Underlie Tumor Progression

  Cutaneous squamous cell carcinoma (cSCC) is the second most common cancer in the United States, affecting over a million people annually, and with significant mortality due to metastasis. The overall scientific objective of this study is to identify and integrate novel tumor mutational data with previously characterized information on host genetic risk factors and clinical risk factors to better understand how cancer risk alleles contribute to the development of cSCCs capable of metastasis. We analyze 290 cSCCs (145 primary cSCCs) that progressed to metastasis and 145 non-metastatic primary cSCCs arising in the well characterized GERA cohort to provide a comprehensive landscape of genomic alterations in cSCCs. The aims of the study are: a) characterize the somatic genome and transcriptome of metastatic and non-metastatic cSCCs, b) integrate somatic mutational analysis with environmental exposure data, and c) develop a risk prediction tool for metastatic-cSCC that integrate genomic and clinical data.

  Study phs003681

• 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

• Genes in Diabetic Retinopathy Project (DRCRnet-Genes)

  The "Genetics in Retinal Diseases Project" (Protocol-GEN) is an ongoing effort to create a repository of genetic material and clinical phenotype information as a resource for the research community, both public and private institutions. Blood samples are collected from consented participants from Diabetic Retinopathy Clinical Research (DRCR) Retina Network trials and sent to a qualified laboratory to harvest DNA and store the materials. This bioresource is available to the research community (e.g., government, academic centers, and industry) who may request samples, together with detailed clinical data, for genotypic analyses. When complete, the project will create a resource that combines high-quality genetic material and uniquely detailed phenotype information.The Network collaborated with Regeneron's Genetics Center for the sequencing of 2,084 samples, with both whole exome and genotype array data, as well as relevant phenotype data for the 8* completed studies (n = 2,074) are available for further analysis efforts. Of these, 850 samples of DME-only patients treated with anti-VEGF agents for 6 or 12 months were included in a GWAS study by the Network, in collaboration with the Mass Eye & Ear Infirmary (MEEI), for statistical analysis of the pharmacogenetics of treatment responses. Quality controlled genotypes from Illumina's Infinium Global Screening Array were imputed using the TOPMed reference panel. Both change in central subfield thickness (CST) and visual acuity (VA) were examined as co-primary phenotype endpoints, with several additional secondary outcomes and time to response. Linear and logistic regression were applied (PLINK2.0) to quantitative and dichotomous outcomes, respectively, on all samples and subpopulations (EUR, AFR, AMR) separately, adjusting for 10 genotype PCs, age, sex, HbA1c, diabetes type and duration, hypertension prior treatment, DR severity, baseline ETDRS and CST, and type/number of anti-VEGF agents received in 6 and 12 months. A cross-ancestry meta-analysis was performed on the 6-month time point using METAL. Replication of significant associations were pursued in a second independent sample set. To prioritize causal genes and pathways, gene and gene-set level association testing was performed using MAGMA. Colocalization analysis between expression and slicing QTLs (e/sQTLs) and significant GWAS loci was performed to further prioritize causal genes for genome-wide significant loci.Multiple loci were significant at a genome-wide significance (PPPIL3 and BICC1. Colocalization analyses with expression and splicing QTLs from GTEx tissues and retina further proposed putative causal genes for several loci. In replication analyses with a second, independent study, one locus on chromosome 5 passed genome-wide significance with a consistent direction of effect between the discovery cohort and replication cohort.Data available through dbGaP includes the entire genotype/sequencing dataset (2,084 samples), supporting documentation including SNP array and CNV calls derived from the sequencing, a linking table for accessing associated phenotype from the completed clinical trials (2,074 samples; URLs are listed in table below), and the GWAS/linkage results (851 samples). ProtocolProtocol DescriptionSamples AvailablePublic DatasetIIntravitreal Ranibizumab or Triamcinolone Acetonide in Combination with Laser Photocoagulation for Diabetic Macular Edema277DownloadMEffect of Diabetes Education during Retinal Ophthalmology Visits on Diabetes Control294DownloadSPrompt Panretinal Photocoagulation versus Intravitreal Ranibizumab with Deferred Panretinal Photocoagulation for Proliferative Diabetic Retinopathy196DownloadTA Comparative Effectiveness Study of Intravitreal Aflibercept, Bevacizumab and Ranibizumab for Diabetic Macular Edema460DownloadTXA Comparative Effectiveness Study of Intravitreal Aflibercept, Bevacizumab and Ranibizumab for Diabetic Macular Edema – Follow-up Extension Study5DownloadUShort-term Evaluation of Combination Corticosteroid+Anti-VEGF Treatment for Persistent Central-Involved Diabetic Macular Edema Following Anti-VEGF Therapy70DownloadVTreatment for Central-Involved Diabetic Macular Edema in Eyes with Very Good Visual Acuity423DownloadAAPeripheral Diabetic Retinopathy (DR) Lesions on Ultrawide-field Fundus Images and Risk of DR Worsening Over Time250DownloadABIntravitreous Anti-VEGF vs. Prompt Vitrectomy for Vitreous Hemorrhage from Proliferative Diabetic Retinopathy99Download*Protocol AD (PROMINENT-Eye Ancillary Study, NCT03345901) ended prematurely due to low recruitment. Samples were collected but insufficient clinical data is available to create a phenotype dataset.

  Study phs004015

• Kids First: The Genomic Architecture of Hirschsprung Disease (HSCR)

  Hirschsprung disease (HSCR) is a male biased developmental disorder associated with a lack of innervation of the gastrointestinal tract. Genetic studies have been instrumental in understanding its multifactorial inheritance, high heritability, syndromic associations, and genetic heterogeneity with variable penetrance and expressivity. At least 24 genes and 9 loci with pathogenic alleles (PAs) are known to underlie HSCR pathogenesis and explain 62% of its population attributable risk (PAR). Despite this heterogeneity, there is functional unity in HSCR: ~53% of HSCR PAs disrupt RET and EDNRB signaling in the developing enteric nervous system (ENS) in which 11 genes comprising a gene regulatory network control RET and EDNRB gene expression. We propose to identify the remaining 30% PAR by studying 857 unrelated HSCR cases, their 125 affected and 1,446 unaffected firstdegree relatives by whole genome sequencing to increase statistical power of gene discovery through improved detection of all types of coding and regulatory PAs. HSCR arises from cell autonomous defects in enteric neural crest cell precursors (ENCCs) affecting their proliferation, differentiation and migration in the ENS, functional studies that will guide our detection of novel genes.

  Study phs003662

• Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS-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 SPIROMICS data available include: SPIROMICS (main, phs001119); NHLBI TOPMed SPIROMICS (phs001927); Genetics and genomics (SPIROMICS Genetics Genomics, phs002399), and C4R SPIROMICS (phs002909).Biospecimens: Access to Biospecimens is through the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biospecimens from SPIROMICS include: bronchial lavage, bronchial wash, oral wash, plasma, serum, sputum, and urine. Please note that use of biospecimens in genetic research is subject to a tiered consent.Available Data: Data available for request include SPIROMICS I main study data as well as SPIROMICS Bridge phone call follow-up period data (period between SPIROMICS I NIH contract and SPIROMICS II grant).Objectives: The SPIROMICS study sought to identify homogeneous subgroups of COPD patients for targeted enrollment in future therapeutic clinical trials, as well as to identify and conduct preliminary validation of intermediate biological or clinical outcomes for use as clinical trial endpoints.Background: Chronic obstructive pulmonary disease (COPD) is a chronic, usually progressive, lung disease characterized by incompletely reversible airflow obstruction. At the time of the SPIROMICS study, COPD affected between 12,000,000 and 24,000,000 people in the US, with no proven medical therapies that significantly reduce mortality, other than supplemental oxygen and smoking cessation. COPD is also a highly heterogeneous disease. For example, cigarette smoke-induced chronic bronchitis and emphysema are subsumed within the COPD definition, despite histological and clinical differences. The recognition of COPD as a systemic disease that affects extra-pulmonary systems, including cardiovascular, sleep and muscle function, further complicates disease classification. Because of clinical and pathological heterogeneity, individual patient subtypes may benefit from unique therapeutic regimens. Thus the SPIROMICS study was initiated to facilitate the identification of important COPD phenotypes, based on disease pathophysiology and biomarkers that track key pathophysiologic processes, in order to focus research efforts and improve treatment options.Participants: Eligible participants were between 40 and 80 years of age, and included never-smokers, current and former smokers without obstructive lung disease, and current and former smokers with COPD. Never smoker was defined as less than 1 pack-year smoking history, and current or former smoker were defined as more than 20 pack-years smoking history. Lung function was also part of the eligibility criteria and was assessed by spirometry with or without inhaled bronchodilators. Non-smokers were required to have pre-bronchodilator FEV1 (forced expiratory volume in one second)/FVC (forced vital capacity) > 0.7 and FVC > LLN (lower limit of normal). Current or former smokers without obstructive lung disease were required to have post-bronchodilator FEV1/FVC > 0.7 and FVC > LLN. Current or former smokers with obstructive lung disease were required to have post-bronchodilator FEV1/FVC 50% predicted.Major exclusion criteria included non-COPD obstructive lung disease or a history of diseases or treatments likely to interfere with interpretation of study tests, BMI > 40 kg/m2 at baseline, hypersensitivity to or intolerance of the bronchodilators used in study assessments, and diagnosis of unstable cardiovascular disease. Design: SPIROMICS was a prospective cohort study that enrolled approximately 2,981 participants at twelve clinical centers over five years. Participants were distributed across four enrollment strata; never-smokers, smokers without COPD, smokers with mild or moderate COPD, and smokers with severe COPD.There were baseline (Visit 1) and three annual in-person follow-up visits (Visits 2–4). Participants also received quarterly follow-up calls to assess health status and determine if an exacerbation occurred. Visits 1, 2 and 4, included anthropometry, seated blood pressure, spirometry, 6-minute walk test, biological specimen collection, and a series of questionnaires. Information was collected on medical history, respiratory exposures and current medications. Visits 1 and 2 included a thoracic computed tomography (CT) scan at maximum inspiration and expiration. Clinical outcomes, including hospitalizations and deaths, were adjudicated centrally. The primary outcome measures up to month 36 were (1) morbidity measured by assessing acute exacerbations, (2) lung function by using spirometry and plethysmography to measure FEV1, FVC, FRC (functional residual capacity), and IC (inspiratory capacity), and (3) mortality. There were several key sub-studies involving SPIROMICS participants. The Repeatability and Replicate Sub-study enrolled 98 participants and repeated the entire baseline clinic visit, including the CT scanning, in order to quantify reliability and short-term within-person variability of study procedures and assay methods. In addition, sites collected blinded replicate samples on 5% of each specimen type at the Baseline, Year 1, and Year 3 visits. The Bronchoscopy Sub-study enrolled a total of 250 participants to undergo bronchoscopy with bronchoalveolar lavage, epithelial brushings and bronchial biopsies. The Exacerbation Sub-study enrolled a total of 214 participants that were followed prospectively and had biological samples (not available via BioLINCC) and clinical information collected at the time of an acute exacerbation.

  Study phs004568