3906 results for "*geneti*"

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• HuBMAP: KULMAP - Human Kidney, Urinary Tract, and Lung Mapping Center

  The major goal of the Human Kidney, Urinary Tract, and Lung Mapping Center (KULMAP) is to generate multi-omic and spatially resolved molecular anatomical maps of the human bladder, ureter and kidneys (BUKMAP) and the lung airways and parenchyma (LAPMAP) at a single cell resolution. This entails sequencing of the transcriptomes and epigenomes of dissociated single cells in a massively parallel manner. These profiles will then inform on highly multiplexed RNA in situ imaging for spatial mapping of hundreds of molecular targets in the tissue sections, at a subcellular resolution. These spatial molecular maps will serve as scaffolds for computational registration of cell types and the associated transcriptome/chromatin maps to the tissue space. The combination of sequencing single dissociated cells and multiplexed in situ mapping will allow the construction of detailed spatial maps for these large organs.

  Study phs002249

• National Cancer Institute Genome-Wide Association Study of Renal Cell Carcinoma

  The National Cancer Institute (NCI) genome-wide association study (GWAS) of renal cell carcinoma (RCC) was conducted to investigate common genetic variants associated with RCC risk. The GWAS includes 1,453 RCC cases and 3,531 controls of European background from 4 studies (3 cohort, 1 case-control), scanned using the Illumina InfiniumHumanHap 550, 610 and 660W chips. This project was supported by the Intramural Research Program of the National Institutes of Health and NCI. Data from this GWAS were pooled with those from another GWAS of RCC (2,639 cases and 5,392 controls) conducted in Europe by the International Agency for Research on Cancer and the Centre National de Gènotypage. Findings from this collaboration are described in an upcoming report (Purdue et al. Nature Genetics 2011;43(1):60-65; PMID: 21131975). Only data from the NCI scan are included in this dbGaP submission.

  Study phs000351

• NHLBI TOPMed: Pharmacogenomics of Hydroxyurea in Sickle Cell Disease (PharmHU)

  Sickle cell disease (SCD) is characterized by the presence of sickle hemoglobin (HbS) within circulating erythrocytes resulting in hemolytic anemia, vascular occlusion, and end organ damage due to alterations in the shape and deformability of the cell membrane. The disease is inherited in an autosomal recessive pattern, and is most commonly caused by a single nucleotide substitution in the hemoglobin subunit beta (HBB) gene located on chromosome 11. Participants in this study include children with SCD treated with hydroxyurea to pharmacologically increase fetal hemoglobin (HbF) levels and reduce disease severity. Therefore, the primary phenotype of interest in this study is the change in HbF levels in response to hydroxyurea treatment. Genetic factors have been shown to influence inter-individual variation in drug response, and identification of novel genes and variants associated with clinical outcomes in SCD will be achieved through collaboration between Baylor College of Medicine, Augusta University, Columbia University Medical Center, Emory University School of Medicine and Children's Healthcare of Atlanta, and St. Jude Children's Research Hospital. The NHLBI TOPMed Program is designed to generate scientific resources to enhance understanding of fundamental biological processes that underlie heart, lung, blood and sleep disorders (HLBS). It is part of a broader Precision Medicine Initiative, which aims to provide disease treatments that are tailored to an individual's unique genes and environment.

  Study phs001466

• deCODE Genetics study on genes contributing to nicotine dependence in humans

  A genome-wide association study on smoking behavior and nicotine dependence in Icelandic smokers, assessed by the number of cigarettes smoked per day, smoking initiation and degree of dependence on nicotine. The number of cigarettes smoked per day was ascertained through questionnaires given to individuals participating in multiple disease projects at deCODE Genetics (n=16,483). Smoking initiation was analyzed by comparing those that have ever smoked (n=16,483) versus those that have never smoked (n=21,667). The nicotine dependence analysis included 3,435 nicotine dependent cases (score 4 or higher on Fagerstrom Test for Nicotine Dependence (FTND) or endorsement of at least three of the seven Diagnostic and Statistical Manual of Mental Disorders 4th edition (DSM-IV) criteria) and 3,344 low-quantity smokers as controls.

  Study phs000393

• Predicting Chemotherapy-Induced Mucositis with Genetic and Clinical Factors

  We hypothesized that genetic variability in the enzymes/proteins involved in drug metabolism, inflammation, and immune function is a major underlying contributor to mucositis incidence and progression and that, based on this variability we can identify variants that influence risk, and develop a mucositis progression prediction model that improves on existing models by incorporating genetic variability along with clinical factors. Using genome wide association study (GWAS) combined with a pathway candidate gene approach and a modified case-control study method, we investigated the hypothesis in a sample of 1092 patients who received a myeloablative dose of melphalan (MEL) followed by autologous hematopoietic stem cell (ASCT) transplantation as treatment for multiple myeloma and for whom banked blood stem cell samples and clinical data were available.

  Study phs000545

• NHLBI TOPMed: Determining the Association of Chromosomal Variants with Non-PV Triggers and Ablation-Outcome in AF (DECAF)

  The DECAF trial was conducted at the Texas Cardiac Arrhythmia Institute (TCAI) in 2013 in collaboration with the University of Texas at Austin. Four hundred consecutive AF patients undergoing catheter ablation were enrolled. All participants provided voluntary informed consents. Blood samples were collected before the ablation procedure and labeled with anonymous patient identifier. The researchers at UT Austin responsible for DNA extraction and genetic analysis were blinded about the clinical characteristics and identification of the study participants. AF cases included adults >18 years of age from both sex and all AF types.

  Study phs001546

• NHLBI TOPMed: GOLDN Epigenetic Determinants of Lipid Response to Dietary Fat and Fenofibrate

  The GOLDN study was initiated to assess how genetic factors interact with environmental (diet and drug) interventions to influence blood levels of triglycerides and other atherogenic lipid species and inflammation markers (registered at clinicaltrials.gov, number NCT00083369). The study recruited Caucasian participants primarily from three-generational pedigrees from two NHLBI Family Heart Study (FHS) field centers (Minneapolis, MN and Salt Lake City, UT). Only families with at least two siblings were recruited and only participants who did not take lipid-lowering agents (pharmaceuticals or nutraceuticals) for at least 4 weeks prior to the initial visit were included. The diet intervention followed the protocol of Patsch et al. (1992). The whipping cream (83% fat) meal had 700 Calories/m2 body surface area (2.93 mJ/m2 body surface area): 3% of calories were derived from protein (instant nonfat dry milk) and 14% from carbohydrate (sugar). The ratio of polyunsaturated to saturated fat was 0.06 and the cholesterol content of the average meal was 240 mg. The mixture was blended with ice and flavorings. Blood samples were drawn immediately before (fasting) and at 3.5 and 6 hours after consuming the high-fat meal. The diet intervention was administered at baseline as well as after a 3-week treatment with 160 mg micronized fenofibrate. Participants were given the option to complete one or both (diet and drug) interventions. Of all participants, 1079 had phenotypic data and provided appropriate consent, and underwent whole genome sequencing through the Trans-Omics for Precision Medicine (TOPMed) program. Comprehensive phenotypic and pedigree data for GOLDN study participants are available through dbGaP phs000741.

  Study phs001359

• University of North Carolina at Chapel Hill (UNC) Hepatocellular Carcinoma Study by Exome Sequencing (HCCSES)

  Genetic alterations in specific driver genes lead to disruption of cellular pathways and are critical events in the instigation and progression of hepatocellular carcinoma. As a prerequisite for individualized cancer treatment, we sought to characterize the landscape of recurrent somatic mutations in hepatocellular carcinoma. We performed whole exome sequencing on 87 hepatocellular carcinomas and matched normal adjacent tissues to an average coverage of 59x. The overall mutation rate was roughly 2 mutations per Mb, with a median of 45 non-synonymous mutations that altered the amino acid sequence (range 2 to 381). We found recurrent mutations in several genes with high transcript levels: TP53 (18%), CTNNB1 (10%), KEAP1 (8%), C16orf62 (8%), MLL4 (7%) and RAC2 (5%). Significantly affected gene families include the nucleotide-binding domain and leucine rich repeat containing family, calcium channel subunits, and histone methyltransferases. In particular, the MLL family methyltransferases for histone H3 lysine 4 were mutated in 20% of tumors. Conclusion: The NFE2L2-KEAP1 and MLL pathways are recurrently mutated in multiple cohorts of hepatocellular carcinoma.

  Study phs000627

• eMERGE: Northwestern (NUgene) WGS

  The NUgene Project is a biorepository with longitudinal medical information from participating patients at Northwestern Medicine affiliated hospitals and outpatient clinics. Participants' DNA samples are coupled with data from a self-reported questionnaire (2 versions were used, 1 before and 1 after February 2006, both are included) and continuously updated data from our Electronic Medical Record (EMR) representing actual clinical care events. Northwestern has a state-of-the art, comprehensive inpatient and outpatient EMR system of over 3 million patients. NUgene has broad access to participant data for all outpatient visits as well as inpatient data via a consolidated enterprise data warehouse. NUgene participants consent to distribution and use of their coded DNA samples and data for a broad range of genetic research by third-party investigators. The electronic MedicalRecords and Genomics (eMERGE) Network is a consortium of 9 clinical sites with EMR linked DNA biobanks, including Northwestern University and its NUgene biobank, funded by the NHGRI (National Human Genome Research Institute) to investigate the use of electronic medical record systems for genomic research. The goal of eMERGE is to conduct genome-wide association studies in approximately 100,000 individuals using EMR-derived phenotypes and DNA from linked biorepositories. Using electronic phenotyping methods, the consortium has been and is using DNA samples from all participating sites to explore the genetic determinants of approximately 80 phenotypes, including both diseases and traits, for which the electronic phenotyping algorithms have or are being published on PheKB.org. Thus, for the eMERGE network, ~900 NUgene subjects were selected, as described in the study inclusion/exclusion criteria section below, to be genotyped using whole genome sequencing (WGS), for use in the eMERGE network as eMERGE subjects. The criteria used below were selected so that these subjects will likely meet the criteria to be cases and/or controls, of diverse races and/or ethnicities, for at least 1 of the ~80 phenotypes being studied within eMERGE, and could be recontacted for future research if needed.

  Study phs001191

• San Francisco Bay Area Latina Breast Cancer Study

  The genome-wide association study (GWAS) includes participants enrolled into two different studies. The first study, the San Francisco Bay Area Cancer Study (SFBCS) is a population-based case-control study of breast cancer conducted in the San Francisco Bay Area and included women ages 35-79 years from three racial/ethnic groups: Non-Hispanic whites, African Americans, and Hispanics/Latinas. For the GWAS, only Hispanic/Latina women were included. Women diagnosed with invasive breast cancer between 1995 and 2002 were identified through the Greater Bay Area Cancer Registry. Controls were identified by random digit dialing and were frequency-matched to cases by age in 5 year increments and by race/ethnicity. Hispanic/Latina ethnicity was assessed by self-report. 175 Hispanic/Latina cases and 307 Hispanic/Latina controls from the SFBCS had given adequate consent and provided biospecimens that were used in the GWAS to be included in this data submission. The second study is the Northern California site of the Breast Cancer Family Registry (NC-BCFR). This population-based family study recruited breast cancer cases ages 18-64 years diagnosed from 1995-2009 that were identified through the Greater Bay Area Cancer Registry. Cases included all women at increased genetic susceptibility for breast cancer who met one or more of the following criteria: (a) being diagnosed with breast cancer at age <35 years; b) having a personal history of ovarian cancer or childhood cancer; (c) being diagnosed with two different breast cancers (bilateral breast cancers), with the first one diagnosed at age <50 years; and d) having one or more first-degree relatives with breast cancer, ovarian cancer or childhood cancer. Cases not meeting these criteria were randomly sampled and racial/ethnic minorities were oversampled. Controls were recruited by random digit dialing and were matched by 5-year age increments and by race/ethnicity. For the current GWAS only Latina/Hispanic cases and controls were included. Latina/Hispanic ethnicity was assessed by self-report. 631 Hispanic/Latina cases and 61 Hispanic/Latina controls from the NC-BCFR had given adequate consent and provided biospecimens that were used in the GWAS to be included in this data submission.

  Study phs000912