3909 results for "*geneti*"

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• Filtering and Annotation of Variants That Are Rare (FAVR)

  The project developed a suite of new methods (FAVR) designed to assist the shortlisting of genetic variants under a rare variant-phenotype/disease model. The methods were designed to work with commonly used massively parallel sequencing analysis pipelines, such as the GATK or ANNOVAR, and have been made publically available as a suite of software tools (https://github.com/bjpop/favr). The FAVR methods use signatures in comparator sequence alignment files to facilitate the filtering of mapping artifacts and common genetic variants, and annotation of genetic variants based on evidence of co-occurrence in individuals. As relevant, FAVR methods can also be used to filter out artifacts derived from imbalanced paired-end sequencing. Pope et al., BMC Bioinformatics, accepted Dec 2012.

  Study phs000601

• Myocardial Infarction Genetics Exome Sequencing Consortium: Italian Atherosclerosis Thrombosis and Vascular Biology

  Italian Atherosclerosis Thrombosis and Vascular Biology study is a prospective, nationwide, case-control study involving 125 coronary care units in Italy. The cases were patients who were hospitalised for a first MI before the age of 45 years and underwent coronary angiography. Acute MI was defined as resting chest pain lasting more than 30 minutes, accompanied by persistent electrocardiographic changes, and confirmed by an increase in total creatine kinase or in the MB fraction to more than twice the upper normal limits. The controls were healthy subjects without a history of thromboembolic disease who were unrelated to the patients, but individually matched with them by age, gender and geographical origin. They were enrolled from among the blood donors or staff of the same participating hospitals. Recruitment of cases and controls took place between 1994 and 2007. All exome sequencing was performed at the Broad Institute of Harvard and MIT; samples sequence capture was performed using Agilent SureSelect Human All Exon Kit v2 and sequencing was performed on an Illumina HiSeq 2000 or 2500.

  Study phs000814

• Center for Common Disease Genomics [CCDG] - Cardiovascular: TexGen

  Cardiovascular disease (CVD), especially coronary heart disease, heart failure and cerebrovascular disease remain the leading causes of death in men and women across all race groups in the United States. Substantial evidence exists for genetic factors underlying CVD risk, and their discovery offers an opportunity to enhance understanding of disease mechanisms, to provide specific diagnostic and prognostic indicators, and to identify novel therapeutic targets. The Centers for Common Disease Genomics (CCDG) are a large-scale genome sequencing effort undertaken as a collaboration to identify rare risk and protective alleles for common chronic diseases, with a current focus on early onset heart disease, hemorrhagic stroke, and autism. In this study, whole genome sequencing (WGS) was performed in 6,146 individuals with any personal or family history of CVD from the TexGen study who were recruited from several institutions in the Texas Medical Center located in Houston, Texas. The participants included patients who were admitted with a variety of diagnoses including acute coronary syndromes, strokes, and transient ischemic attacks, or who underwent percutaneous coronary interventions or coronary artery bypass grafting (CABG) (Virani SS et al. Am J Cardiology 107:1504-1509, 2011). Patients in the TexGen cohort with a confirmed diagnosis of acute coronary syndrome (ACS) or CABG when discharged from the hospital between 2001-2008 were eligible for a follow-up study of recurrent myocardial infarction (Virani SS et al. Circulation J 76:950-956, 2012), while those presenting with ACS beginning in 2007 were recruited for an investigation of the role of depressive symptoms in the risk of major adverse coronary events (Sanner J et al. Biol Res Nurs 20:168-176, 2018). In addition, the initial criterion for enrollment in a third TexGen sub-study undertaken between 2007 and 2013 was the occurrence of premature acute myocardial infarction in men ≤ 50 years and women ≤ 55 years in order to establish a blood sample collection resource with the intention of localizing genes that contribute to disease risk. This definition was later expanded to include individuals with a clinical history of premature coronary heart disease such as CABG or percutaneous coronary interventions.

  Study phs003010

• Genome Wide Association Study of Asthma

  This data forms part of an ongoing genome wide association study into the genetic variants that predispose to pediatric asthma at the Children's Hospital of Philadelphia (CHOP). All cases and controls were recruited at CHOP and genotyped at the Center for Applied Genomics (CAG). The data set includes 793 cases and 1988 controls. The inclusion criteria to this case control study are detailed below.

  Study phs000233

• Kids First: Whole Genome Sequencing of Nonsyndromic Craniosynostosis

  The Gabriella Miller Kids First Pediatric Research Program (Kids First) is a trans-NIH effort initiated in response to the 2014 Gabriella Miller Kids First Research Act and supported by the NIH Common Fund. This program focuses on gene discovery in pediatric cancers and structural birth defects and the development of the Gabriella Miller Kids First Pediatric Data Resource (Kids First Data Resource). All of the WGS and phenotypic data from this study are accessible through dbGaP and kidsfirstdrc.org, where other Kids First datasets can also be accessed. Nonsyndromic craniosynostosis (NCS) is a common, major structural birth defect - due to the premature fusion of one or more cranial sutures - that requires extensive surgical correction and is associated with considerable ongoing medical problems and health care costs. Because little is known about the causes of NCS, whole genome sequencing will help advance knowledge of genetic factors contributing to the etiology of NCS. Data from this project will lead to a better understanding of biological processes involved in the etiology of NCS and provide critical insights for development of early diagnostic tools and therapeutic strategies.

  Study phs001806

• Exome Sequencing for Head and Neck Cancer Susceptibility

  This study seeks to find low frequency or rare genetic variants in genes carried by subjects from families with unexplained familial risk of head and neck cancer. Whole exome sequencing was used to identify genetic variation in head and neck cancer cases.

  Study phs002571

• LCCC1122: Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212

  In this study the investigators looked at adaptive reprogramming impact on the kinome when a MEK inhibitor called GSK1120212 (trametinib) was administered in a "window of opportunity" trial. GSK1120212 is not yet approved by the FDA for use in breast cancer patients. The investigators gave GSK1120212 for a short period of time (one week) to examine MEK and the other kinase expression in cancer cells both before and after the study drug is given. The investigators gave this drug for research purposes only. The length of time it was given is not intended to treat cancer. Recently researchers at UNC developed a process that can comprehensively profile the majority of the individual kinases in the kinome and examine the impact on kinase expression of kinase inhibitors (Duncan et al, Cell 2012, PMID: 22500798). This can tell us which kinases need to be concurrently blocked to augment responsiveness and prevent acquired resistance so that the investigators can design the best combinations of kinase blocking drugs for triple negative breast cancer. This is especially important for individuals with triple negative breast cancer (TNBC) because there are no targeted drugs available that can block molecules that affect tumor growth. The investigators believe that kinase-blocking drugs have the potential to be a more effective treatment for people with TNBC. In this recently published study (Zawistowski et al, Cancer Discovery 2017, PMID: 28108460), TNBC patients treated with trametinib for 7 days resulted in a transcriptional response characterized by significant reprogramming of the tyrosine kinome, and this adaptive bypass response in human tumors was found to be similar to that seen in preclinical models including TNBC cell lines and mouse xenografts. In this study we also examined whether reprogramming differed between TNBC molecular subtypes, finding that basal-like and claudin-low human TNBC cells and mouse tumor subtypes had different adaptive transcriptional responses to MEK-ERK inhibition. Mechanistically we found that genome-wide enhancer remodeling drove the adaptive transcriptional response, suggesting that epigenetic approaches to reprogramming may be more durable than kinase inhibitor polypharmacology.

  Study phs001405

• Molecular Profiling of Gallbladder Cancer (MPOG)

  The purpose of this study is to investigate the underlying genetic factors involved in gallbladder cancer.

  Study phs001404

• National Institute of General Medical Sciences (NIGMS) Human Genetic Cell Repository Human Variation Panels including 100 African-Americans (HD100AA), 100 Caucasians (HD100CAU), 100 Han People of Los Angeles (HD100CHI) and 100 Mexican American Community of Los Angeles (HD100MEX)

  The Human Genetic Cell Repository is sponsored by the National Institute of General Medical Sciences (NIGMS) with the mission of supplying scientists with the materials for accelerating disease gene discovery and functional studies. The resources available include highly-characterized, contaminant-free cell cultures and high quality, well-characterized DNA samples derived from these cultures, both subjected to rigorous quality control. The Repository was established in 1972 at Coriell and contains more than 9,500 cell lines, primarily fibroblasts and transformed lymphoblasts. The Repository has a major emphasis on inherited diseases and chromosomally aberrant cell lines. In addition, it contains a large collection dedicated to understanding human variation that includes samples from populations around the world, the CEPH collection, the Polymorphism Discovery Resource, Human Variation and many apparently healthy controls. The Human Variation collection provides cell lines and DNA samples from a variety of populations. The panels of African-Americans (HD100AA) and Caucasians (100CAU) used for this study are comprised of samples present in the Repository that were originally collected over the years from apparently healthy people to be used as "controls", for example, unaffected family members of persons with identified mono-genetic diseases. The samples for the Han people of Los Angeles (HD100CHI) and the Mexican American Community of Los Angeles (HD100MEX), however, were collected relatively recently from volunteers, identified as member of these communities, specifically for use in these panels. The Coriell Genotyping and Microarray Center in conjunction with the NIGMS repository used the Affymetrix Genome-Wide Human SNP 6.0 platform to genotype 400 samples from the NIGMS human variation panels. The populations genotyped included Americans of African, Caucasian, Mexican, and Han Chinese ancestry. The Affymetrix SNP 6.0 array detects approximately 940,000 SNPs and provides copy number information for more than 900,000 additional locations across the genome.

  Study phs000211

• Genetic Modifiers of Huntington's Disease

  Huntington's disease (HD) is a neurodegenerative disorder typically diagnosed in mid-life that is caused by expansion of an otherwise polymorphic CAG trinucleotide repeat. The mutation causes a gain-of-function of the huntingtin protein to trigger a pathogenic process that produces detectable phenotypic differences many years before the traditional diagnosis, which is based upon characteristic motor symptoms. The prediagnosis phase of pathogenesis is now the subject of intense scrutiny by an NINDS-funded longitudinal study, PREDICT-HD, in which undiagnosed gene carriers are followed longitudinally and subjected to detailed phenotyping (PREDICT-HD Huntington Disease Study -- dbGaP Study Accession: phs000222). This powerful approach, which offers the potential for moving the focus of therapeutic development to the decades prior to neurological disease diagnosis, is enabled by the fact that all individuals with HD have the same type of mutation, which can be determined at any time in life by a single HD CAG repeat PCR amplification assay. The precise length of the HD CAG repeat differs between individuals. There is a strong negative correlation between the number of CAG repeats and the age at onset of diagnostic neurological abnormalities in HD, such that the CAG repeat accounts for ~50% of the variation in age at diagnosis. Analysis of the remaining variance not explained by the length of the CAG repeat has shown that it is highly heritable, being due to genetic variation, elsewhere in the genome. The intent of the Genetic Modifiers of Huntington's Disease study is to identify genetic modifiers of HD pathogenesis by using genomewide association techniques in diagnosed HD individuals to identify genetic factors associated with the residual variance in age at onset not explained by the CAG repeat, and to extend these analyses to pre-diagnosis phenotypes, for example, those defined in the PREDICT-HD study. Identification of modifier genes is a top priority for HD research (and an example of an approach that can be applied in other late-onset genetic disorders), as it could provide clues to developing rational treatments that delay or prevent the pathogenic process from causing the ravages of the disease that ensue in the ~15 years of inexorable decline to ultimate death that now follows clinical diagnosis. To further that goal, the release of study version 2 makes available whole exome sequencing data of n=221 study participants.

  Study phs000371