Deep sequencing of RYR3 gene identifies rare and common variants associated with increased carotid intima-media thickness (cIMT) in HIV-infected individuals.
Degui Zhi, Aditi Shendre, Rebecca Scherzer, Marguerite R Irvin, Rodney T Perry, Shawn Levy, Donna K Arnett, Carl Grunfeld, Sadeep Shrestha
Open access · bronzeAbstract readMulticenter Study
Article in Journal of human genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1citing papers in PubMed
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5 · Who and what money
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9 authors at 4 institutions in 1 country.
Degui ZhiDepartment of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA.
Aditi ShendreDepartment of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA.
Rebecca ScherzerDepartment of Medicine, San Francisco VA Medical Center, and University of California, San Francisco, CA, USA.
Marguerite R IrvinDepartment of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA.
Rodney T PerryDepartment of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA.
Shawn LevyHudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Donna K ArnettDepartment of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA.
Carl GrunfeldDepartment of Medicine, San Francisco VA Medical Center, and University of California, San Francisco, CA, USA.
Sadeep ShresthaDepartment of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA.
University of Alabama at Birmingham · USHudsonAlpha Institute for Biotechnology · USSan Francisco VA Medical Center · USUniversity of California, San Francisco · US
Funding
UCSF CLINICAL AND TRANSLATIONAL SCIENCE INSTITUTEUL1RR024131 · NCRR · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI JOHNSTON, S. CLAIBORNE · 2006 to 2011
$111.2M
Virology CoreP30AI027767 · NIAID · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI Latesha Ellen Elopre · 1988 to 2026
$84.1M
ZOPOLRESTAT PHARMACOKINETICS IN DIABETICS WITH VARYING RENAL FUNCTIONM01RR000051 · NCRR · UNIVERSITY OF COLORADO DENVER · PI ALBERT, RICHARD K · 1985 to 2008
$52.6M
ZDV &3TC NEVIRAPINE COMBINATION THERAPY IN HIV 1 INFECTED INFANTS &M01RR000865 · NCRR · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI WASHINGTON, ARNOLD E. · 1985 to 2011
$43.4M
ZINC AND CA EDTA THERAPY OF PLUMBISMM01RR000052 · NCRR · JOHNS HOPKINS UNIVERSITY · PI MARSH, LAURA · 1985 to 2007
$37.3M
YOGA FOR THE MANAGEMENT OF HIV-METABOLIC SYNDROMESM01RR000036 · NCRR · WASHINGTON UNIVERSITY · PI REEDS, DOMINIC N · 1985 to 2007
$25.4M
WELFARE REFORM AND THE PERINATAL HEALTH OF IMMIGRANTSM01RR000083 · NCRR · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KESSLER, DAVID A · 1985 to 2006
$21.1M
ZIDOVUDINE &LAMIVUDINE ALONE OR IN COMBINATION ON BODY COMPOSITIONM01RR000054 · NCRR · TUFTS MEDICAL CENTER · PI MENON, VANDANA · 1985 to 2005
$12.2M
Fat Redistribution and Metabolic Change in HIV InfectionR01HL074814 · NHLBI · NORTHERN CALIFORNIA INSTITUTE RES &EDUC · PI GRUNFELD, CARL · 2003 to 2006
$11.0M
FAT REDISTRIBUTION AND METABOLIC CHANGE IN HIV INFECTIONR01DK057508 · NIDDK · NORTHERN CALIFORNIA INSTITUTE RES &EDUC · PI GRUNFELD, CARL · 1999 to 2002
$5.8M
VISCERAL FAT, METABOLIC RATE AND CVD IN YOUNG ADULTSR01HL053359 · NHLBI · KAISER FOUNDATION RESEARCH INSTITUTE · PI SIDNEY, STEPHEN · 1995 to 2002
$1.5M
Gender Effects of HIV and HCV on lipodystrophy, glucose disorders, and steatosisK23AI066943 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI TIEN, PHYLLIS C · 2005 to 2009
Carotid intima-media thickness (cIMT) is a subclinical measure of atherosclerosis with mounting evidence that higher cIMT confers an increased risk of cardiovascular disease. The ryanodine receptor 3 gene (RYR3) has previously been linked to increased cIMT; however, the causal variants have not yet been localized. Therefore, we sequenced 339,480 bp encompassing 104 exons and 2 kb flanking region of the RYR3 gene in 96 HIV-positive white men from the extremes of the distribution of common cIMT from the Fat Redistribution and Metabolic Changes in HIV infection study (FRAM). We identified 2710 confirmed variants (2414 single-nucleotide polymorphisms (SNPs) and 296 insertion/deletions (indels)), with a mean count of 736 SNPs (ranging from 528 to 1032) and 170 indels (ranging from 128 to 214) distributed in each individual. There were 39 variants in the exons and 15 of these were non-synonymous, of which with only 4 were common variants and the remaining 11 were rare variants, one was a novel SNP. We confirmed that the common variant rs2229116 was significantly associated with cIMT in this design (P<7.9 × 10(-9)), and observed seven other significantly associated SNPs (P<10(-8)). These variants including the private non-synonymous SNPs need to be followed up in a larger sample size and also tested with clinical atherosclerotic outcomes.
Indexed as
Carotid Intima-Media ThicknessPolymorphism, Single NucleotideAdultAllelesAtherosclerosisFemaleGene FrequencyGenetic Predisposition to DiseaseHigh-Throughput Nucleotide SequencingHIV InfectionsHumansINDEL MutationLinkage DisequilibriumMaleMiddle AgedMultivariate AnalysisRyanodine Receptor Calcium Release Channel
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.
Deep sequencing of RYR3 gene identifies rare and common variants associated with increased carotid intima-media thickness (cIMT) in HIV-infected individuals. · full record | OpenQuestion