title: Rare and Coding Region Genetic Variants Associated With Risk of Ischemic Stroke: The NHLBI Exome Sequence Project.
abstract: OBJECTIVE
  Stroke is the second leading cause of death and the third leading cause of years of life lost. Genetic factors contribute to stroke prevalence, and candidate gene and genome-wide association studies (GWAS) have identified variants associated with ischemic stroke risk. These variants often have small effects without obvious biological significance. Exome sequencing may discover predicted protein-altering variants with a potentially large effect on ischemic stroke risk.
  
  
  OBJECTIVE
  To investigate the contribution of rare and common genetic variants to ischemic stroke risk by targeting the protein-coding regions of the human genome.
  
  
  METHODS
  The National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project (ESP) analyzed approximately 6000 participants from numerous cohorts of European and African ancestry. For discovery, 365 cases of ischemic stroke (small-vessel and large-vessel subtypes) and 809 European ancestry controls were sequenced; for replication, 47 affected sibpairs concordant for stroke subtype and an African American case-control series were sequenced, with 1672 cases and 4509 European ancestry controls genotyped. The ESP's exome sequencing and genotyping started on January 1, 2010, and continued through June 30, 2012. Analyses were conducted on the full data set between July 12, 2012, and July 13, 2013.
  
  
  METHODS
  Discovery of new variants or genes contributing to ischemic stroke risk and subtype (primary analysis) and determination of support for protein-coding variants contributing to risk in previously published candidate genes (secondary analysis).
  
  
  RESULTS
  We identified 2 novel genes associated with an increased risk of ischemic stroke: a protein-coding variant in PDE4DIP (rs1778155; odds ratio, 2.15; P = 2.63 × 10(-8)) with an intracellular signal transduction mechanism and in ACOT4 (rs35724886; odds ratio, 2.04; P = 1.24 × 10(-7)) with a fatty acid metabolism; confirmation of PDE4DIP was observed in affected sibpair families with large-vessel stroke subtype and in African Americans. Replication of protein-coding variants in candidate genes was observed for 2 previously reported GWAS associations: ZFHX3 (cardioembolic stroke) and ABCA1 (large-vessel stroke).
  
  
  CONCLUSIONS
  Exome sequencing discovered 2 novel genes and mechanisms, PDE4DIP and ACOT4, associated with increased risk for ischemic stroke. In addition, ZFHX3 and ABCA1 were discovered to have protein-coding variants associated with ischemic stroke. These results suggest that genetic variation in novel pathways contributes to ischemic stroke risk and serves as a target for prediction, prevention, and therapy.
authors.affiliation: Joseph J. Zilber School of Public Health, University of Wisconsin, Milwaukee2Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Paul L
authors.initials: PL
authors.lastname: Auer
authors.affiliation: Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland.
authors.forename: Mike
authors.initials: M
authors.lastname: Nalls
authors.affiliation: Department of Neurology, Mayo Clinic, Jacksonville, Florida.
authors.forename: James F
authors.initials: JF
authors.lastname: Meschia
authors.affiliation: Department of Neurology, University of Virginia, Charlottesville.
authors.forename: Bradford B
authors.initials: BB
authors.lastname: Worrall
authors.affiliation: Department of Neurology, University of Washington, Seattle.
authors.forename: W T
authors.initials: WT
authors.lastname: Longstreth
authors.affiliation: Department of Neurology, Boston University School of Medicine, Boston, Massachusetts.
authors.forename: Sudha
authors.initials: S
authors.lastname: Seshadri
authors.affiliation: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Charles
authors.initials: C
authors.lastname: Kooperberg
authors.affiliation: Department of Neurology, George Washington University Hospital, Washington, DC.
authors.forename: Kathleen M
authors.initials: KM
authors.lastname: Burger
authors.affiliation: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Carlson
authors.affiliation: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Cara L
authors.initials: CL
authors.lastname: Carty
authors.affiliation: Center for Public Health Genomics, University of Virginia, Charlottesville.
authors.forename: Wei-Min
authors.initials: WM
authors.lastname: Chen
authors.affiliation: Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts.
authors.forename: L Adrienne
authors.initials: LA
authors.lastname: Cupples
authors.affiliation: Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts.
authors.forename: Anita L
authors.initials: AL
authors.lastname: DeStefano
authors.affiliation: Institute for Molecular Medicine, University of Texas Health Science Center, Houston.
authors.forename: Myriam
authors.initials: M
authors.lastname: Fornage
authors.affiliation: Department of Neuroscience, Reta Lila Weston Institute, University College London, London, England.
authors.forename: John
authors.initials: J
authors.lastname: Hardy
authors.affiliation: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Li
authors.initials: L
authors.lastname: Hsu
authors.affiliation: Department of Internal Medicine, The Ohio State University, Columbus.
authors.forename: Rebecca D
authors.initials: RD
authors.lastname: Jackson
authors.affiliation: Department of Medicine, University of Washington, Seattle.
authors.forename: Gail P
authors.initials: GP
authors.lastname: Jarvik
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle.
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Kim
authors.affiliation: Department of Neurology, University of Minnesota, Minneapolis.
authors.forename: Kamakshi
authors.initials: K
authors.lastname: Lakshminarayan
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill.
authors.forename: Leslie A
authors.initials: LA
authors.lastname: Lange
authors.affiliation: Center for Public Health Genomics, University of Virginia, Charlottesville.
authors.forename: Ani
authors.initials: A
authors.lastname: Manichaikul
authors.affiliation: Center for Public Health Genomics, University of Virginia, Charlottesville.
authors.forename: Aaron R
authors.initials: AR
authors.lastname: Quinlan
authors.affiliation: Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland.
authors.forename: Andrew B
authors.initials: AB
authors.lastname: Singleton
authors.affiliation: Department of Biostatistics, University of Washington, Seattle.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Thornton
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle.
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Nickerson
authors.affiliation: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Peters
authors.affiliation: Center for Public Health Genomics, University of Virginia, Charlottesville.
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Rich
mesh_terms: D048868:Adaptor Proteins, Signal Transducing; D000368:Aged; D002545:Brain Ischemia / Q000175:diagnosis / Q000235:genetics*; D003598:Cytoskeletal Proteins; D059472:Exome / Q000235:genetics*; D005260:Female; D020022:Genetic Predisposition to Disease / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods; D006801:Humans; D008297:Male; D008875:Middle Aged; D009124:Muscle Proteins / Q000235:genetics*; D054555:National Heart, Lung, and Blood Institute (U.S.); D009687:Nuclear Proteins / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics; D010170:Palmitoyl-CoA Hydrolase / Q000235:genetics*; D020521:Stroke / Q000175:diagnosis / Q000453:epidemiology / Q000235:genetics*; D014481:United States / Q000453:epidemiology
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D003598:Cytoskeletal Proteins; D009124:Muscle Proteins; D009687:Nuclear Proteins; C432971:PDE4DIP protein, human; C506774:ACOT4 protein, human; D010170:Palmitoyl-CoA Hydrolase