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JAMA Neurol. 2015 Jul;72(7):781-8. doi: 10.1001/jamaneurol.2015.0582.

Rare and Coding Region Genetic Variants Associated With Risk of Ischemic Stroke: The NHLBI Exome Sequence Project.

Collaborators (396)

Gabriel SB, Altshuler DM, Abecasis GR, Allayee H, Cresci S, Daly MJ, de Bakker PI, DePristo MA, Do R, Donnelly P, Farlow DN, Fennell T, Garimella K, Hazen SL, Hu Y, Jordan DM, Jun G, Kathiresan S, Kang HM, Kiezun A, Lettre G, Li B, Li M, Newton-Cheh CH, Padmanabhan S, Peloso G, Pulit S, Rader DJ, Reich D, Reilly MP, Rivas MA, Schwartz S, Scott L, Siscovick DS, Spertus JA, Stitziel NO, Stoletzki N, Sunyaev SR, Voight BF, Willer CJ, Rich SS, Akylbekova E, Atwood LD, Ballantyne CM, Barbalic M, Barr RG, Benjamin EJ, Bis J, Boerwinkle E, Bowden DW, Brody J, Budoff M, Burke G, Buxbaum S, Carr J, Chen DT, Chen IY, Chen WM, Concannon P, Crosby J, Cupples LA, D'Agostino R, DeStefano AL, Dreisbach A, Dupuis J, Durda JP, Ellis J, Folsom AR, Fornage M, Fox CS, Fox E, Funari V, Ganesh SK, Gardin J, Goff D, Gordon O, Grody W, Gross M, Guo X, Hall IM, Heard-Costa NL, Heckbert SR, Heintz N, Herrington DM, Hickson D, Huang J, Hwang SJ, Jacobs DR, Jenny NS, Johnson AD, Johnson CW, Kawut S, Kronmal R, Kurz R, Lange EM, Lange LA, Larson MG, Lawson M, Lewis CE, Levy D, Li D, Lin H, Liu C, Liu J, Liu K, Liu X, Liu Y, Longstreth WT Jr, Loria C, Lumley T, Lunetta K, Mackey AJ, Mackey R, Manichaikul A, Maxwell T, McKnight B, Meigs JB, Morrison AC, Musani SK, Mychaleckyj JC, Nettleton JA, North K, O'Donnell CJ, O'Leary D, Ong FS, Palmas W, Pankow JS, Pankratz ND, Paul S, Perez M, Person SD, Polak J, Post WS, Psaty BM, Quinlan AR, Raffel LJ, Ramachandran VS, Reiner AP, Rice K, Rotter JI, Sanders JP, Schreiner P, Seshadri S, Shea S, Sidney S, Silverstein K, Siscovick DS, Smith NL, Sotoodehnia N, Srinivasan A, Taylor HA, Taylor K, Thomas F, Tracy RP, Tsai MY, Volcik KA, Wassel CL, Watson K, Wei G, White W, Wiggins KL, Wilk JB, Williams OD, Wilson G, Wilson JG, Wolf P, Zakai NA, Hardy J, Meschia JF, Nalls M, Rich SS, Singleton A, Worrall B, Bamshad MJ, Barnes KC, Abdulhamid I, Accurso F, Anbar R, Beaty T, Bigham A, Black P, Bleecker E, Buckingham K, Cairns AM, Chen WM, Caplan D, Chatfield B, Chidekel A, Cho M, Christiani DC, Crapo JD, Crouch J, Daley D, Dang A, Dang H, De Paula A, DeCelie-Germana J, Dozor A, Drumm M, Dyson M, Emerson J, Emond MJ, Ferkol T, Fink R, Foster C, Froh D, Gao L, Gershan W, Gibson RL, Godwin E, Gondor M, Gutierrez H, Hansel NN, Hassoun PM, Hiatt P, Hokanson JE, Howenstine M, Hummer LK, Jamal SM, Kanga J, Kim Y, Knowles MR, Konstan M, Lahiri T, Laird N, Lange C, Lin L, Lin X, Louie TL, Lynch D, Make B, Martin TR, Mathai SC, Mathias RA, McNamara J, McNamara S, Meyers D, Millard S, Mogayzel P, Moss R, Murray T, Nielson D, Noyes B, O'Neal W, Orenstein D, O'Sullivan B, Pace R, Pare P, Parker HW, Passero MA, Perkett E, Prestridge A, Rafaels NM, Ramsey B, Regan E, Ren C, Retsch-Bogart G, Rock M, Rosen A, Rosenfeld M, Ruczinski I, Sanford A, Schaeffer D, Sell C, Sheehan D, Silverman EK, Sin D, Spencer T, Stonebraker J, Tabor HK, Varlotta L, Vergara CI, Weiss R, Wigley F, Wise RA, Wright FA, Wurfel MM, Zanni R, Zou F, Nickerson DA, Rieder MJ, Green P, Shendure J, Akey JM, Bamshad MJ, Bucasas KL, Bustamante CD, Crosslin DR, Eichler EE, Fox PK, Fu W, Gordon A, Gravel S, Jarvik GP, Johnsen JM, Kan M, Kenny EE, Kidd JM, Lara-Garduno F, Leal SM, Liu DJ, McGee S, O'Connor TD, Paeper B, Robertson PD, Smith JD, Staples JC, Tennessen JA, Turner EH, Wang G, Yi Q, Jackson R, North K, Peters U, Carlson CS, Anderson G, Anton-Culver H, Assimes TL, Auer PL, Beresford S, Bizon C, Black H, Brunner R, Brzyski R, Burwen D, Caan B, Carty CL, Chlebowski R, Cummings S, Curb JD, Eaton CB, Ford L, Franceschini N, Fullerton SM, Gass M, Geller N, Heiss G, Howard BV, Hsu L, Hutter CM, Ioannidis J, Jiao S, Johnson KC, Kooperberg C, Kuller L, LaCroix A, Lakshminarayan K, Lane D, Lange EM, Lange LA, Lasser N, LeBlanc E, Lewis CE, Li KP, Limacher M, Lin DY, Logsdon BA, Ludlam S, Manson JE, Margolis K, Martin L, McGowan J, Monda KL, Morley Kotchen J, Nathan L, Ockene J, O'Sullivan MJ, Phillips LS, Prentice RL, Reiner AP, Robbins J, Robinson JG, Rossouw JE, Sangi-Haghpeykar H, Sarto GE, Shumaker S, Simon MS, Stefanick ML, Stein E, Tang H, Taylor KC, Thomson CA, Thornton TA, Van Horn L, Vitolins M, Wactawski-Wende J, Wallace R, Wassertheil-Smoller S, Zeng D, Applebaum-Bowden D, Feolo M, Gan W, Paltoo DN, Rossouw JE, Sholinsky P, Sturcke A.

Author information

1
Joseph J. Zilber School of Public Health, University of Wisconsin, Milwaukee2Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.
2
Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland.
3
Department of Neurology, Mayo Clinic, Jacksonville, Florida.
4
Department of Neurology, University of Virginia, Charlottesville.
5
Department of Neurology, University of Washington, Seattle.
6
Department of Neurology, Boston University School of Medicine, Boston, Massachusetts.
7
Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.
8
Department of Neurology, George Washington University Hospital, Washington, DC.
9
Center for Public Health Genomics, University of Virginia, Charlottesville.
10
Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts.
11
Institute for Molecular Medicine, University of Texas Health Science Center, Houston.
12
Department of Neuroscience, Reta Lila Weston Institute, University College London, London, England.
13
Department of Internal Medicine, The Ohio State University, Columbus.
14
Department of Medicine, University of Washington, Seattle.
15
Department of Genome Sciences, University of Washington, Seattle.
16
Department of Neurology, University of Minnesota, Minneapolis.
17
Department of Genetics, University of North Carolina, Chapel Hill.
18
Department of Biostatistics, University of Washington, Seattle.

Abstract

IMPORTANCE:

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.

DESIGN, SETTING, AND PARTICIPANTS:

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.

MAIN OUTCOMES AND MEASURES:

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 AND RELEVANCE:

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.

PMID:
25961151
PMCID:
PMC4673986
DOI:
10.1001/jamaneurol.2015.0582
[Indexed for MEDLINE]
Free PMC Article

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