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A genome-wide scan for common alleles affecting risk for autism

Lookup NU author(s): Dr Thomas Berney, Professor Jeremy Parr


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Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 x 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 x 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.

Publication metadata

Author(s): Anney R, Klei L, Pinto D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Sykes N, Pagnamenta AT, Almeida J, Bacchelli E, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bolte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Carson AR, Casallo G, Casey J, Chu SH, Cochrane L, Corsello C, Crawford EL, Crossett A, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Melhem NM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Piven J, Osey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang ZZ, Wassink TH, Wing K, Wittemeyer K, Wood S, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Betancur C, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Gallagher L, Geschwind DH, Gill M, Haines JL, Miller J, Monaco AP, Nurnberger JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Scherer SW, Sutcliffe JS, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Devlin B, Ennis S, Hallmayer J

Publication type: Article

Publication status: Published

Journal: Human Molecular Genetics

Year: 2010

Volume: 19

Issue: 20

Pages: 4072-4082

Print publication date: 27/07/2010

ISSN (print): 0964-6906

ISSN (electronic): 1460-2083

Publisher: Oxford University Press


DOI: 10.1093/hmg/ddq307


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Funder referenceFunder name
Assistance Publique - Hopitaux de Paris (France)
Autism Speaks (USA)
Canadian Institutes for Health Research (CIHR)
Centre for Applied Genomics (Canada)
Fondation de France
Fondation Orange (France)
Fondation pour la Recherche Medicale (France)
Gene Environment Association Studies (GENEVA) under GEI
Genome Canada/Ontario Genomics Institute
Health Research Board (HRB, Ireland)
Hilibrand Foundation (USA)
Hospital for Sick Children Foundation
INSERM (France)
John P. Hussman Foundation (USA)
Medical Research Council (MRC; UK)
National Institute on Drug Abuse
Ontario Ministry of Research and Innovation (Canada)
Seaver Foundation (USA)
University of Toronto (Canada)
Utah Autism Foundation (USA)
Autism Speaks
Canada Foundation for Innovation/Ontario Innovation Trust
Fondation FondaMental (France)
Fundacao Calouste Gulbenkian (Portugal)
Fundacao para a Ciencia e Tecnologia (Portugal)
GlaxoSmithKline-CIHR Pathfinder Chair (Canada)
Institut Pasteur (France)
Italian Ministry of Health
McLaughlin Centre (Canada)
National Institute on Alcohol Abuse and Alcoholism
Swedish Science Council
075491/Z/04 UKWellcome Trust
825.06.031Netherlands Organization for Scientific Research
HD055782US National Institutes of Health
HD055751US National Institutes of Health
HD055784US National Institutes of Health
HD35465US National Institutes of Health
MH057881US National Institutes of Health
MH061009US National Institutes of Health
MH06359US National Institutes of Health
MH066673US National Institutes of Health
MH077930US National Institutes of Health
MH52708US National Institutes of Health
NS026630US National Institutes of Health
MH080647US National Institutes of Health
MH081754US National Institutes of Health
MH55284US National Institutes of Health
MH66766US National Institutes of Health
Po 255/17-4Deutsche Forschungsgemeinschaft (Germany)
NS042165US National Institutes of Health
NS049261US National Institutes of Health
U01 HG004422NIH Genes, Environment and Health Initiative [GEI]
U01 HG004438NIH Genes, Environment and Health Initiative [GEI]
TMF/DA/5801Royal Netherlands Academy of Arts and Sciences