Article | Published:

Mapping autism risk loci using genetic linkage and chromosomal rearrangements

Nature Genetics volume 39, pages 319328 (2007) | Download Citation

  • A Corrigendum to this article was published on 01 October 2007

This article has been updated


Autism spectrum disorders (ASDs) are common, heritable neurodevelopmental conditions. The genetic architecture of ASDs is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASDs by using Affymetrix 10K SNP arrays and 1,181 families with at least two affected individuals, performing the largest linkage scan to date while also analyzing copy number variation in these families. Linkage and copy number variation analyses implicate chromosome 11p12–p13 and neurexins, respectively, among other candidate loci. Neurexins team with previously implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for contributing to ASDs.

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Change history

  • 26 September 2007

    In the version of this article initially published, Kacie J. Meyer (University of Iowa, Iowa City) was inadvertently omitted from the author list, and the names of three authors (Frederieke Koop, Marjolein Langemeijer and Channa Hijmans) were misspelled. There were also minor errors in the abstract (“1,168 families” should read “1,181 families”) and in the final paragraph of the Discussion (“11q13–12” should read “11p13–12”). These errors have been corrected in the HTML and PDF versions of the article.


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The authors are indebted to the participating families for their contribution of time and effort in support of this study. We gratefully acknowledge Autism Speaks, formerly the National Alliance for Autism Research, for financial support for data pooling, SNP genotyping and data analysis.

The Autism Genetics Cooperative thanks Assistance Publique-Hôpitaux de Paris, Canadian Institutes for Health Research (CIHR grant 11350 to P.S.), Catherine and Maxwell Meighan Foundation, Fondation de France, Fondation France Télécom, Fondation pour la Recherche Médicale, Genome Canada/Ontario Genomics Institute, The Hospital for Sick Children Foundation, Howard Hughes Medical Institute, INSERM, McLaughlin Centre for Molecular Medicine, National Institute of Child Health and Human Development, National Institute of Mental Health (MH066673 to J.D.B.; MH55135 to S.E.F.; MH52708 to N. Risch (University of California, San Francisco); MH061009 to J.S.S.), National Institute of Neurological Disorders and Stroke (NS042165 to J.H.; NS026630 and NS036738 to M.A.P.-V.; NS049261 to J.S.S.; NS043550 to T.H.W.), Swedish Science Council, Seaver Autism Research Foundation and The Centre for Applied Genomics (Toronto). S.W.S. is an Investigator of the CIHR and an HHMI International Scholar.

The Autism Genetic Resource Exchange Consortium gratefully acknowledges the resources provided by the participating families. The Autism Genetic Resource Exchange is a program of Cure Autism Now and is supported, in part, by the National Institute of Mental Health (MH64547 to D.H.G.).

The Collaborative Programs of Excellence thank the National Center for Research Resources (M01-RR00064), National Institute of Child Health and Human Development (U19HD34565 G.D. and G.S.), NIMH (MH057881), NINDS (5 U19 HD035476 to W.M.McM.) and the Utah Autism Foundation.

The International Molecular Genetic Study of Autism Consortium thanks the UK Medical Research Council, Wellcome Trust, BIOMED 2 (CT-97-2759), EC Fifth Framework (QLG2-CT-1999-0094), Telethon-Italy (GGP030227), Janus Korczak Foundation, Deutsche Forschungsgemeinschaft, Fondation France Telecom, Conseil Regional Midi-Pyrenees, Danish Medical Research Council, Sofiefonden, Beatrice Surovell Haskells Fond for Child Mental Health Research of Copenhagen, Danish Natural Science Research Council (9802210) and the US National Institutes of Health (U19 HD35482, MO1 RR06022, K05 MH01196, K02 MH01389). A.J.B. is the Cheryl and Reece Scott Professor of Psychiatry. A.P.M. is a Wellcome Trust Principal Research Fellow.

Requests for data or methods should be addressed to B.D. ( or S.W.S. (

Author information

Author notes

    • Peter Szatmari
    • , Andrew D Paterson
    • , Stephen W Scherer
    • , Veronica J Vieland
    • , Margaret A Pericak-Vance
    • , Catalina Betancur
    • , Joseph D Buxbaum
    • , Joachim Hallmayer
    • , James S Sutcliffe
    • , Jonathan L Haines
    • , Joseph Piven
    • , Thomas H Wassink
    • , Daniel H Geschwind
    • , Rita M Cantor
    • , Stan Nelson
    • , Geraldine Dawson
    • , Bernie Devlin
    • , William M McMahon
    • , Gerard D Schellenberg
    • , Ellen M Wijsman
    • , Anthony J Bailey
    • , Anthony P Monaco
    •  & Edwin H Cook

    These authors contributed equally to this work.


  1. Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.

    • Peter Szatmari
    • , Ann P Thompson
    •  & Ping Guo Tepper
  2. The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children and University of Toronto, Toronto, Ontario M5G 1X8, Canada.

    • Andrew D Paterson
    • , Xiao-Qing Liu
    • , Jennifer L Skaug
    • , Lars Feuk
    • , Cheng Qian
    • , Christian R Marshall
    •  & Stephen W Scherer
  3. Department of Pediatrics, McMaster University, Hamilton, Ontario L8N 3Z5 Canada.

    • Lonnie Zwaigenbaum
  4. Autism Research Unit, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.

    • Wendy Roberts
    • , Jessica Brian
    •  & Lili Senman
  5. Centre for Addiction and Mental Health, Clarke Institute and Department of Psychiatry, University of Toronto, Toronto, Ontario M5G 1X8, Canada.

    • John B Vincent
  6. Departments of Pediatrics and Psychology, Izaak Walton Killam Health Centre – Dalhousie University, Halifax, Nova Scotia B3K 6R8, Canada.

    • Susan E Bryson
  7. Department of Neural and Behavioral Sciences, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA.

    • Marshall B Jones
  8. Columbus Children's Research Institute, Center for Quantitative and Computational Biology, Columbus, Ohio 43205 USA.

    • Veronica J Vieland
    • , Christopher Bartlett
    •  & La Vonne Mangin
  9. University of Iowa, Department of Computer Science, Iowa City, Iowa 52242, USA.

    • Rhinda Goedken
    •  & Alberto Segre
  10. Miami Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida 33101, USA.

    • Margaret A Pericak-Vance
    • , Michael L Cuccaro
    •  & John R Gilbert
  11. W.S. Hall Psychiatric Institute, University of South Carolina, Columbia, South Carolina 29208, USA.

    • Harry H Wright
    •  & Ruth K Abramson
  12. INSERM U513, Université Paris XII, Créteil 94000, France.

    • Catalina Betancur
    •  & Marion Leboyer
  13. Human Genetics and Cognitive Functions, Institut Pasteur, Paris 75015, France.

    • Thomas Bourgeron
  14. Department of Child and Adolescent Psychiatry, Goteborg University, Goteborg 41119, Sweden.

    • Christopher Gillberg
  15. Department of Psychiatry, Groupe hospitalier Henri Mondor-Albert Chenevier, AP-HP, Créteil 94000, France.

    • Marion Leboyer
  16. Seaver Autism Research Center and the Greater New York Autism Research Center for Excellence, Department of Psychiatry, Mount Sinai School of Medicine, New York, New York 10029, USA.

    • Joseph D Buxbaum
    • , Kenneth L Davis
    • , Eric Hollander
    •  & Jeremy M Silverman
  17. Stanford University, Department of Psychiatry, Stanford, California 94304, USA.

    • Joachim Hallmayer
    •  & Linda Lotspeich
  18. Center for Molecular Neuroscience, Vanderbilt University, Nashville, Tennessee 37232, USA.

    • James S Sutcliffe
  19. Center for Human Genetics Research, Vanderbilt University, Nashville 37232, Tennessee, USA.

    • James S Sutcliffe
    •  & Jonathan L Haines
  20. Department of Psychiatry, Johns Hopkins University, Baltimore, Maryland 21287, USA.

    • Susan E Folstein
  21. University of North Carolina, Chapel Hill, North Carolina 27599, USA.

    • Joseph Piven
  22. University of Iowa, Iowa City, Iowa 52242, USA.

    • Thomas H Wassink
    • , Kacie J Meyer
    •  & Val Sheffield
  23. Department of Neurology, University of California - Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, USA.

    • Daniel H Geschwind
  24. University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

    • Maja Bucan
  25. New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA.

    • W Ted Brown
  26. Department of Human Genetics, UCLA School of Medicine, Los Angeles, California 90095, USA.

    • Rita M Cantor
    •  & Stan Nelson
  27. Washington University School of Medicine, St. Louis, Missouri, USA.

    • John N Constantino
  28. University of Chicago, Chicago 60637, Illinois, USA.

    • T Conrad Gilliam
  29. Harvard Medical School, Boston, Massachusetts 02115, USA.

    • Martha Herbert
  30. Cure Autism Now, Los Angeles, California 90036, USA.

    • Clara LaJonchere
    •  & Janet Miller
  31. Emory University, Atlanta, Georgia 30322, USA.

    • David H Ledbetter
    •  & Christa Lese-Martin
  32. George Washington University, Washington, D.C. 20052, USA.

    • Carol A Samango-Sprouse
  33. UCLA, Los Angeles, California 90095, USA.

    • Sarah Spence
  34. Yale University Child Study Center, New Haven, Connecticut 06520, USA.

    • Matthew State
    •  & Fred Volkmar
  35. Massachusetts General Hospital, Boston, Massachusetts 02114, USA.

    • Rudolph E Tanzi
  36. Department of Psychiatry, University of Utah, Salt Lake City 84132, USA.

    • Hilary Coon
    •  & William M McMahon
  37. Department of Psychology and the Center on Human Development and Disability, University of Washington, Seattle, Washington 98195, USA.

    • Geraldine Dawson
    •  & Jeff Munson
  38. Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington 98195, USA.

    • Geraldine Dawson
    •  & Annette Estes
  39. Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.

    • Bernie Devlin
    • , Lambertus Klei
    •  & Nancy Minshew
  40. Department of Pediatrics, University of California, Irvine, California 92697, USA.

    • Pamela Flodman
    • , Moyra Smith
    •  & M Anne Spence
  41. Geriatrics Research Education and Clinical Center, Puget Sound Veterans Affairs Medical Center, Seattle, Washington 98108, USA.

    • Elena Korvatska
    • , Gerard D Schellenberg
    •  & Chang-En Yu
  42. Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, Washington 98104, USA.

    • Elena Korvatska
    • , Gerard D Schellenberg
    •  & Chang-En Yu
  43. Department of OB/GYN, University of Rochester Medical Center, Rochester, New York 14642, USA.

    • Patricia M Rodier
    •  & Chris Stodgell
  44. Departments of Neurology and Pharmacology, University of Washington, Seattle, Washington 98195, USA.

    • Gerard D Schellenberg
  45. Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington 98195, USA.

    • Ellen M Wijsman
  46. Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA.

    • Ellen M Wijsman
  47. Université de Toulouse Le Mirail, Centre d'Etudes et de Recherches en Psychopathologie (CERPP), 31058 Toulouse, France.

    • Bernadette Rogé
    • , Carine Mantoulan
    •  & Kerstin Wittemeyer
  48. Deutsches Krebsforschungszentrum (DKFZ), Division of Molecular Genome Analysis, D-69120 Heidelberg, Germany.

    • Annemarie Poustka
    • , Bärbel Felder
    • , Sabine M Klauck
    •  & Claudia Schuster
  49. J W Goethe Universität Frankfurt, Klinik für Psychiatrie und Psychotherapie des Kindes- und Jugendalters, D-60528 Frankfurt, Germany.

    • Fritz Poustka
    • , Sven Bölte
    • , Sabine Feineis-Matthews
    • , Evelyn Herbrecht
    •  & Gabi Schmötzer
  50. National and Kapodistrian University of Athens, Department of Child Psychiatry, “Agia Sophia” Children's Hospital, Athens 115 27, Greece.

    • John Tsiantis
    •  & Katerina Papanikolaou
  51. Department of Biology, University of Bologna, 40126 Bologna, Italy.

    • Elena Maestrini
    • , Elena Bacchelli
    • , Francesca Blasi
    • , Simona Carone
    •  & Claudio Toma
  52. University Medical Center, Utrecht, Department of Child and Adolescent Psychiatry, 3508 GA Utrecht, The Netherlands.

    • Herman Van Engeland
    • , Maretha de Jonge
    • , Chantal Kemner
    • , Frederieke Koop
    • , Marjolein Langemeijer
    • , Channa Hijmans
    •  & Wouter G Staal
  53. Guy's Hospital, Newcomen Centre, London SE1 9RT, UK.

    • Gillian Baird
  54. Institute of Psychiatry, Department of Child and Adolescent Psychiatry, London, UK.

    • Patrick F Bolton
  55. Institute of Psychiatry, Social, Genetic and Developmental Psychiatry Centre (SGDP), London SE5 8AF, UK.

    • Michael L Rutter
  56. University of Cambridge Clinical School, Cambridge CB2 2AH, UK.

    • Emma Weisblatt
  57. University of Manchester Department of Child Psychiatry, Booth Hall Children's Hospital, Manchester M9 7AA, UK.

    • Jonathan Green
    • , Catherine Aldred
    •  & Julie-Anne Wilkinson
  58. University of Manchester School of Epidemiology and Health Science, Manchester M13 9P, UK.

    • Andrew Pickles
  59. University of Newcastle, Child and Adolescent Mental Health, Sir James Spence Institute, Newcastle upon Tyne NE1 4LP, UK.

    • Ann Le Couteur
    • , Tom Berney
    •  & Helen McConachie
  60. University of Oxford Department of Psychiatry, Oxford OX3 7LQ, UK.

    • Anthony J Bailey
    • , Kostas Francis
    • , Gemma Honeyman
    • , Aislinn Hutchinson
    • , Jeremy R Parr
    •  & Simon Wallace
  61. Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK.

    • Anthony P Monaco
    • , Gabrielle Barnby
    • , Kazuhiro Kobayashi
    • , Janine A Lamb
    • , Ines Sousa
    •  & Nuala Sykes
  62. Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, 60608, USA.

    • Edwin H Cook
    • , Stephen J Guter
    • , Bennett L Leventhal
    •  & Jeff Salt
  63. University of Michigan Autism and Communicative Disorders Center (UMACC), Ann Arbor, Michigan, 48109, USA.

    • Catherine Lord
    • , Christina Corsello
    •  & Vanessa Hus
  64. University of Pittsburgh Department of Human Genetics, Pittsburgh, Pennsylvania 15213, USA.

    • Daniel E Weeks
  65. Service de pédiatrie et génétique médicale, CHU de Toulouse, Toulouse, France.

    • Maïté Tauber
  66. Montreal Children's Hospital, McGill University, Montreal, Canada.

    • Eric Fombonne
  67. Autism Speaks, 2 Park Avenue, New York, New York 10016, USA.

    • Andy Shih


  1. The Autism Genome Project Consortium



    P.S., A.D.P., S.W.S., V.J.V., M.A.P.-V., C.B., J.D.B., J.H., J.S.S., J.H., J.L.H., J.P., T.H.W., D.H.G., R.C., S.N., G.D., G.D.S., B.D., W.M.M., E.M.W., A.J.B., A.P.M. and E.H.C. were lead AGP investigators and contributed equally to this project.

    The Autism Genome Project (AGP). The AGP comprises four existing consortia of partners or countries (listed alphabetically below).

    Autism Genetics Cooperative. Canagen: P.S., A.D.P., L.Z., W.R., J.B., X.-Q.L., J.B.V., J.L.S., A.P.T., L.S., L.F., C.Q., S.E.B., M.B.J., C.R.M. and S.W.S. Iowa Data Coordinating Center: V.J.V., C.B., L.V.M., R.G. and A.S. University of Miami: M.A.P.-V., M.L.C. and J.R.G. University of South Carolina: H.H.W., R.K.A. Paris Autism Research: International Sibpair Study: C.B., T.B., C.G. and M.L. Seaver Autism Research Center: J.D.B., K.L.D., E.H. and J.M.S. Stanford University: J.H. and L.L. Vanderbilt University: J.S.S., J.L.H. and S.E.F. University of North Carolina/University of Iowa: J.P., T.H.W., K.J.M. and V.S.

    The Autism Genetic Resource Exchange Consortium. D.H.G., M.B., W.T.B., R.M.C., J.N.C., T.C.G., M.H., C.LaJ., D.H.L., C.L.-M., J.M., S.N. C.A.S.-S., S.S., M.S. and R.E.T.

    The Collaborative Programs of Excellence in Autism. H.C., G.D., B.D., A.E., P.F., L.K., W.M.McM., N.M., J.M., E.K., P.M.R., G.D.S., M.S., M.A.S., C.S., P.G.T., E.M.W. and C.-E.Y.

    The International Molecular Genetic Study of Autism Consortium. France: B.R., C.M., K.W. and M.T. Germany: A.P., B.F., S.M.K., C.S., F.P., S.B., S.F.-M., E.H. and G.S. Greece: J.T., K.P. Italy: E.M., E.B., F.B., S.C. and C.T. The Netherlands: H.V.E., M. de J., C.K., F.K., M.L., C.H. and W.G.S. UK: G.B., P.F.B., M.L.R., E.W., J.G., C.A., J.-A.W., A.P., A.LeC., T.B., H.McC., A.J.B., K.F., G.H., A.H., J.R.P., S.W., A.P.M., G.B., K.K., J.A.L., I.S. and N.S. USA: E.H.C., S.J.G., B.L.L., J.S., C.L., C.C., V.H., D.E.W. and F.V. Canada: E.F.

    Scientific management. A.S.

    Competing interests

    The author declare no competing financial interests.

    Corresponding authors

    Correspondence to Stephen W Scherer or Bernie Devlin.

    Supplementary information

    PDF files

    1. 1.

      Supplementary Fig. 1

      Binned size distribution of CNVs in batch, plate and filtered analyses.

    2. 2.

      Supplementary Fig. 2

      Linkage results due to removing families in which affected individuals putatively carry CNV.

    3. 3.

      Supplementary Fig. 3

      Principal component plot used to infer ancestry.

    4. 4.

      Supplementary Fig. 4

      Linkage results obtained by analyzing families inferred to be of homogeneous European ancestry.

    5. 5.

      Supplementary Table 1

      List of 624 CNVs in filtered analysis.

    6. 6.

      Supplementary Table 2

      List of 254 CNVs in affected individuals.

    7. 7.

      Supplementary Table 3

      Breakdown of CNVs in affected individuals.

    8. 8.

      Supplementary Table 4

      List of validated CNVs.

    9. 9.

      Supplementary Methods

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