Autism spectrum disorders (ASDs) represent a group of childhood neurodevelopmental and neuropsychiatric disorders characterized by deficits in verbal communication, impairment of social interaction, and restricted and repetitive patterns of interests and behaviour. To identify common genetic risk factors underlying ASDs, here we present the results of genome-wide association studies on a cohort of 780 families (3,101 subjects) with affected children, and a second cohort of 1,204 affected subjects and 6,491 control subjects, all of whom were of European ancestry. Six single nucleotide polymorphisms between cadherin 10 (CDH10) and cadherin 9 (CDH9)—two genes encoding neuronal cell-adhesion molecules—revealed strong association signals, with the most significant SNP being rs4307059 (P = 3.4 × 10-8, odds ratio = 1.19). These signals were replicated in two independent cohorts, with combined P values ranging from 7.4 × 10-8 to 2.1 × 10-10. Our results implicate neuronal cell-adhesion molecules in the pathogenesis of ASDs, and represent, to our knowledge, the first demonstration of genome-wide significant association of common variants with susceptibility to ASDs.

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We gratefully thank all the children with ASDs and their families at the participating study sites who were enrolled in this study and all the control subjects who donated blood samples to Children’s Hospital of Philadelphia (CHOP) for genetic research purposes. We also acknowledge the resources provided by the AGRE Consortium (D. H. Geschwind, M. Bucan, W. T. Brown, J. D. Buxbaum, R. M. Cantor, J. N. Constantino, T. C. Gilliam, C. M. Lajonchere, D. H. Ledbetter, C. Lese-Martin, J. Miller, S. F. Nelson, G. D. Schellenberg, C. A. Samango-Sprouse, S. Spence, M. State, R. E. Tanzi) and the participating families. AGRE is a program of Autism Speaks and is at present supported, in part, by grant 1U24MH081810 from the National Institute of Mental Health to C. M. Lajonchere (PI), and formerly by grant MH64547 to D. H. Geschwind (PI). We thank the technical staff at the Center for Applied Genomics at CHOP for producing the genotypes used for analyses, and the nursing, medical assistant and medical staff for their help with recruitment of patient and control subjects for the study. We thank R. Liu and I. Lindquist for helping with CNV validation. We thank D. J. Hedges, H. N. Cukier, J. L. McCauley, G. W. Beecham, H. H. Wright, R. K. Abramson, E. R. Martin and J. P. Hussman for their comments, advice and statistical support, and the laboratory core and the autism clinical personnel at the Miami Institute for Human Genomics and the autism clinical staff at the Vanderbilt Center for Human Genetics Research. A subset of the CAP participants was ascertained while M.A.P.-V. was a faculty member at Duke University. We thank the National Institutes of Health (NIH)-funded Developmental Brain and Tissue Bank at University of Maryland for access to the fetal brain tissues used in these studies (National Institute of Child Health and Human Development Contract no. NO1-HD-4-3368 and NO1-HD-4-3383). All genotyping of the AGRE and ACC cohort was supported by an Institutional Development Award to the Center for Applied Genomics (H.H.) at the Children’s Hospital of Philadelphia. The study was supported in part by a Research Award from the Margaret Q. Landenberger Foundation (H.H.), a Research Development Award from the Cotswold Foundation (H.H. and S.F.A.G), UL1-RR024134-03 (H.H.), an Alavi-Dabiri fellowship from Mental Retardation and Developmental Disability Research Center at CHOP (K.W.), the Beatrice and Stanley A. Seaver Foundation (J.D.B.), the Department of Veterans Affairs (G.D.S.), NIH grants HD055782-01 (J.Munson, A.E., O.K., G.D. and G.D.S.), MH0666730 (J.D.B.), MH061009 and NS049261 (J.S.S.), HD055751 (E.H.C.), MH69359, M01-RR00064 and the Utah Autism Foundation (H.C., J.Miller and W.M.M.), MH64547, MH081754 (D.H.G.), HD055784 (D.H.G. and M.S.), NS26630, NS36768, MH080647 and a gift from the Hussman Foundation (M.A.P.-V.), the Autism Genome Project Consortium (B.S.A., J.P., C.W.B., D.H.G., T.H.W., W.M.M., H.C., J.I.N., J.S.S., E.H.C., J.Munson, A.E., O.K., J.D.B., B.D. and G.D.S.) funded by Autism Speaks, the Medical Research Council (UK) and the Health Research Board (Ireland). We also acknowledge the partial support to CAP cohort from the Autism Genome Project.

Author Contributions H.H. and G.D.S. designed the study and H.H. supervised the genotyping, data analysis and interpretation. K.W., H.Z. and D.M. analysed the AGRE, ACC/CART and CAP data sets, respectively. K.W. drafted the manuscript, and H.H., G.D.S. and other authors edited the manuscript. M.B., J.T.G, M.I., J.P.B., P.M.A.S., C.E.K., C.H., E.F., R.C., C.M.L., R.M.C. and S.F.A.G. helped generate data and assisted with data analysis of the AGRE cohort. D.M., D.S., J.R.G. and M.L.C. generated data for the CAP replication cohort. B.S.A., L.I.S., A.I.A.R., E.I.H., H.D., T.H., M.S., S.O. and A.K. performed in situ hybridization, and generated data for the CART replication cohort. K.W., C.E.K. and E.R. performed qPCR validation of CNVs. N.T., T.S. and J.D.B. preformed MLPA validation of CNVs. J.Munson, A.E., O.K., J.P., T.O., J.A.S. C.W.B., R.B. J.R.G., W.M.M., J.Miller, M.W.S., T.H.W., H.C., S.E.L., R.T.S., J.I.N., J.L.H., J.S.S., E.H.C., N.J.M., J.D.B., G.D., D.H.G., M.A.P.-V. and G.D.S. collected samples, contributed phenotype data for the study, helped with interpretation of data, and assisted with manuscript preparation. D.H.G. and M.A.P.-V. contributed equally to this work.

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Author notes

    • Kai Wang
    • , Haitao Zhang
    •  & Deqiong Ma

    These authors contributed equally to this work.


  1. Center for Applied Genomics, Children’s Hospital of Philadelphia, Pennsylvania 19104, USA

    • Kai Wang
    • , Haitao Zhang
    • , Joseph T. Glessner
    • , Marcin Imielinski
    • , Jonathan P. Bradfield
    • , Patrick M. A. Sleiman
    • , Cecilia E. Kim
    • , Cuiping Hou
    • , Edward Frackelton
    • , Rosetta Chiavacci
    • , Struan F. A. Grant
    •  & Hakon Hakonarson
  2. The Miami Institute for Human Genomics and Department of Human Genetics, University of Miami, Miami, Florida 33101, USA

    • Deqiong Ma
    • , Daria Salyakina
    • , John R. Gilbert
    • , Michael L. Cuccaro
    •  & Margaret A. Pericak-Vance
  3. Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19014, USA

    • Maja Bucan
  4. Department of Neurology and Center for Autism Research and Treatment, University of California Los Angeles, Los Angeles, California 90095, USA

    • Brett S. Abrahams
    • , Lisa I. Sonnenblick
    • , Ana I. Alvarez Retuerto
    • , Edward I. Herman
    • , Hongmei Dong
    • , Ted Hutman
    • , Marian Sigman
    •  & Daniel H. Geschwind
  5. Seaver Autism Center for Research and Treatment, Department of Psychiatry, Mount Sinai School of Medicine, New York, New York 10029, USA

    • Nagahide Takahashi
    • , Takeshi Sakurai
    •  & Joseph D. Buxbaum
  6. Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19014, USA

    • Eric Rappaport
    • , Susan E. Levy
    • , Robert T. Schultz
    • , Struan F. A. Grant
    •  & Hakon Hakonarson
  7. Department of Biomedical Engineering, University of Southern California and Autism Speaks, Los Angeles, California 90089, USA

    • Clara M. Lajonchere
  8. Department of Psychiatry, University of Washington, Seattle, Washington 98105, USA

    • Jeffrey Munson
    • , Annette Estes
    • , Olena Korvatska
    • , Raphael Bernier
    •  & Geraldine Dawson
  9. Department of Psychiatry, University of North Carolina and Carolina Institute for Developmental Disabilities, Chapel Hill, North Carolina 27599, USA

    • Joseph Piven
  10. The M.I.N.D. Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis, Sacramento, California 95817, USA

    • Sally Ozonoff
  11. Department of Genetics and Child Study Center, Yale University, New Haven, Connecticut 06520, USA

    • Ami Klin
    •  & Matthew W. State
  12. Institute for Juvenile Research and Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois 60608, USA

    • Thomas Owley
    • , John A. Sweeney
    • , Camille W. Brune
    •  & Edwin H. Cook
  13. Department of Human Genetics, University of California Los Angeles, Los Angeles, California 90095, USA

    • Rita M. Cantor
  14. Department of Psychiatry, University of Utah, Salt Lake City, Utah 84132, USA

    • William M. McMahon
    • , Judith Miller
    •  & Hilary Coon
  15. Department of Psychiatry, University of Iowa, Iowa City, Iowa 84112, USA

    • Thomas H. Wassink
  16. Institute of Psychiatric Research, Indiana University, Indianapolis, Indiana 46202, USA

    • John I. Nurnberger
  17. Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee 37232, USA

    • Jonathan L. Haines
  18. Center for Molecular Neuroscience and Vanderbilt Kennedy Center, Vanderbilt University, Nashville, Tennessee 37232, USA

    • James S. Sutcliffe
  19. Departments of Psychiatry and Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA

    • Nancy J. Minshew
  20. Departments of Psychiatry, Neuroscience, and Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York 10029, USA

    • Joseph D. Buxbaum
  21. Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19014, USA

    • Gerard D. Schellenberg


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Corresponding author

Correspondence to Hakon Hakonarson.

The AGRE data set was genotyped by the Center for Applied Genomics at CHOP, and the complete sets of genotype and signal intensity data have been released to the public domain. AGRE-approved academic researchers can acquire the data sets from AGRE ( In addition, the summary statistics for the full data set will be made available in the repository of the NIH Genotype and Phenotype database (dbGAP;

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