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Author notes

1. These authors contributed equally: Xueya Zhou, Pamela Feliciano, Chang Shu, Tianyun Wang, Irina Astrovskaya.

2. These authors jointly supervised this work: Yufeng Shen, Wendy K. Chung.

Authors and Affiliations

1. Department of Pediatrics, Columbia University Medical Center, New York, NY, USA

   Xueya Zhou, Chang Shu, Joseph U. Obiajulu & Wendy K. Chung

2. Department of Systems Biology, Columbia University Medical Center, New York, NY, USA

   Xueya Zhou, Chang Shu, Joseph U. Obiajulu, Alex Kitaygorodsky & Yufeng Shen

3. Simons Foundation, New York, NY, USA

   Pamela Feliciano, Irina Astrovskaya, Jacob B. Hall, Jessica R. Wright, Simon Xuming Xu, Olena Marchenko, Christopher Fleisch, Sarah D. Barns, LeeAnne Green Snyder, Bing Han, Alpha Amatya, Asif Bashar, Alex E. Lash, Alexandra Goler, Alison Holbrook, Andrea J. Ace, Amy M. Daniels, Anup Mankar, Alexandra N. Stephens, Ai Nhu Nguyen, Beverly E. Robertson, Bill Jensen, Brianna M. Vernoia, Brady Schwind, Cheryl Cohen, Chris Diggins, Chris Rigby, Casey White-Lehman, Dennis Vasquez Montes, Dave Cho, Elizabeth Brooks, Erica Jones, Eirene O’Connor, Esmeralda Perez, Emily Singer, Hana Zaydens, John Acampado, Jennylyn Brown, Jessica Hernandez, J. Kiely Law, Julie Manoharan, Jibrielle Polite, Jennifer Tjernagel, Jaimie Toroney, Katharine Diehl, Lindsey A. Cartner, Lori Mann, Luke P. Grosvenor, Malcolm D. Mallardi, Martin E. Butler, Misia Kowanda, Mahfuza Sabiha, Marina Sarris, Noah Lawson, Nathan Lo, Natalie Nagpal, Neelay Shah, Richard Marini, Rishiraj Rana, Richard Remington, Swami Ganesan, Stanley Jean, Swapnil Shah, Sabrina Xiao, Simon Xu, Tunisia Greene, Vincent J. Myers, Wubin Chin, Natalia Volfovsky & Wendy K. Chung

4. Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA

   Tianyun Wang, Shwetha C. Murali, William T. Harvey & Evan E. Eichler

5. Department of Medical Genetics, Center for Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China

   Tianyun Wang

6. Neuroscience Research Institute, Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center; Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing, China

   Tianyun Wang

7. Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA

   Shwetha C. Murali & Evan E. Eichler

8. Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA

   Leo Brueggeman, Taylor R. Thomas, Cate Buescher, Ethan Bahl, Lucas Casten, Sydney Kramer, Tanner Koomar & Jacob J. Michaelson

9. Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA

   Timothy S. Chang, Daniel H. Geschwind & Elizabeth Ruzzo

10. Department of Genetics, Washington University, St. Louis, MO, USA

    Tychele N. Turner

11. Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA

    Andrew Nishida & Brian J. O’Roak

12. Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA

    Yufeng Shen

13. Department of Medicine, Columbia University Medical Center, New York, NY, USA

    Wendy K. Chung

14. Department of Psychiatry and Behavioral Sciences, Rush University Medical Center, Chicago, IL, USA

    Adrienne Adams, Anna Hirshman, Allison L. Wainer, Caroline Leonczyk, Cynthia Pierre, Diamond Phillips, Edith Ocampo, Holly Lechniak, Kathryn A. Schweers, Latha V. Soorya, Lisa Yeh, Madison Printen, Natalie Berger, Norma Calderon, Nicole M. Russo-Ponsaran, Rachel A. Gordon, Soo J. Lee & Sarely Licona

15. Department of Pediatrics, University of Utah, Salt Lake City, UT, USA

    Alicia Andrus, Dawn Bentley, Gabriele Baraghoshi, Gregory Schoonover, Laurie Lesher & Paul S. Carbone

16. Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA

    Anna Berman, Alexandra Miceli, Amy Swanson, Ellen Grimes, Nicole Bardett, Nina Harris & S. Carpenter

17. Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, MD, USA

    Alison Brown, Alexander P. McKenzie, Bonnie VanMetre, Catherine Edmonson, Emily Dillon, Ericka L. Wodka, Hanna Hutter, Jason Neely, Katrina Pama, Melinda Koza, Megan McTaggart, Nicolas Alvarez, Rebecca J. Landa, Roman Shikov, Sarah Michaels & Vini Singh

18. Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, USA

    Alexies Camba, Amanda C. Gulsrud, Catherine Lord, Ivette Arriaga, James T. McCracken, Karla Murillo, Katherine Tsai, Monica Haley, Maira Tafolla, Sophia Sandhu & Wha S. Yang

19. PreventionGenetics, Marshfield, WI, USA

    Anthony D. Krentz, Angela J. Gruber, Gregory J. Fischer & Marc A. Popp

20. Thompson Center for Autism and Neurodevelopmental Disorders, University of Missouri, Columbia, MO, USA

    Amanda D. Shocklee, Hannah Cottrell, Jennifer Delaporte, Kathy Hirst, Kerri Nowell, Megan Sweeney, Nicole Takahashi, Shelby Birdwell, Samantha Hunter & Stephen M. Kanne

21. Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA

    Amy Esler

22. Child Study Center, Yale School of Medicine, New Haven, CT, USA

    Anne Fanta, Abha R. Gupta, Catherine A. W. Sullivan, Hope Koene, Jane Jurayj, Roger Jou & Sarah Boland

23. Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA

    Ali Fatemi

24. Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA

    Angela Fish, Annes Kim, Ashley Raven, Allyson Zick, Costanza Colombi, Fiona K. Miller, Jessyca Judge, Kate D. Fitzgerald, Mohammad Ghaziuddin, Sharmista Chintalapalli & Sarah Mohiuddin

25. Department of Psychology, University of Miami’s Center for Autism and Related Disabilities (UM-CARD), Coral Gables, FL, USA

    Antonio Gonzalez, Anibal Gutierrez Jr., Brandon Lobisi, Cindy Zha, Dahriana Correa, David Giancarla, Hoa Lam Schneider, Joaquin Comitre, Jacob Rosewater, Lynette M. Herbert, Michael Alessandri, Michele Cutri, Melissa N. Hale, Madelyn Rayos & Nickelle Decius

26. Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA

    Antonio Hardan, Daniela Rojas, Elizabeth Orrick, Jared Gong, Margot Frayne, Morgan Steele, Robin Libove & Sandy Littlefield

27. Division of Pediatric Psychology and Neuropsychology, Nationwide Children’s Hospital (Child Development Center), Columbus, OH, USA

    Amy Hess, Charles Albright, Daniel Lee Coury, Erin Given, Elizabeth Kryszak, Eric M. Butter, Gabrielle Tiede, Jessica Scherr, Kevin Stephenson, Megan Norris, Nancy Long, Nicholas Russell, Sara Eldred & Teresa Ibanez

28. John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA

    Anthony J. Griswold

29. Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA

    Andrea Jarratt, Alissa Jorgenson, Angela Tesng, Claudia Campo-Soria, Dain Howes, Dalia Istephanous, Desiree Rambeck, Diksha Srishyla, Gregory Hooks, Jaclyn Gunderson, Katie Beard, Laura Simon, Lucy Wasserburg, Megan DuBois, Natasha Lillie, Olivia Newman, Sunday Francis, Suma Jacob & Wenteng CaI

30. Department of Psychiatry and Behavioral Neuroscience, Cincinnati Children’s Hospital Medical Center – Research Foundation, Cincinnati, OH, USA

    Anna Jelinek, Craig A. Erickson, Carrie Fassler, Elizabeth Blank, Erica Lampert, Ernest V. Pedapati, Jose Polanco, Kaela O’Brien, Natalie Madi, Nicole Mccoy, Patricia Manning, Rebecca C. Shaffer, Stephanie Booker, Sophia Melnyk & Shelley Randall

31. Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA

    A. Pablo Juarez, Amy Nicholson & Zachary E. Warren

32. Department of Psychiatry, Oregon Health & Science University, Portland, OR, USA

    Addie Luo, Desi Limpoco, Eric J. Fombonne, Faris Fazal, Hadley Morotti, Landon Beeson, Leigh Coppola, Lillian D. Pacheco, Lark Y. Huang-Storms, Shelley Aberle & Sarah Mastel

33. Department of Pediatrics, JFK Partners/University of Colorado School of Medicine, Aurora, CO, USA

    Angela L. Rachubinski, Amber Tallbull, Cordelia R. Rosenberg, Jeanette Cordova, Lisa Cordiero, Nicole Targalia, Susan Hepburn, Sandra L. Friedman & Tamim Shaikh

34. Department of Neurosciences, University of California, San Diego and SARRC Phoenix, La Jolla, CA, USA

    Andrew Mason, Anthony Sziklay, Chris Smith, Erin Bower, Eric Courchesne, Hannah E. Kaplan, Hongjian Qi, Haicang Zhang, Haoquan Zhao, Jiayao Wang, Kendra Coleman, Karen L. Pierce, Mojeeb Shir, Sidi Xu, Tia Chen & Tiziano Pramparo

35. Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA

    Anna Milliken, Christopher Zaro, Emily T. Matthews, Gabriella Aberbach, Katherine G. Pawlowski, Lisa M. Prock, Michelle Coughlin & Margaret Hojlo

36. Department of Pediatrics, Montefiore Medical Center and The Albert Einstein College of Medicine, Bronx, NY, USA

    Amy Morales-Lara, Lisa H. Shulman, Molly O’Neil & Maria Valicenti-McDermott

37. Department of Psychiatry, Weill Cornell Medicine, White Plains, NY, USA

    Anna Marie Paolicelli, Michelle Heyman & Shanping Qiu

38. Department of Pediatrics, Medical University of South Carolina, Charleston, SC, USA

    Anna Rhea, Audrey Ward, Brandi Bell, Catherine C. Bradley, Caitlin McCarthy, Crissy Ortiz, Casey Roche, Clara Shrier, Candace Van Wade, Erin Doyle, Harper Richardson, Jessie Montezuma, Laura Carpenter, Sarah Conyers, Sophia D’Ambrosi & Virginia Galbraith

39. Department of Pediatrics, Texas Children’s Hospital (Baylor College of Medicine), Houston, TX, USA

    Andrea Simon, Danica Limon, Gabrielle Duhon, Gabriela Marzano, Jessica Orobio, Kelli Baalman & Robin P. Goin-Kochel

40. Department of Medicine, Boston Children’s Hospital, Boston, MA, USA

    Aubrie Soucy, Ryan N. Doan & Timothy W. Yu

41. MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Sacramento, CA, USA

    Brittani A. Hilscher, Claudine Anglo, David G. Amaral, Deana Li, Kaitlin Smith, Leonard Abbeduto, Nicki Rodriguez & Samantha Thompson

42. Children’s Specialized Hospital, Toms River, NJ, USA

    Barbara Enright, Jill F. Harris, Malia Beckwith, Myriam Casseus, Marilyn Lopez & Natalia Gonzalez

43. Department of Psychiatry, University of North Carolina (UNC, TEACCH, CIDD), Chapel Hill, NC, USA

    Brenda Hauf, Catherine Gray, Corrie H. Walston, Elena Lamarche, Gabriel S. Dichter, Joseph Piven, Kailey Murray, Kelli Real, Mary Currin, Michelle Jordy & Renee D. Clark

44. Department of Psychiatry and Behavioral Sciences, Emory University and Marcus Autism Center, Atlanta, GA, USA

    Catherine E. Rice, Joseph F. Cubells, Michael J. Morrier & Opal Y. Ousley

45. Department of Pediatrics, Emory University and Marcus Autism Center, Atlanta, GA, USA

    Chris Gunter, Cheryl Klaiman, Megan Dunlevy, Sheena Mathai & Stormi White

46. Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA, USA

    Christa Lese Martin, Cora M. Taylor, Kate Dent, Kaitlyn Singer, Lauren Kasperson Walsh & William Curtis Weaver

47. Department of Pediatrics, Rush University Medical Center, Chicago, IL, USA

    Cesar Ochoa-Lubinoff, Elizabeth Berry-Kravis, Hai Li, Josh Beeson, Kelsey Gonring, Lorena Ferreira Corzo, Melissa Baer, Peter Heydemann & Thao Tran

48. Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, USA

    Dustin E. Sarver, Danielle Stamps, Kristen Callahan, Lacy Malloch, Robert D. Annett & Sabrina White

49. Department of Psychiatry and Behavioral Sciences, University of Washington/Seattle Children’s Autism Center, Seattle, WA, USA

    Daniel Cho, Emily A. Fox, Haidar Ghina, Jennifer A. Gerdts, Katie Ahlers, Raphael A. Bernier, Rachel K. Earl, Theodore Ho & Tara Rutter

50. Department of Psychology, University of Michigan, Ann Arbor, MI, USA

    Ivy F. Tso

51. Center for Autism Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    Juhi Pandey, Lindsey DeMarco, Robert T. Schultz, Susannah Horner, Samiza Palmer, Samantha Plate & Vaikunt Ranganathan

52. Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA

    James S. Sutcliffe

53. Department of Psychiatry, Columbia University Medical Center, New York, NY, USA

    Jeremy Veenstra-Vanderweele

54. Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA

    McLeod F. Gwynette

55. Department of Neurology, Boston Children’s Hospital, Boston, MA, USA

    Mustafa Sahin

56. Maine Medical Center Research Institute, Scarborough, ME, USA

    Matthew Siegel, Mary Verdi & Susan Santangelo

57. Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA, USA

    Megan Y. Dennis

58. Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA, USA

    Stephanie J. Brewster

59. Center for Autism and the Developing Brain (CADB), Weill Cornell Medicine, White Plains, NY, USA

    So Hyun & Y. B. Choi

60. Department of Health Psychology, University of Missouri, Columbia, MO, USA

    Stephen M. Kanne

61. Greenwood Genetic Center, Greenwood, SC, USA

    Steve Skinner

62. Department of Pediatrics, University of California, San Diego and SARRC Phoenix, La Jolla, CA, USA

    Vahid Gazestani

Consortia

Contributions

I. Astrovskaya, J.B.H., J.J.M., N.V., P.F., C. Shu, T.W., W.K.C., X.Z. and Y.S. designed and conceived this study. A. Adams, A. Andrus, A. Berman, A. Brown, A.C., A.C.G., A.D.S., A.E., A. Fanta, A. Fatemi, A. Fish, A. Goler, A. Gonzalez, A. Gutierrez Jr., A. Hardan, A. Hess, A. Hirshman, A. Holbrook, A.J.A., A.J. Griswold, A. Jarratt, A. Jelinek, A. Jorgenson, A. Juarez, A. Kim, A. Kitaygorodsky, A.L., A.L.R., A.L.W., A.M.D., A. Mankar, A. Mason, A. Miceli, A. Milliken, A.M.-L., A.N.S., A. Nguyen, A. Nicholson, A. Nishida, A.P., A.P.M., A.R.G., A. Raven, A. Rhea, A. Simon, A. Swanson, A. Sziklay, A. Tallbull, A. Tesng, A.W., A.Z., B.A.H., B.B., B.E., B.E.R., B. Hauf, B.J.O., B.L., B.M.V., B.S., B.V., C.A.E., C.A.W.S., C. Albright, C. Anglo, C.B., C.C.B., C.C.-S., C. Cohen, C. Colombi, C.D., C.E., C.E.R., C. Fassler, C. Gray, C. Gunter, C.H.W., C.K., C. Leonczyk, C.L.M., C. Lord, C.M.T., C.M., C.O.-L., C. Ortiz, C.P., C.R.R., C. Roche, C. Shrier, C. Smith, C.V., C.W.-L., C. Zaro, C. Zha, D.B., Daniel Cho, D. Correa, D.E.S., D.G., D.G.A., D.H., D.I., D.L.C., D. Li, D. Limon, D. Limpoco, D.P., D. Rambeck, D. Rojas, D. Srishyla, D. Stamps, E.A.F., E. Bahl, E.B.-K., E. Blank, E. Bower, E. Brooks, E.C., E. Dillon, E. Doyle, E. Given, E. Grimes, E.J., E.J.F., E.K., E.L.W., E. Lamarche, E. Lampert, E.M.B., E. O’Connor, E. Ocampo, E. Orrick, E.P., E.R., E.S., E.T.M., E.V.P., F.F., F.K.M., G.A., G.B., G.D., G.H., G.M., G.S., G.S.D., G.T., H.C., H.E.K., H.G., H.H., H.K., H.L.S., H. Lechniak, H. Li, H.M., H.R., H. Zaydens, I. Arriaga, I.F.T., J.A., J.A.G., J. Beeson, J. Brown, J. Comitre, J. Cordova, J.D., J.F.C., J.F.H., J. Gong, J. Gunderson, J.H., J.J.M., J. Judge, J. Jurayj, J.K.L., J. Manoharan, J. Montezuma, J.N., J.O., J. Pandey, J. Piven, J. Polanco, J. Polite, J.R., J.R.W., J.S., J.S.S., J.T.M., J. Tjernagel, J. Toroney, J.V.-V., J.W., K.A., K.A.S., K. Baalman, K. Beard, K. Callahan, K. Coleman, K.D.F., K. Dent, K. Diehl, K.G., K.G.P., K.H., K.L.P., K. Murillo, K. Murray, K.N., K.O., K. Pama, K.R., K. Singer, K. Smith, K. Stephenson, K.T., L.A., L.A.C., L. Beeson, L. Carpenter, L. Casten, L. Coppola, L. Cordiero, L.D., L.D.P., L.F.C., L.G.S., L.H.S., L.K.W., L.L., L.M.H., L.M.P., L. Malloch, L. Mann, L.P.G., L.S., L.V.S., L.W., L.Y., L.Y.-H., M.A., M. Baer, M. Beckwith, M. Casseus, M. Coughlin, M. Currin, M. Cutri, M. DuBois, M. Dunlevy, M.F., M.F.G., M.G., M. Haley, M. Heyman, M. Hojlo, M.J., M.J.M., M. Kowanda, M. Koza, M.L., M.M., M.N., M.N.H., M.O., M.P., M.R., M. Sabiha, M. Sahin, M. Sarris, M. Shir, M. Siegel, M. Steele, M. Sweeney, M.T., M.V.-M., M. Verdi, M.Y.D., N.A., N. Bardett, N. Berger, N.C., N.D., N.G., N.H., N. Lillie, N. Long, N.M.R.-P., N. Madi, N. Mccoy, N.N., N. Rodriguez, N. Russell, N.S., N. Takahashi, N. Targalia, N.V., O.N., O.Y.O., P.F., P.H., P.M., P.S.C., R.A.B., R.A.G., R.C.S., R.D.A., R.D.C., R.J., R.J.L., R.K.E., R.L., R.P.G.-K., R. Remington, R.S., R.T.S., S.A., S. Birdwell, S. Boland, S. Booker, S. Carpenter, S. Chintalapalli, S. Conyers, S.D., S.D.B., S.E., S.F., S.G., S. Hepburn, S. Horner, S. Hunter, S.J.B., S.J.L., S. Jacob, S. Jean, S. Kim, S. Kramer, S.L.F., S. Licona, S. Littlefield, S.M.K., S. Mastel, S. Mathai, S. Melnyk, S. Michaels, S. Mohiuddin, S. Palmer, S. Plate, S.Q., S.R., S. Sandhu, S. Santangelo, S. Skinner, S.T., S. Xu, S. Xiao, Sabrina White, Stormi White, T.C., T.G., T.H., T.I., T.K., T.P., T.R., T.S., T.R.T., T.T., V. Galbraith, V. Gazestani, V.J.M., V.R., V.S., W.C.W., W. Cal, W.K.C., W.S.Y., Y.C. and Z.E.W. recruited participants and collected clinical data and biospecimens. A. Amatya, A. Bashar, A.E.L., A. Mankar, A. Nguyen, B.J., C. Rigby, Dave Cho, D.V.M., E. O’Connor, J.A., M.D.M., M.E.B., N. Lawson, N. Lo, N.V., R.M., R. Rana, S.G., S. Jean, S. Shah and W. Chin built and supported the SPARKforAutism.org website, software, databases and systems, and managed SPARK data. A.D.K., A.J. Gruber, A. Nishida, B. Han, B.J.O., C. Fleisch, C. Shu, D.V.M., E. Brooks, G.J.F., I. Astrovskaya, J.B.H., J.J.M., J.R.W., J.U.O., L. Brueggeman, L.G.S., M.A.P., N. Lo, N.V., O.M., P.F., S.D.B., S.C.M., S.X.X., T.N.T., T.S.C., T.W., W.T.H., X.Z. and Y.S. performed analyses, processed biospecimens and sequenced DNA samples. A. Fatemi, A. Kitaygorodsky, A. Soucy, C. Shu, D.H.G., E.B.-K., E.E.E., E.R., H.Q., H. Zhang, H. Zhao, I. Astrovskaya, J.B.H., J.J.M., J.R.W., J.U.O., L. Brueggeman, L.G.S., M.Y.D., N.V., O.M., P.F., R.N.D., S.D.B., S.C.M., S.X.X., T.K., T.N.T., T.P., T.S., T.R.T., T.W., T.W.Y., W.K.C., X.Z. and Y.S. helped with data interpretation. A.E.L., E.E.E., J.J.M., N.V., P.F., W.K.C. and X.Z. supervised the work. B.J.O., I. Astrovskaya, J.B.H., J.J.M., J.U.O., C. Shu, J.R.W., N.V., P.F., T.N.T., T.W., W.K.C., X.Z. and Y.S. wrote this paper.

Corresponding author

Correspondence to
Wendy K. Chung.

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