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Talkowski ME, Rosenfeld JA, Blumenthal I, Pillalamarri V, Chiang C, Heilbut A, Ernst C, Hanscom C, Rossin E, Lindgren A, Pereira S, Ruderfer D, Kirby A, Ripke S, Harris D, Lee JH, Ha K, Kim HG, Solomon BD, Gropman AL, Lucente D, Sims K, Ohsumi TK, Borowsky ML, Loranger S, Quade B, Lage K, Miles J, Wu BL, Shen Y, Neale B, Shaffer LG, Daly MJ, Morton CC, Gusella JF. Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries. Cell 2012; 149:525-37. [PMID: 22521361 PMCID: PMC3340505 DOI: 10.1016/j.cell.2012.03.028] [Citation(s) in RCA: 425] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 02/27/2012] [Accepted: 03/28/2012] [Indexed: 01/18/2023]
Abstract
Balanced chromosomal abnormalities (BCAs) represent a relatively untapped reservoir of single-gene disruptions in neurodevelopmental disorders (NDDs). We sequenced BCAs in patients with autism or related NDDs, revealing disruption of 33 loci in four general categories: (1) genes previously associated with abnormal neurodevelopment (e.g., AUTS2, FOXP1, and CDKL5), (2) single-gene contributors to microdeletion syndromes (MBD5, SATB2, EHMT1, and SNURF-SNRPN), (3) novel risk loci (e.g., CHD8, KIRREL3, and ZNF507), and (4) genes associated with later-onset psychiatric disorders (e.g., TCF4, ZNF804A, PDE10A, GRIN2B, and ANK3). We also discovered among neurodevelopmental cases a profoundly increased burden of copy-number variants from these 33 loci and a significant enrichment of polygenic risk alleles from genome-wide association studies of autism and schizophrenia. Our findings suggest a polygenic risk model of autism and reveal that some neurodevelopmental genes are sensitive to perturbation by multiple mutational mechanisms, leading to variable phenotypic outcomes that manifest at different life stages.
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Affiliation(s)
- Michael E. Talkowski
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Department of Neurology, Harvard Medical School, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | | | - Ian Blumenthal
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Vamsee Pillalamarri
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Colby Chiang
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Adrian Heilbut
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Carl Ernst
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Carrie Hanscom
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Elizabeth Rossin
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Amelia Lindgren
- Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA
| | - Shahrin Pereira
- Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA
| | - Douglas Ruderfer
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Andrew Kirby
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Stephan Ripke
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - David Harris
- Division of Clinical Genetics, Children’s Hospital of Boston, Boston, MA
| | - Ji-Hyun Lee
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Kyungsoo Ha
- Cancer Research Center, Georgia Health Sciences University, Augusta, GA
| | - Hyung-Goo Kim
- Department of OB/GYN, IMMAG, Georgia Health Sciences University, Augusta, GA
| | - Benjamin D. Solomon
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Andrea L. Gropman
- Department of Neurology, Children’s National Medical Center, Washington, DC, USA
- Department of Neurology, George Washington University of Health Sciences, Washington, DC, USA
| | - Diane Lucente
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Katherine Sims
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Toshiro K. Ohsumi
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
| | - Mark L. Borowsky
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
| | | | - Bradley Quade
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Kasper Lage
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
- Pediatric Surgical Research Laboratories, MassGeneral Hospital for Children, Massachusetts General Hospital, Boston, MA, USA
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Judith Miles
- Departments of Pediatrics, Medical Genetics & Pathology, The Thompson Center for Autism & Neurodevelopmental Disorders, University of Missouri Hospitals and Clinics, Columbia, MO
| | - Bai-Lin Wu
- Department of Pathology, Massachusetts General Hospital, Boston, MA
- Department of Laboratory Medicine, Children’s Hospital Boston, Boston, MA
- Children’s Hospital and Institutes of Biomedical Science, Fudan University, Shanghai, China
| | - Yiping Shen
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
- Department of Laboratory Medicine, Children’s Hospital Boston, Boston, MA
- Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Benjamin Neale
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Lisa G. Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA
| | - Mark J. Daly
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
- Autism Consortium of Boston, Boston, MA
| | - Cynthia C. Morton
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - James F. Gusella
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Autism Consortium of Boston, Boston, MA
- Department of Genetics, Harvard Medical School, Boston, MA
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