Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries
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 associate...
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| Published in | Cell Vol. 149; no. 3; pp. 525 - 537 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
27.04.2012
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0092-8674 1097-4172 1097-4172 |
| DOI | 10.1016/j.cell.2012.03.028 |
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| 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.
[Display omitted]
▸ Mechanisms of epigenetic and transcriptional regulation implicated in autism ▸ Balanced chromosomal abnormality breakpoints harbor individual strong-effect genes ▸ Dosage-sensitive loci confer risk to autism from a spectrum of mutational mechanisms ▸ Different alterations in a gene are associated with diverse clinical outcomes
Sequencing of balanced chromosomal abnormalities, combined with convergent genomic studies of gene expression, copy-number variation, and genome-wide association, identifies 22 new loci that contribute to autism and related neurodevelopmental disorders. These data support a polygenic risk model for autism and provide new insight into how different types of mutations of the same genes can lead to variable disease phenotypes that manifest at different stages of life. |
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| AbstractList | 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.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. 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. [Display omitted] ▸ Mechanisms of epigenetic and transcriptional regulation implicated in autism ▸ Balanced chromosomal abnormality breakpoints harbor individual strong-effect genes ▸ Dosage-sensitive loci confer risk to autism from a spectrum of mutational mechanisms ▸ Different alterations in a gene are associated with diverse clinical outcomes Sequencing of balanced chromosomal abnormalities, combined with convergent genomic studies of gene expression, copy-number variation, and genome-wide association, identifies 22 new loci that contribute to autism and related neurodevelopmental disorders. These data support a polygenic risk model for autism and provide new insight into how different types of mutations of the same genes can lead to variable disease phenotypes that manifest at different stages of life. 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. Balanced chromosomal abnormalities (BCAs) represent a reservoir of single gene disruptions in neurodevelopmental disorders (NDD). We sequenced BCAs in autism and related NDDs, revealing disruption of 33 loci in four general categories: 1) genes associated with abnormal neurodevelopment (e.g., AUTS2, FOXP1, CDKL5 ), 2) single gene contributors to microdeletion syndromes ( MBD5, SATB2, EHMT1, SNURF-SNRPN ), 3) novel risk loci (e.g., CHD8, KIRREL3 , ZNF507 ), and 4) genes associated with later onset psychiatric disorders (e.g., TCF4, ZNF804A, PDE10A, GRIN2B, ANK3 ). We also discovered profoundly increased burden of copy number variants among 19,556 neurodevelopmental cases compared to 13,991 controls (p = 2.07×10 −47 ) and enrichment of polygenic risk alleles from autism and schizophrenia genome-wide association studies (p = 0.0018 and 0.0009, respectively). Our findings suggest a polygenic risk model of autism incorporating loci of strong effect and indicate that some neurodevelopmental genes are sensitive to perturbation by multiple mutational mechanisms, leading to variable phenotypic outcomes that manifest at different life stages. 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. |
| Author | Kim, Hyung-Goo Lucente, Diane Chiang, Colby Solomon, Benjamin D. Sims, Katherine Pereira, Shahrin Blumenthal, Ian Morton, Cynthia C. Harris, David J. Shen, Yiping Talkowski, Michael E. Hanscom, Carrie Lage, Kasper Ripke, Stephan Borowsky, Mark L. Shaffer, Lisa G. Pillalamarri, Vamsee Quade, Bradley Ruderfer, Douglas Gropman, Andrea L. Rosenfeld, Jill A. Ohsumi, Toshiro K. Gusella, James F. Lee, Ji-Hyun Miles, Judith Wu, Bai-Lin Daly, Mark J. Neale, Benjamin Rossin, Elizabeth Loranger, Stephanie Ha, Kyungsoo Ernst, Carl Lindgren, Amelia M. Kirby, Andrew Heilbut, Adrian |
| AuthorAffiliation | 13 Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 8 Cancer Research Center, Georgia Health Sciences University, Augusta, GA 3 Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 9 Department of OB/GYN, IMMAG, Georgia Health Sciences University, Augusta, GA 4 Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 17 Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark 22 Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China 5 Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 6 Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA 11 Department of Neurology, Children’s National Medical Center, Washington, DC, USA 2 Department of Neurology, Harvard Medical School, Boston, MA 15 Department of Pathology, Massachusetts General Hospital, Boston, |
| AuthorAffiliation_xml | – name: 14 Autism Consortium of Boston, Boston, MA – name: 2 Department of Neurology, Harvard Medical School, Boston, MA – name: 3 Program in Medical and Population Genetics, Broad Institute, Cambridge, MA – name: 15 Department of Pathology, Massachusetts General Hospital, Boston, MA – name: 4 Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA – name: 21 Children’s Hospital and Institutes of Biomedical Science, Fudan University, Shanghai, China – name: 6 Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA – name: 7 Division of Clinical Genetics, Children’s Hospital of Boston, Boston, MA – name: 5 Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA – name: 13 Department of Molecular Biology, Massachusetts General Hospital, Boston, MA – name: 9 Department of OB/GYN, IMMAG, Georgia Health Sciences University, Augusta, GA – name: 17 Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark – name: 23 Department of Genetics, Harvard Medical School, Boston, MA – name: 8 Cancer Research Center, Georgia Health Sciences University, Augusta, GA – name: 1 Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA – name: 11 Department of Neurology, Children’s National Medical Center, Washington, DC, USA – name: 10 Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA – name: 16 Pediatric Surgical Research Laboratories, MassGeneral Hospital for Children, Massachusetts General Hospital, Boston, MA, USA – name: 12 Department of Neurology, George Washington University of Health Sciences, Washington, DC, USA – name: 20 Department of Laboratory Medicine, Children’s Hospital Boston, Boston, MA – name: 18 Center for Protein Research, University of Copenhagen, Copenhagen, Denmark – name: 19 Departments of Pediatrics, Medical Genetics & Pathology, The Thompson Center for Autism & Neurodevelopmental Disorders, University of Missouri Hospitals and Clinics, Columbia, MO – name: 22 Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China |
| Author_xml | – sequence: 1 givenname: Michael E. surname: Talkowski fullname: Talkowski, Michael E. organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 2 givenname: Jill A. surname: Rosenfeld fullname: Rosenfeld, Jill A. organization: Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207, USA – sequence: 3 givenname: Ian surname: Blumenthal fullname: Blumenthal, Ian organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 4 givenname: Vamsee surname: Pillalamarri fullname: Pillalamarri, Vamsee organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 5 givenname: Colby surname: Chiang fullname: Chiang, Colby organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 6 givenname: Adrian surname: Heilbut fullname: Heilbut, Adrian organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 7 givenname: Carl surname: Ernst fullname: Ernst, Carl organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 8 givenname: Carrie surname: Hanscom fullname: Hanscom, Carrie organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 9 givenname: Elizabeth surname: Rossin fullname: Rossin, Elizabeth organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 10 givenname: Amelia M. surname: Lindgren fullname: Lindgren, Amelia M. organization: Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA – sequence: 11 givenname: Shahrin surname: Pereira fullname: Pereira, Shahrin organization: Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA – sequence: 12 givenname: Douglas surname: Ruderfer fullname: Ruderfer, Douglas organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 13 givenname: Andrew surname: Kirby fullname: Kirby, Andrew organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 14 givenname: Stephan surname: Ripke fullname: Ripke, Stephan organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 15 givenname: David J. surname: Harris fullname: Harris, David J. organization: Division of Clinical Genetics, Children's Hospital Boston, Boston, MA 02115, USA – sequence: 16 givenname: Ji-Hyun surname: Lee fullname: Lee, Ji-Hyun organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 17 givenname: Kyungsoo surname: Ha fullname: Ha, Kyungsoo organization: Cancer Research Center, Georgia Health Sciences University, Augusta, GA 30912, USA – sequence: 18 givenname: Hyung-Goo surname: Kim fullname: Kim, Hyung-Goo organization: Department of Obstetrics and Gynecology, Institute of Molecular Medicine and Genetics, Georgia Health Sciences University, Augusta, GA 30912, USA – sequence: 19 givenname: Benjamin D. surname: Solomon fullname: Solomon, Benjamin D. organization: Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA – sequence: 20 givenname: Andrea L. surname: Gropman fullname: Gropman, Andrea L. organization: Department of Neurology, Children's National Medical Center, Washington, DC 20010, USA – sequence: 21 givenname: Diane surname: Lucente fullname: Lucente, Diane organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 22 givenname: Katherine surname: Sims fullname: Sims, Katherine organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 23 givenname: Toshiro K. surname: Ohsumi fullname: Ohsumi, Toshiro K. organization: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 24 givenname: Mark L. surname: Borowsky fullname: Borowsky, Mark L. organization: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 25 givenname: Stephanie surname: Loranger fullname: Loranger, Stephanie organization: Autism Consortium of Boston, Boston, MA 02115, USA – sequence: 26 givenname: Bradley surname: Quade fullname: Quade, Bradley organization: Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 27 givenname: Kasper surname: Lage fullname: Lage, Kasper organization: Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 28 givenname: Judith surname: Miles fullname: Miles, Judith organization: Departments of Pediatrics, Medical Genetics and Pathology, The Thompson Center for Autism and Neurodevelopmental Disorders, University of Missouri Hospitals and Clinics, Columbia, MO 65201, USA – sequence: 29 givenname: Bai-Lin surname: Wu fullname: Wu, Bai-Lin organization: Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 30 givenname: Yiping surname: Shen fullname: Shen, Yiping organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 31 givenname: Benjamin surname: Neale fullname: Neale, Benjamin organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 32 givenname: Lisa G. surname: Shaffer fullname: Shaffer, Lisa G. organization: Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207, USA – sequence: 33 givenname: Mark J. surname: Daly fullname: Daly, Mark J. organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 34 givenname: Cynthia C. surname: Morton fullname: Morton, Cynthia C. organization: Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA – sequence: 35 givenname: James F. surname: Gusella fullname: Gusella, James F. email: gusella@helix.mgh.harvard.edu organization: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/22521361$$D View this record in MEDLINE/PubMed |
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| Snippet | Balanced chromosomal abnormalities (BCAs) represent a relatively untapped reservoir of single-gene disruptions in neurodevelopmental disorders (NDDs). We... Balanced chromosomal abnormalities (BCAs) represent a reservoir of single gene disruptions in neurodevelopmental disorders (NDD). We sequenced BCAs in autism... |
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| SubjectTerms | alleles Autism Autistic Disorder - diagnosis Autistic Disorder - genetics Boundaries Child Child Development Disorders, Pervasive - diagnosis Child Development Disorders, Pervasive - genetics Chromosome Aberrations Chromosome Breakage Chromosome Deletion Developmental stages DNA Copy Number Variations Foxp1 protein Genetic Predisposition to Disease Genome-Wide Association Study Humans loci Mental disorders Nervous System - growth & development neurodevelopment Neurodevelopmental disorders patients risk Schizophrenia Schizophrenia - genetics Sequence Analysis, DNA Signal Transduction |
| Title | Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries |
| URI | https://dx.doi.org/10.1016/j.cell.2012.03.028 https://www.ncbi.nlm.nih.gov/pubmed/22521361 https://www.proquest.com/docview/1010494875 https://www.proquest.com/docview/1028023045 https://www.proquest.com/docview/2000021571 https://pubmed.ncbi.nlm.nih.gov/PMC3340505 |
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