1
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Constantino JN, Abbacchi AM, May BK, Klaiman C, Zhang Y, Lowe JK, Marrus N, Klin A, Geschwind DH. Prospects for Leveling the Playing Field for Black Children With Autism. J Am Acad Child Adolesc Psychiatry 2023; 62:949-952. [PMID: 37196781 PMCID: PMC10948275 DOI: 10.1016/j.jaac.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/04/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023]
Abstract
Among the many race-based health disparities that have persistently plagued the US population,1 the disproportionate burden of adverse neurodevelopmental outcomes to Black children affected by autism spectrum disorder (ASD) is particularly devastating given its major lifelong consequences. Recently, in 3 successive reports from the Autism and Developmental Disabilities Monitoring (ADDM) program of the US Centers for Disease Control and Prevention (CDC) (birth cohort years 2014, 2016, and 2018), we and our collaborators reported that although the prevalence of community-diagnosed ASD had equalized for Black and non-Hispanic White (NHW) children in the United States, there has persisted a pronounced racial disparity in the proportion of ASD-affected children with comorbid intellectual disability (ID), on the order of 50% for Black children with ASD vs 20% for White children with ASD.2 Here, we provide data to support the following: much earlier diagnosis is possible; early diagnosis alone is not likely to close the ID comorbidity disparity; and judicious efforts over care as usual are necessary to ensure that Black children have access to timely implementation of developmental therapy, for which we observed promising associations with improved cognitive and adaptive outcomes in our sample.
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Affiliation(s)
| | - Anna M Abbacchi
- Washington University School of Medicine, St. Louis, Missouri
| | - Brandon K May
- Washington University School of Medicine, St. Louis, Missouri
| | - Cheryl Klaiman
- Marcus Autism Center, School of Medicine, Emory University, Atlanta, Georgia
| | - Yi Zhang
- Washington University School of Medicine, St. Louis, Missouri
| | - Jennifer K Lowe
- David Geffen School of Medicine, University of California, Los Angeles, California
| | - Natasha Marrus
- Washington University School of Medicine, St. Louis, Missouri
| | - Ami Klin
- Marcus Autism Center, School of Medicine, Emory University, Atlanta, Georgia
| | - Daniel H Geschwind
- David Geffen School of Medicine, University of California, Los Angeles, California
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2
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Cirnigliaro M, Chang TS, Arteaga SA, Pérez-Cano L, Ruzzo EK, Gordon A, Bicks LK, Jung JY, Lowe JK, Wall DP, Geschwind DH. The contributions of rare inherited and polygenic risk to ASD in multiplex families. Proc Natl Acad Sci U S A 2023; 120:e2215632120. [PMID: 37506195 PMCID: PMC10400943 DOI: 10.1073/pnas.2215632120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 06/13/2023] [Indexed: 07/30/2023] Open
Abstract
Autism spectrum disorder (ASD) has a complex genetic architecture involving contributions from both de novo and inherited variation. Few studies have been designed to address the role of rare inherited variation or its interaction with common polygenic risk in ASD. Here, we performed whole-genome sequencing of the largest cohort of multiplex families to date, consisting of 4,551 individuals in 1,004 families having two or more autistic children. Using this study design, we identify seven previously unrecognized ASD risk genes supported by a majority of rare inherited variants, finding support for a total of 74 genes in our cohort and a total of 152 genes after combined analysis with other studies. Autistic children from multiplex families demonstrate an increased burden of rare inherited protein-truncating variants in known ASD risk genes. We also find that ASD polygenic score (PGS) is overtransmitted from nonautistic parents to autistic children who also harbor rare inherited variants, consistent with combinatorial effects in the offspring, which may explain the reduced penetrance of these rare variants in parents. We also observe that in addition to social dysfunction, language delay is associated with ASD PGS overtransmission. These results are consistent with an additive complex genetic risk architecture of ASD involving rare and common variation and further suggest that language delay is a core biological feature of ASD.
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Affiliation(s)
- Matilde Cirnigliaro
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Timothy S. Chang
- Movement Disorders Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Stephanie A. Arteaga
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Laura Pérez-Cano
- STALICLA Discovery and Data Science Unit, World Trade Center, Barcelona08039, Spain
| | - Elizabeth K. Ruzzo
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Aaron Gordon
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Lucy K. Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Jae-Yoon Jung
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA94304
- Department of Biomedical Data Science, Stanford University, Stanford, CA94305
| | - Jennifer K. Lowe
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Dennis P. Wall
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA94304
- Department of Biomedical Data Science, Stanford University, Stanford, CA94305
| | - Daniel H. Geschwind
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Movement Disorders Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
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3
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Lawrence KE, Hernandez LM, Fuster E, Padgaonkar NT, Patterson G, Jung J, Okada NJ, Lowe JK, Hoekstra JN, Jack A, Aylward E, Gaab N, Van Horn JD, Bernier RA, McPartland JC, Webb SJ, Pelphrey KA, Green SA, Bookheimer SY, Geschwind DH, Dapretto M. Impact of autism genetic risk on brain connectivity: a mechanism for the female protective effect. Brain 2021; 145:378-387. [PMID: 34050743 PMCID: PMC8967090 DOI: 10.1093/brain/awab204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 04/23/2021] [Accepted: 05/11/2021] [Indexed: 01/27/2023] Open
Abstract
The biological mechanisms underlying the greater prevalence of autism spectrum disorder in males than females remain poorly understood. One hypothesis posits that this female protective effect arises from genetic load for autism spectrum disorder differentially impacting male and female brains. To test this hypothesis, we investigated the impact of cumulative genetic risk for autism spectrum disorder on functional brain connectivity in a balanced sample of boys and girls with autism spectrum disorder and typically developing boys and girls (127 youth, ages 8-17). Brain connectivity analyses focused on the salience network, a core intrinsic functional connectivity network which has previously been implicated in autism spectrum disorder. The effects of polygenic risk on salience network functional connectivity were significantly modulated by participant sex, with genetic load for autism spectrum disorder influencing functional connectivity in boys with and without autism spectrum disorder but not girls. These findings support the hypothesis that autism spectrum disorder risk genes interact with sex differential processes, thereby contributing to the male bias in autism prevalence and proposing an underlying neurobiological mechanism for the female protective effect.
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Affiliation(s)
- Katherine E Lawrence
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA,Correspondence to: Mirella Dapretto Ahmanson-Lovelace Brain Mapping Center 660 Charles E. Young Drive South Los Angeles, CA 90095, USA E-mail:
| | - Leanna M Hernandez
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Emily Fuster
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Namita T Padgaonkar
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Genevieve Patterson
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jiwon Jung
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Nana J Okada
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jennifer K Lowe
- Department of Neurology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jackson N Hoekstra
- Department of Neurology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Allison Jack
- Department of Psychology, George Mason University, Fairfax, VA 22030, USA
| | - Elizabeth Aylward
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Nadine Gaab
- Harvard Graduate School of Education, Cambridge, MA 02138, USA
| | - John D Van Horn
- Department of Psychology and School of Data Science, University of Virginia, Charlottesville, VA 22904, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | | | - Sara J Webb
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA,Center on Child Health, Behavior, and Development, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Kevin A Pelphrey
- Department of Neurology, University of Virginia, Charlottesville, VA 22904, USA
| | - Shulamite A Green
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Susan Y Bookheimer
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel H Geschwind
- Department of Neurology, University of California Los Angeles, Los Angeles, CA 90095, USA,Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Mirella Dapretto
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA
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4
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Constantino JN, Abbacchi AM, Saulnier C, Klaiman C, Mandell DS, Zhang Y, Hawks Z, Bates J, Klin A, Shattuck P, Molholm S, Fitzgerald R, Roux A, Lowe JK, Geschwind DH. Timing of the Diagnosis of Autism in African American Children. Pediatrics 2020; 146:peds.2019-3629. [PMID: 32839243 PMCID: PMC7461218 DOI: 10.1542/peds.2019-3629] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/29/2020] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES African American (AA) children affected by autism spectrum disorder (ASD) experience delays in diagnosis and obstacles to service access, as well as a disproportionate burden of intellectual disability (ID) as documented in surveillance data recently published by the US Centers for Disease Control and Prevention. Our objective in this study was to analyze data from the largest-available repository of diagnostic and phenotypic information on AA children with ASD, and to explore the wide variation in outcome within the cohort as a function of sociodemographic risk and specific obstacles to service access for the purpose of informing a national approach to resolution of these disparities. METHODS Parents of 584 AA children with autism consecutively enrolled in the Autism Genetic Resource Exchange across 4 US data collection sites completed event history calendar interviews of the diagnostic odysseys for their children with ASD. These data were examined in relation to developmental outcomes of the children with autism and their unaffected siblings. RESULTS The average age of ASD diagnosis was 64.9 months (±49.6), on average 42.3 months (±45.1) after parents' first concerns about their children's development. The relationship between timing of diagnosis and ASD severity was complex, and ID comorbidity was not predicted in a straightforward manner by familial factors associated with cognitive variation in the general population. CONCLUSIONS These findings document significant opportunity to expedite diagnosis, the need to further understand causes of ID comorbidity, and the necessity to identify effective approaches to the resolution of disparities in severity-of-outcome for AA children with autism.
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Affiliation(s)
- John N. Constantino
- Department of Psychiatry, School of Medicine,
Washington University, St Louis, Missouri;,Contributed equally as co-first authors
| | - Anna M. Abbacchi
- Department of Psychiatry, School of Medicine,
Washington University, St Louis, Missouri;,Contributed equally as co-first authors
| | - Celine Saulnier
- Marcus Autism Center, School of Medicine, Emory
University, Atlanta, Georgia;,Neurodevelopmental Assessment and Consulting
Services, Atlanta, Georgia
| | - Cheryl Klaiman
- Marcus Autism Center, School of Medicine, Emory
University, Atlanta, Georgia
| | - David S. Mandell
- Department of Psychiatry, Perelman School of
Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yi Zhang
- Department of Psychiatry, School of Medicine,
Washington University, St Louis, Missouri
| | - Zoe Hawks
- Department of Psychiatry, School of Medicine,
Washington University, St Louis, Missouri
| | - Julianna Bates
- Departments of Pediatrics, Neuroscience, and
Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx,
New York
| | - Ami Klin
- Marcus Autism Center, School of Medicine, Emory
University, Atlanta, Georgia
| | - Paul Shattuck
- Drexel Autism Institute, Drexel University,
Philadelphia, Pennsylvania; and
| | - Sophie Molholm
- Departments of Pediatrics, Neuroscience, and
Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx,
New York
| | - Robert Fitzgerald
- Department of Psychiatry, School of Medicine,
Washington University, St Louis, Missouri
| | - Anne Roux
- Drexel Autism Institute, Drexel University,
Philadelphia, Pennsylvania; and
| | - Jennifer K. Lowe
- Departments of Neurology, Psychiatry, and Human
Genetics, David Geffen School of Medicine, University of California, Los
Angeles, California
| | - Daniel H. Geschwind
- Departments of Neurology, Psychiatry, and Human
Genetics, David Geffen School of Medicine, University of California, Los
Angeles, California
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5
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Hernandez LM, Lawrence KE, Padgaonkar NT, Inada M, Hoekstra JN, Lowe JK, Eilbott J, Jack A, Aylward E, Gaab N, Van Horn JD, Bernier RA, McPartland JC, Webb SJ, Pelphrey KA, Green SA, Geschwind DH, Bookheimer SY, Dapretto M. Imaging-genetics of sex differences in ASD: distinct effects of OXTR variants on brain connectivity. Transl Psychiatry 2020; 10:82. [PMID: 32127526 PMCID: PMC7054353 DOI: 10.1038/s41398-020-0750-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/19/2019] [Accepted: 01/08/2020] [Indexed: 01/07/2023] Open
Abstract
Autism spectrum disorder (ASD) is more prevalent in males than in females, but the neurobiological mechanisms that give rise to this sex-bias are poorly understood. The female protective hypothesis suggests that the manifestation of ASD in females requires higher cumulative genetic and environmental risk relative to males. Here, we test this hypothesis by assessing the additive impact of several ASD-associated OXTR variants on reward network resting-state functional connectivity in males and females with and without ASD, and explore how genotype, sex, and diagnosis relate to heterogeneity in neuroendophenotypes. Females with ASD who carried a greater number of ASD-associated risk alleles in the OXTR gene showed greater functional connectivity between the nucleus accumbens (NAcc; hub of the reward network) and subcortical brain areas important for motor learning. Relative to males with ASD, females with ASD and higher OXTR risk-allele-dosage showed increased connectivity between the NAcc, subcortical regions, and prefrontal brain areas involved in mentalizing. This increased connectivity between NAcc and prefrontal cortex mirrored the relationship between genetic risk and brain connectivity observed in neurotypical males showing that, under increased OXTR genetic risk load, females with ASD and neurotypical males displayed increased connectivity between reward-related brain regions and prefrontal cortex. These results indicate that females with ASD differentially modulate the effects of increased genetic risk on brain connectivity relative to males with ASD, providing new insights into the neurobiological mechanisms through which the female protective effect may manifest.
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Affiliation(s)
- Leanna M Hernandez
- Ahmanson-Lovelace Brain Mapping Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Katherine E Lawrence
- Ahmanson-Lovelace Brain Mapping Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - N Tanya Padgaonkar
- Ahmanson-Lovelace Brain Mapping Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Marisa Inada
- Ahmanson-Lovelace Brain Mapping Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jackson N Hoekstra
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jennifer K Lowe
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jeffrey Eilbott
- Autism & Neurodevelopmental Disorders Institute, The George Washington University, Washington, DC, USA
| | - Allison Jack
- Autism & Neurodevelopmental Disorders Institute, The George Washington University, Washington, DC, USA
| | - Elizabeth Aylward
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Nadine Gaab
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - John D Van Horn
- USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | | | - Sara J Webb
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Kevin A Pelphrey
- University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Shulamite A Green
- Ahmanson-Lovelace Brain Mapping Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Susan Y Bookheimer
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Mirella Dapretto
- Ahmanson-Lovelace Brain Mapping Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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6
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Ruzzo EK, Pérez-Cano L, Jung JY, Wang LK, Kashef-Haghighi D, Hartl C, Singh C, Xu J, Hoekstra JN, Leventhal O, Leppä VM, Gandal MJ, Paskov K, Stockham N, Polioudakis D, Lowe JK, Prober DA, Geschwind DH, Wall DP. Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks. Cell 2019; 178:850-866.e26. [PMID: 31398340 PMCID: PMC7102900 DOI: 10.1016/j.cell.2019.07.015] [Citation(s) in RCA: 233] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/08/2019] [Accepted: 07/11/2019] [Indexed: 02/08/2023]
Abstract
We performed a comprehensive assessment of rare inherited variation in autism spectrum disorder (ASD) by analyzing whole-genome sequences of 2,308 individuals from families with multiple affected children. We implicate 69 genes in ASD risk, including 24 passing genome-wide Bonferroni correction and 16 new ASD risk genes, most supported by rare inherited variants, a substantial extension of previous findings. Biological pathways enriched for genes harboring inherited variants represent cytoskeletal organization and ion transport, which are distinct from pathways implicated in previous studies. Nevertheless, the de novo and inherited genes contribute to a common protein-protein interaction network. We also identified structural variants (SVs) affecting non-coding regions, implicating recurrent deletions in the promoters of DLG2 and NR3C2. Loss of nr3c2 function in zebrafish disrupts sleep and social function, overlapping with human ASD-related phenotypes. These data support the utility of studying multiplex families in ASD and are available through the Hartwell Autism Research and Technology portal.
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Affiliation(s)
- Elizabeth K Ruzzo
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Laura Pérez-Cano
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jae-Yoon Jung
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Lee-Kai Wang
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Dorna Kashef-Haghighi
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Chris Hartl
- Bioinformatics IDP, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chanpreet Singh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jin Xu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jackson N Hoekstra
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Olivia Leventhal
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Virpi M Leppä
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Kelley Paskov
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Nate Stockham
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Damon Polioudakis
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jennifer K Lowe
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - David A Prober
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Daniel H Geschwind
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
| | - Dennis P Wall
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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7
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Polioudakis D, de la Torre-Ubieta L, Langerman J, Elkins AG, Shi X, Stein JL, Vuong CK, Nichterwitz S, Gevorgian M, Opland CK, Lu D, Connell W, Ruzzo EK, Lowe JK, Hadzic T, Hinz FI, Sabri S, Lowry WE, Gerstein MB, Plath K, Geschwind DH. A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation. Neuron 2019; 103:785-801.e8. [PMID: 31303374 DOI: 10.1016/j.neuron.2019.06.011] [Citation(s) in RCA: 241] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/20/2019] [Accepted: 06/12/2019] [Indexed: 01/05/2023]
Abstract
We performed RNA sequencing on 40,000 cells to create a high-resolution single-cell gene expression atlas of developing human cortex, providing the first single-cell characterization of previously uncharacterized cell types, including human subplate neurons, comparisons with bulk tissue, and systematic analyses of technical factors. These data permit deconvolution of regulatory networks connecting regulatory elements and transcriptional drivers to single-cell gene expression programs, significantly extending our understanding of human neurogenesis, cortical evolution, and the cellular basis of neuropsychiatric disease. We tie cell-cycle progression with early cell fate decisions during neurogenesis, demonstrating that differentiation occurs on a transcriptomic continuum; rather than only expressing a few transcription factors that drive cell fates, differentiating cells express broad, mixed cell-type transcriptomes before telophase. By mapping neuropsychiatric disease genes to cell types, we implicate dysregulation of specific cell types in ASD, ID, and epilepsy. We developed CoDEx, an online portal to facilitate data access and browsing.
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Affiliation(s)
- Damon Polioudakis
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Luis de la Torre-Ubieta
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Justin Langerman
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Andrew G Elkins
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Xu Shi
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jason L Stein
- Department of Genetics & UNC Neuroscience Center, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Celine K Vuong
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Susanne Nichterwitz
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Melinda Gevorgian
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Biology, CSUN, Northridge, CA, USA
| | - Carli K Opland
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Daning Lu
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - William Connell
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Elizabeth K Ruzzo
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jennifer K Lowe
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Tarik Hadzic
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Flora I Hinz
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Shan Sabri
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - William E Lowry
- Department of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
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8
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Chen Z, Chen JA, Shatunov A, Jones AR, Kravitz SN, Huang AY, Lawrence L, Lowe JK, Lewis CM, Payan CAM, Lieb W, Franke A, Deloukas P, Amouyel P, Tzourio C, Dartigues JF, Ludolph A, Bensimon G, Leigh PN, Bronstein JM, Coppola G, Geschwind DH, Al-Chalabi A. Genome-wide survey of copy number variants finds MAPT duplications in progressive supranuclear palsy. Mov Disord 2019; 34:1049-1059. [PMID: 31059154 DOI: 10.1002/mds.27702] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/01/2019] [Accepted: 02/26/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Progressive supranuclear palsy is a neurodegenerative tauopathy manifesting clinically as a progressive akinetic-rigid syndrome. In this study, we sought to identify genetic variants influencing PSP susceptibility through a genome-wide association analysis of a cohort of well-characterized patients who had participated in the Neuroprotection and Natural History in Parkinson Plus Syndromes and Blood Brain Barrier in Parkinson Plus Syndromes studies. METHODS We genotyped single-nucleotide polymorphisms in 283 PSP cases from the United Kingdom, Germany, and France and compared these with genotypes from 4472 controls. Copy number variants were identified from genotyping data. RESULTS We observed associations on chromosome 17 within or close to the MAPT gene and explored the genetic architecture at this locus. We confirmed the previously reported association of rs1768208 in the MOBP gene (P = 3.29 × 10-13 ) and rs1411478 in STX6 (P = 3.45 × 10-10 ). The population-attributable risk from the MAPT, MOBP, and STX6 single-nucleotide polymorphisms was found to be 0.37, 0.26, and 0.08, respectively. In addition, we found 2 instances of copy number variants spanning the MAPT gene in patients with PSP. These copy number variants include tau but few other genes within the chromosome 17 haplotype region, providing additional support for the direct pathogenicity of MAPT in PSP. CONCLUSIONS Clinicians should also be aware of MAPT duplication as a possible genetic cause of PSP, especially in patients presenting with young age at onset. © 2019 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Zhongbo Chen
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Jason A Chen
- Interdepartmental Program in Bioinformatics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Stephanie N Kravitz
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Alden Y Huang
- Interdepartmental Program in Bioinformatics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Lauren Lawrence
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Jennifer K Lowe
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, and Department of Medical and Molecular Genetics, King's College London, UK
| | - Christine A M Payan
- Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpétrière, Assistance Publique Hôpitaux de Paris, Paris; Pharmacologie, Universités Paris-Sorbonne, UPMC Paris 06, Paris, France
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Christian Albrechts Universitat zu Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts Universitat zu Kiel, Kiel, Germany
| | - Panagiotis Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | - Philippe Amouyel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factor and Molecular Determinants of Aging Diseases, Labex-Distalz, Lille, France
| | - Christophe Tzourio
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, UMR-1219, CHU Bordeaux, France
| | - Jean-François Dartigues
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, UMR-1219, CHU Bordeaux, France
| | - Albert Ludolph
- Department of Neurology, University of Ulm, Oberer Eselsberg, Ulm, Germany
| | - Gilbert Bensimon
- Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpétrière, Assistance Publique Hôpitaux de Paris, Paris; Pharmacologie, Universités Paris-Sorbonne, UPMC Paris 06, Paris, France
| | - P Nigel Leigh
- Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton, UK
| | - Jeff M Bronstein
- Program in Movement Disorders, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Giovanni Coppola
- Interdepartmental Program in Bioinformatics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Center for Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Social, Genetic and Developmental Psychiatry Centre, and Department of Medical and Molecular Genetics, King's College London, UK
- Department of Human Genetics, University of California, Los Angeles, California, USA
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
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9
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Chen JA, Chen Z, Won H, Huang AY, Lowe JK, Wojta K, Yokoyama JS, Bensimon G, Leigh PN, Payan C, Shatunov A, Jones AR, Lewis CM, Deloukas P, Amouyel P, Tzourio C, Dartigues JF, Ludolph A, Boxer AL, Bronstein JM, Al-Chalabi A, Geschwind DH, Coppola G. Joint genome-wide association study of progressive supranuclear palsy identifies novel susceptibility loci and genetic correlation to neurodegenerative diseases. Mol Neurodegener 2018; 13:41. [PMID: 30089514 PMCID: PMC6083608 DOI: 10.1186/s13024-018-0270-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/29/2018] [Indexed: 11/21/2022] Open
Abstract
Background Progressive supranuclear palsy (PSP) is a rare neurodegenerative disease for which the genetic contribution is incompletely understood. Methods We conducted a joint analysis of 5,523,934 imputed SNPs in two newly-genotyped progressive supranuclear palsy cohorts, primarily derived from two clinical trials (Allon davunetide and NNIPPS riluzole trials in PSP) and a previously published genome-wide association study (GWAS), in total comprising 1646 cases and 10,662 controls of European ancestry. Results We identified 5 associated loci at a genome-wide significance threshold P < 5 × 10− 8, including replication of 3 loci from previous studies and 2 novel loci at 6p21.1 and 12p12.1 (near RUNX2 and SLCO1A2, respectively). At the 17q21.31 locus, stepwise regression analysis confirmed the presence of multiple independent loci (localized near MAPT and KANSL1). An additional 4 loci were highly suggestive of association (P < 1 × 10− 6). We analyzed the genetic correlation with multiple neurodegenerative diseases, and found that PSP had shared polygenic heritability with Parkinson’s disease and amyotrophic lateral sclerosis. Conclusions In total, we identified 6 additional significant or suggestive SNP associations with PSP, and discovered genetic overlap with other neurodegenerative diseases. These findings clarify the pathogenesis and genetic architecture of PSP. Electronic supplementary material The online version of this article (10.1186/s13024-018-0270-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jason A Chen
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, 90095, USA
| | - Zhongbo Chen
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9RX, UK
| | - Hyejung Won
- Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Alden Y Huang
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, 90095, USA
| | - Jennifer K Lowe
- Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Kevin Wojta
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, 90095, USA
| | - Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, 94158, USA
| | - Gilbert Bensimon
- BESPIM, CHU-Nîmes, Nîmes, France.,Dept Pharmacologie Clinique, Pitié-Salpêtrière Hospital, AP-PH, Paris, France.,Pharmacology UPMC-Paris VI, Universite Paris-Sorbonne, Paris, France
| | - P Nigel Leigh
- Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton, UK
| | - Christine Payan
- BESPIM, CHU-Nîmes, Nîmes, France.,Dept Pharmacologie Clinique, Pitié-Salpêtrière Hospital, AP-PH, Paris, France
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9RX, UK
| | - Ashley R Jones
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9RX, UK
| | - Cathryn M Lewis
- Medical Research Council Social, Genetic and Developmental Psychiatry Centre, and Department of Medical and Molecular Genetics, King's College London, London, SE5 8AF, UK
| | - Panagiotis Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Philippe Amouyel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factor and molecular determinants of aging diseases, Labex-Distalz, F-59000, Lille, France
| | - Christophe Tzourio
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, CHU Bordeaux, F-33000 Bordeaux, France
| | - Jean-Francois Dartigues
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, CHU Bordeaux, F-33000 Bordeaux, France
| | - Albert Ludolph
- Department of Neurology, University of Ulm, Oberer Eselsberg, Ulm, Germany
| | - Adam L Boxer
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, 94158, USA
| | - Jeff M Bronstein
- Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9RX, UK
| | - Daniel H Geschwind
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, 90095, USA.,Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Giovanni Coppola
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, 90095, USA. .,Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA. .,Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, 90095, USA. .,Departments of Psychiatry and Neurology, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E Young Dr. South, Gonda Bldg, Rm 1524, Los Angeles, CA, 90095, USA.
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10
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Parikshak NN, Swarup V, Belgard TG, Irimia M, Ramaswami G, Gandal MJ, Hartl C, Leppa V, de la Torre Ubieta L, Huang J, Lowe JK, Blencowe BJ, Horvath S, Geschwind DH. Author Correction: Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism. Nature 2018; 560:E30. [DOI: 10.1038/s41586-018-0295-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Cantor RM, Navarro L, Won H, Walker RL, Lowe JK, Geschwind DH. ASD restricted and repetitive behaviors associated at 17q21.33: genes prioritized by expression in fetal brains. Mol Psychiatry 2018; 23:993-1000. [PMID: 28533516 PMCID: PMC5700871 DOI: 10.1038/mp.2017.114] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 04/07/2017] [Accepted: 04/17/2017] [Indexed: 12/18/2022]
Abstract
Autism spectrum disorder (ASD) is a behaviorally defined condition that manifests in infancy or early childhood as deficits in communication skills and social interactions. Often, restricted and repetitive behaviors (RRBs) accompany this disorder. ASD is polygenic and genetically complex, so we hypothesized that focusing analyses on intermediate core component phenotypes, such as RRBs, can reduce genetic heterogeneity and improve statistical power. Applying this approach, we mined Caucasian genome-wide association studies (GWAS) data from two of the largest ASD family cohorts, the Autism Genetics Resource Exchange and Autism Genome Project (AGP). Of the 12 RRBs measured by the Autism Diagnostic Interview-Revised, seven were found to be significantly familial and substantially variable, and hence, were tested for genome-wide association in 3104 ASD-affected children from 2045 families. Using a stringent significance threshold (P<7.1 × 10-9), GWAS in the AGP revealed an association between 'the degree of the repetitive use of objects or interest in parts of objects' and rs2898883 (P<6.8 × 10-9), which resides within the sixth intron of PHB. To identify the candidate target genes of the associated single-nucleotide polymorphisms at that locus, we applied chromosome conformation studies in developing human brains and implicated three additional genes: SLC35B1, CALCOCO2 and DLX3. Gene expression, brain imaging and fetal brain expression quantitative trait locus studies prioritize SLC35B1 and PHB. These analyses indicate that GWAS of single heritable features of genetically complex disorders followed by chromosome conformation studies in relevant tissues can be successful in revealing novel risk genes for single core features of ASD.
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Affiliation(s)
- Rita M. Cantor
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive, South, Los Angeles, CA 90095 – 7088
- Center for Neurobehavioral Genetics, Department of Psychiatry, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive, South, Los Angeles, CA 90095 – 7088
| | - Linda Navarro
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive, South, Los Angeles, CA 90095 – 7088
| | - Hyejung Won
- Neurogenetics Program, Department of Neurology, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive, South, Los Angeles, CA 90095 – 7088
| | - Rebecca L. Walker
- Neurogenetics Program, Department of Neurology, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive, South, Los Angeles, CA 90095 – 7088
| | - Jennifer K. Lowe
- Neurogenetics Program, Department of Neurology, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive, South, Los Angeles, CA 90095 – 7088
| | - Daniel H. Geschwind
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive, South, Los Angeles, CA 90095 – 7088
- Center for Neurobehavioral Genetics, Department of Psychiatry, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive, South, Los Angeles, CA 90095 – 7088
- Neurogenetics Program, Department of Neurology, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive, South, Los Angeles, CA 90095 – 7088
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12
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Leppa VM, Kravitz SN, Martin CL, Andrieux J, Le Caignec C, Martin-Coignard D, DyBuncio C, Sanders SJ, Lowe JK, Cantor RM, Geschwind DH. Rare Inherited and De Novo CNVs Reveal Complex Contributions to ASD Risk in Multiplex Families. Am J Hum Genet 2016; 99:540-554. [PMID: 27569545 PMCID: PMC5011063 DOI: 10.1016/j.ajhg.2016.06.036] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 06/28/2016] [Indexed: 11/17/2022] Open
Abstract
Rare mutations, including copy-number variants (CNVs), contribute significantly to autism spectrum disorder (ASD) risk. Although their importance has been established in families with only one affected child (simplex families), the contribution of both de novo and inherited CNVs to ASD in families with multiple affected individuals (multiplex families) is less well understood. We analyzed 1,532 families from the Autism Genetic Resource Exchange (AGRE) to assess the impact of de novo and rare CNVs on ASD risk in multiplex families. We observed a higher burden of large, rare CNVs, including inherited events, in individuals with ASD than in their unaffected siblings (odds ratio [OR] = 1.7), but the rate of de novo events was significantly lower than in simplex families. In previously characterized ASD risk loci, we identified 49 CNVs, comprising 24 inherited events, 19 de novo events, and 6 events of unknown inheritance, a significant enrichment in affected versus control individuals (OR = 3.3). In 21 of the 30 families (71%) in whom at least one affected sibling harbored an established ASD major risk CNV, including five families harboring inherited CNVs, the CNV was not shared by all affected siblings, indicating that other risk factors are contributing. We also identified a rare risk locus for ASD and language delay at chromosomal region 2q24 (implicating NR4A2) and another lower-penetrance locus involving inherited deletions and duplications of WWOX. The genetic architecture in multiplex families differs from that in simplex families and is complex, warranting more complete genetic characterization of larger multiplex ASD cohorts.
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Affiliation(s)
- Virpi M Leppa
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Stephanie N Kravitz
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger Health System, Lewisburg, PA 18704, USA
| | - Joris Andrieux
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, Centre Hospitalier Régional Universitaire de Lille, Lille 59037, France
| | - Cedric Le Caignec
- Service de Génétique Medicale, Centre Hospitalier Universitaire Nantes, 9 Quai Moncousu, Nantes 44093, France; Laboratoire de Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, INSERM UMR-957, Nantes 44000, France
| | | | - Christina DyBuncio
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stephan J Sanders
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jennifer K Lowe
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Rita M Cantor
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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13
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Chaste P, Klei L, Sanders SJ, Hus V, Murtha MT, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Mane SM, Martin DM, Morrow EM, Walsh CA, Sutcliffe JS, Martin CL, Beaudet AL, Lord C, State MW, Cook EH, Devlin B. A genome-wide association study of autism using the Simons Simplex Collection: Does reducing phenotypic heterogeneity in autism increase genetic homogeneity? Biol Psychiatry 2015; 77:775-84. [PMID: 25534755 PMCID: PMC4379124 DOI: 10.1016/j.biopsych.2014.09.017] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 09/02/2014] [Accepted: 09/03/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Phenotypic heterogeneity in autism has long been conjectured to be a major hindrance to the discovery of genetic risk factors, leading to numerous attempts to stratify children based on phenotype to increase power of discovery studies. This approach, however, is based on the hypothesis that phenotypic heterogeneity closely maps to genetic variation, which has not been tested. Our study examines the impact of subphenotyping of a well-characterized autism spectrum disorder (ASD) sample on genetic homogeneity and the ability to discover common genetic variants conferring liability to ASD. METHODS Genome-wide genotypic data of 2576 families from the Simons Simplex Collection were analyzed in the overall sample and phenotypic subgroups defined on the basis of diagnosis, IQ, and symptom profiles. We conducted a family-based association study, as well as estimating heritability and evaluating allele scores for each phenotypic subgroup. RESULTS Association analyses revealed no genome-wide significant association signal. Subphenotyping did not increase power substantially. Moreover, allele scores built from the most associated single nucleotide polymorphisms, based on the odds ratio in the full sample, predicted case status in subsets of the sample equally well and heritability estimates were very similar for all subgroups. CONCLUSIONS In genome-wide association analysis of the Simons Simplex Collection sample, reducing phenotypic heterogeneity had at most a modest impact on genetic homogeneity. Our results are based on a relatively small sample, one with greater homogeneity than the entire population; if they apply more broadly, they imply that analysis of subphenotypes is not a productive path forward for discovering genetic risk variants in ASD.
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Affiliation(s)
- Pauline Chaste
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; FondaMental Foundation, Créteil; Centre Hospitalier Sainte Anne, Paris, France.
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of
Medicine, Pittsburgh, Pennsylvania, USA
| | - Stephan J. Sanders
- Department of Genetics, Yale University School of Medicine, New
Haven, Connecticut, USA,Department of Psychiatry, University of California at San Francisco,
California, USA
| | - Vanessa Hus
- Department of Psychology, University of Michigan, Ann Arbor, MI,
USA
| | - Michael T. Murtha
- Program on Neurogenetics, Yale University School of Medicine, New
Haven, Connecticut, USA
| | - Jennifer K. Lowe
- Neurogenetics Program, Department of Neurology and Center for Autism
Research and Treatment, Semel Institute, David Geffen School of Medicine, University
of California Los Angeles, Los Angeles, California, USA
| | - A. Jeremy Willsey
- Department of Genetics, Yale University School of Medicine, New
Haven, Connecticut, USA,Department of Psychiatry, University of California at San Francisco,
California, USA
| | - Daniel Moreno-De-Luca
- Program on Neurogenetics, Yale University School of Medicine, New
Haven, Connecticut, USA,Department of Psychiatry, Yale University School of Medicine, New
Haven, Connecticut, USA
| | - Timothy W. Yu
- Division of Genetics, Children's Hospital Boston, Harvard
Medical School, Boston, Massachusetts, USA
| | - Eric Fombonne
- Department of Psychiatry and Institute for Development and
disability, Oregon Health & Science University, Portland, Oregon, USA
| | - Daniel Geschwind
- Neurogenetics Program, Department of Neurology and Center for
Autism Research and Treatment, Semel Institute, David Geffen School of Medicine,
University of California Los Angeles, Los Angeles, California, USA
| | - Dorothy E. Grice
- Department of Psychiatry, Mount Sinai School of Medicine, New York,
New York, USA
| | - David H. Ledbetter
- Autism and Developmental Medicine Institute, Geisinger Health
System, Danville, Pennsylvania, USA
| | | | - Donna M. Martin
- Departments of Pediatrics and Human Genetics, University of
Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Eric M. Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry,
Brown University, Providence, Rhode Island, USA,Department of Psychiatry and Human Behavior, Brown University,
Providence, Rhode Island, USA
| | - Christopher A. Walsh
- Howard Hughes Medical Institute and Division of Genetics,
Children's Hospital Boston, and Neurology and Pediatrics, Harvard Medical
School Center for Life Sciences, Boston, Massachusetts, USA
| | - James S. Sutcliffe
- Departments of Molecular Physiology & Biophysics and
Psychiatry, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN,
USA
| | - Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger Health
System, Danville, Pennsylvania, USA
| | - Arthur L. Beaudet
- Department of Human and Molecular Genetics, Baylor College of
Medicine, Houston, Texas, USA
| | - Catherine Lord
- Center for Autism and the Developing Brain, Weill Cornell Medical
College, White Plains, New York, USA
| | - Matthew W. State
- Department of Genetics, Yale University School of Medicine, New
Haven, Connecticut, USA,Department of Psychiatry, University of California at San Francisco,
California, USA
| | - Edwin H. Cook
- Institute for Juvenile Research, Department of Psychiatry,
University of Illinois at Chicago, Chicago, Illinois, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of
Medicine, Pittsburgh, Pennsylvania, USA
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Lowe JK, Werling DM, Constantino JN, Cantor RM, Geschwind DH. Social responsiveness, an autism endophenotype: genomewide significant linkage to two regions on chromosome 8. Am J Psychiatry 2015; 172:266-75. [PMID: 25727539 PMCID: PMC4523091 DOI: 10.1176/appi.ajp.2014.14050576] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Autism spectrum disorder is characterized by deficits in social function and the presence of repetitive and restrictive behaviors. Following a previous test of principle, the authors adopted a quantitative approach to discovering genes contributing to the broader autism phenotype by using social responsiveness as an endophenotype for autism spectrum disorder. METHOD Linkage analyses using scores from the Social Responsiveness Scale were performed in 590 families from the Autism Genetic Resource Exchange, a largely multiplex autism spectrum disorder cohort. Regional and genomewide association analyses were performed to search for common variants contributing to social responsiveness. RESULTS Social Responsiveness Scale scores were unimodally distributed in male offspring from multiplex autism families, in contrast with a bimodal distribution observed in female offspring. In correlated analyses differing by Social Responsiveness Scale respondent, genomewide significant linkage for social responsiveness was identified at chr8p21.3 (multipoint LOD=4.11; teacher/parent scores) and chr8q24.22 (multipoint LOD=4.54; parent-only scores), respectively. Genomewide or linkage-directed association analyses did not detect common variants contributing to social responsiveness. CONCLUSIONS The sex-differential distributions of Social Responsiveness Scale scores in multiplex autism families likely reflect mechanisms contributing to the sex ratio for autism observed in the general population and form a quantitative signature of reduced penetrance of inherited liability to autism spectrum disorder among females. The identification of two strong loci for social responsiveness validates the endophenotype approach for the identification of genetic variants contributing to complex traits such as autism spectrum disorder. While causal mutations have yet to be identified, these findings are consistent with segregation of rare genetic variants influencing social responsiveness and underscore the increasingly recognized role of rare inherited variants in the genetic architecture of autism spectrum disorder.
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Affiliation(s)
- Jennifer K. Lowe
- Neurogenetics Program and Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095,Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095,Center for Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Donna M. Werling
- Interdepartmental PhD Program in Neuroscience, Brain Research Institute, University of California, Los Angeles, Los Angeles, CA 90095
| | - John N. Constantino
- Departments of Psychiatry and Pediatrics, Washington University School of Medicine, St Louis, MO 63110
| | - Rita M. Cantor
- Center for Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095,Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095
| | - Daniel H. Geschwind
- Neurogenetics Program and Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095,Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095,Center for Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095,Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095
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15
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Stein JL, de la Torre-Ubieta L, Tian Y, Parikshak NN, Hernández IA, Marchetto MC, Baker DK, Lu D, Hinman CR, Lowe JK, Wexler EM, Muotri AR, Gage FH, Kosik KS, Geschwind DH. A quantitative framework to evaluate modeling of cortical development by neural stem cells. Neuron 2014; 83:69-86. [PMID: 24991955 DOI: 10.1016/j.neuron.2014.05.035] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2014] [Indexed: 01/19/2023]
Abstract
Neural stem cells have been adopted to model a wide range of neuropsychiatric conditions in vitro. However, how well such models correspond to in vivo brain has not been evaluated in an unbiased, comprehensive manner. We used transcriptomic analyses to compare in vitro systems to developing human fetal brain and observed strong conservation of in vivo gene expression and network architecture in differentiating primary human neural progenitor cells (phNPCs). Conserved modules are enriched in genes associated with ASD, supporting the utility of phNPCs for studying neuropsychiatric disease. We also developed and validated a machine learning approach called CoNTExT that identifies the developmental maturity and regional identity of in vitro models. We observed strong differences between in vitro models, including hiPSC-derived neural progenitors from multiple laboratories. This work provides a systems biology framework for evaluating in vitro systems and supports their value in studying the molecular mechanisms of human neurodevelopmental disease.
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Affiliation(s)
- Jason L Stein
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Luis de la Torre-Ubieta
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yuan Tian
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Neelroop N Parikshak
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Israel A Hernández
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Maria C Marchetto
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Dylan K Baker
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daning Lu
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Cassidy R Hinman
- Center for Stem Cell Biology and Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Jennifer K Lowe
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric M Wexler
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alysson R Muotri
- School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fred H Gage
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kenneth S Kosik
- Molecular, Cellular and Developmental Biology and Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Daniel H Geschwind
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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16
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Chaste P, Sanders SJ, Mohan KN, Klei L, Song Y, Murtha MT, Hus V, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Lord C, Mane SM, Martin DM, Morrow EM, Walsh CA, Sutcliffe JS, State MW, Martin CL, Devlin B, Beaudet AL, Cook EH, Kim SJ. Modest impact on risk for autism spectrum disorder of rare copy number variants at 15q11.2, specifically breakpoints 1 to 2. Autism Res 2014; 7:355-62. [PMID: 24821083 PMCID: PMC6003409 DOI: 10.1002/aur.1378] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 03/19/2014] [Indexed: 01/24/2023]
Abstract
The proximal region of chromosome 15 is one of the genomic hotspots for copy number variants (CNVs). Among the rearrangements observed in this region, CNVs from the interval between the common breakpoints 1 and 2 (BP1 and BP2) have been reported cosegregating with autism spectrum disorder (ASD). Although evidence supporting an association between BP1-BP2 CNVs and autism accumulates, the magnitude of the effect of BP1-BP2 CNVs remains elusive, posing a great challenge to recurrence-risk counseling. To gain further insight into their pathogenicity for ASD, we estimated the penetrance of the BP1-BP2 CNVs for ASD as well as their effects on ASD-related phenotypes in a well-characterized ASD sample (n = 2525 families). Transmission disequilibrium test revealed significant preferential transmission only for the duplicated chromosome in probands (20T:9NT). The penetrance of the BP1-BP2 CNVs for ASD was low, conferring additional risks of 0.3% (deletion) and 0.8% (duplication). Stepwise regression analyses suggest a greater effect of the CNVs on ASD-related phenotype in males and when maternally inherited. Taken together, the results are consistent with BP1-BP2 CNVs as risk factors for autism. However, their effect is modest, more akin to that seen for common variants. To be consistent with the current American College of Medical Genetics guidelines for interpretation of postnatal CNV, the BP1-BP2 deletion and duplication CNVs would probably best be classified as variants of uncertain significance (VOUS): they appear to have an impact on risk, but one so modest that these CNVs do not merit pathogenic status.
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Affiliation(s)
- Pauline Chaste
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- FondaMental Foundation, Créteil, France
| | - Stephan J. Sanders
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, University of California at San Francisco, California, USA
| | - Kommu N. Mohan
- Department of Biological Sciences, BITS Pilani-Hyderabad Campus, Hyderabad, India
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Youeun Song
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michael T. Murtha
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Vanessa Hus
- Department of Psychology, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer K. Lowe
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - A. Jeremy Willsey
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, University of California at San Francisco, California, USA
| | - Daniel Moreno-De-Luca
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Timothy W. Yu
- Division of Genetics, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric Fombonne
- Department of Psychiatry, Oregon Health & Science University, Portland, Oregon, USA
| | - Daniel Geschwind
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Dorothy E. Grice
- Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, USA
| | - David H. Ledbetter
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Catherine Lord
- Center for Autism and the Developing Brain, Weill Cornell Medical College, White Plains, New York, USA
| | | | - Donna M. Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Eric M. Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
- Department of Psychiatry and Human Behavior, Brown University, Providence, Rhode Island, USA
| | - Christopher A. Walsh
- Howard Hughes Medical Institute and Division of Genetics, Children's Hospital Boston, and Neurology and Pediatrics, Harvard Medical School Center for Life Sciences, Boston, Massachusetts, USA
| | - James S. Sutcliffe
- Departments of Molecular Physiology & Biophysics and Psychiatry, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Matthew W. State
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, University of California at San Francisco, California, USA
| | - Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Arthur L. Beaudet
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Edwin H. Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Soo-Jeong Kim
- Center for Integrative Brain Research, Seattle Children's Research Institute & Department of Psychiatry and Behavioral Science, University of Washington, Seattle, WA, USA
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17
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Pinto D, Delaby E, Merico D, Barbosa M, Merikangas A, Klei L, Thiruvahindrapuram B, Xu X, Ziman R, Wang Z, Vorstman JAS, Thompson A, Regan R, Pilorge M, Pellecchia G, Pagnamenta AT, Oliveira B, Marshall CR, Magalhaes TR, Lowe JK, Howe JL, Griswold AJ, Gilbert J, Duketis E, Dombroski BA, De Jonge MV, Cuccaro M, Crawford EL, Correia CT, Conroy J, Conceição IC, Chiocchetti AG, Casey JP, Cai G, Cabrol C, Bolshakova N, Bacchelli E, Anney R, Gallinger S, Cotterchio M, Casey G, Zwaigenbaum L, Wittemeyer K, Wing K, Wallace S, van Engeland H, Tryfon A, Thomson S, Soorya L, Rogé B, Roberts W, Poustka F, Mouga S, Minshew N, McInnes LA, McGrew SG, Lord C, Leboyer M, Le Couteur AS, Kolevzon A, Jiménez González P, Jacob S, Holt R, Guter S, Green J, Green A, Gillberg C, Fernandez BA, Duque F, Delorme R, Dawson G, Chaste P, Café C, Brennan S, Bourgeron T, Bolton PF, Bölte S, Bernier R, Baird G, Bailey AJ, Anagnostou E, Almeida J, Wijsman EM, Vieland VJ, Vicente AM, Schellenberg GD, Pericak-Vance M, Paterson AD, Parr JR, Oliveira G, Nurnberger JI, Monaco AP, Maestrini E, Klauck SM, Hakonarson H, Haines JL, Geschwind DH, Freitag CM, Folstein SE, Ennis S, Coon H, Battaglia A, Szatmari P, Sutcliffe JS, Hallmayer J, Gill M, Cook EH, Buxbaum JD, Devlin B, Gallagher L, Betancur C, Scherer SW. Convergence of genes and cellular pathways dysregulated in autism spectrum disorders. Am J Hum Genet 2014; 94:677-94. [PMID: 24768552 PMCID: PMC4067558 DOI: 10.1016/j.ajhg.2014.03.018] [Citation(s) in RCA: 659] [Impact Index Per Article: 65.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 03/25/2014] [Indexed: 12/15/2022] Open
Abstract
Rare copy-number variation (CNV) is an important source of risk for autism spectrum disorders (ASDs). We analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0 × 10−5) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability (odds ratio = 12.62, p = 2.7 × 10−15, ∼3% of ASD subjects). Pathogenic CNVs, often showing variable expressivity, included rare de novo and inherited events at 36 loci, implicating ASD-associated genes (CHD2, HDAC4, and GDI1) previously linked to other neurodevelopmental disorders, as well as other genes such as SETD5, MIR137, and HDAC9. Consistent with hypothesized gender-specific modulators, females with ASD were more likely to have highly penetrant CNVs (p = 0.017) and were also overrepresented among subjects with fragile X syndrome protein targets (p = 0.02). Genes affected by de novo CNVs and/or loss-of-function single-nucleotide variants converged on networks related to neuronal signaling and development, synapse function, and chromatin regulation.
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Affiliation(s)
- Dalila Pinto
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elsa Delaby
- Institut National de la Santé et de la Recherche Médicale U1130, 75005 Paris, France; Centre National de la Recherche Scientifique UMR 8246, 75005 Paris, France; Neuroscience Paris Seine, Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 75005 Paris, France
| | - Daniele Merico
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Mafalda Barbosa
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alison Merikangas
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Bhooma Thiruvahindrapuram
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Xiao Xu
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert Ziman
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Zhuozhi Wang
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Jacob A S Vorstman
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Ann Thompson
- Department of Psychiatry and Behavioural Neurosciences, Offord Centre for Child Studies, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Regina Regan
- National Children's Research Centre, Our Lady's Children's Hospital, Dublin 12, Ireland; Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - Marion Pilorge
- Institut National de la Santé et de la Recherche Médicale U1130, 75005 Paris, France; Centre National de la Recherche Scientifique UMR 8246, 75005 Paris, France; Neuroscience Paris Seine, Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 75005 Paris, France
| | - Giovanna Pellecchia
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | | | - Bárbara Oliveira
- Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; Center for Biodiversity, Functional, & Integrative Genomics, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal
| | - Christian R Marshall
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Tiago R Magalhaes
- National Children's Research Centre, Our Lady's Children's Hospital, Dublin 12, Ireland; Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - Jennifer K Lowe
- Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jennifer L Howe
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - John Gilbert
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Eftichia Duketis
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Goethe University, 60528 Frankfurt am Main, Germany
| | - Beth A Dombroski
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maretha V De Jonge
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Michael Cuccaro
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Emily L Crawford
- Vanderbilt Brain Institute, Center for Human Genetics Research, and Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Catarina T Correia
- Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; Center for Biodiversity, Functional, & Integrative Genomics, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal
| | - Judith Conroy
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland; Children's University Hospital Temple Street, Dublin 1, Ireland
| | - Inês C Conceição
- Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; Center for Biodiversity, Functional, & Integrative Genomics, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal
| | - Andreas G Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Goethe University, 60528 Frankfurt am Main, Germany
| | - Jillian P Casey
- National Children's Research Centre, Our Lady's Children's Hospital, Dublin 12, Ireland; Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - Guiqing Cai
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christelle Cabrol
- Institut National de la Santé et de la Recherche Médicale U1130, 75005 Paris, France; Centre National de la Recherche Scientifique UMR 8246, 75005 Paris, France; Neuroscience Paris Seine, Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 75005 Paris, France
| | - Nadia Bolshakova
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Richard Anney
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Steven Gallinger
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | | | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Lonnie Zwaigenbaum
- Department of Pediatrics, University of Alberta, Edmonton, AB T6B 2H3, Canada
| | | | - Kirsty Wing
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Simon Wallace
- Department of Psychiatry, University of Oxford and Warneford Hospital, Oxford OX3 7JX, UK
| | - Herman van Engeland
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Ana Tryfon
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Susanne Thomson
- Vanderbilt Brain Institute, Center for Human Genetics Research, and Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Latha Soorya
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bernadette Rogé
- Unité de Recherche Interdisciplinaire Octogone, Centre d'Etudes et de Recherches en Psychopathologie, Toulouse 2 University, 31058 Toulouse, France
| | - Wendy Roberts
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Fritz Poustka
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Goethe University, 60528 Frankfurt am Main, Germany
| | - Susana Mouga
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal; University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Nancy Minshew
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - L Alison McInnes
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Susan G McGrew
- Department of Pediatrics, Vanderbilt University, Nashville, TN 37232, USA
| | - Catherine Lord
- NewYork-Presbyterian/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Marion Leboyer
- FondaMental Foundation, 94010 Créteil, France; Institut National de la Santé et de la Recherche U955, Psychiatrie Génétique, 94010 Créteil, France; Faculté de Médecine, Université Paris Est, 94010 Créteil, France; Department of Psychiatry, Henri Mondor-Albert Chenevier Hospital, Assistance Publique - Hôpitaux de Paris, 94010 Créteil, France
| | - Ann S Le Couteur
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne NE1 4LP, UK
| | - Alexander Kolevzon
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patricia Jiménez González
- Child Developmental and Behavioral Unit, Hospital Nacional de Niños Dr. Sáenz Herrera, Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Suma Jacob
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA; Institute of Translational Neuroscience and Department of Psychiatry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Richard Holt
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Stephen Guter
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA
| | - Jonathan Green
- Institute of Brain, Behaviour, and Mental Health, University of Manchester, Manchester M13 9PL, UK; Manchester Academic Health Sciences Centre, Manchester M13 9NT, UK
| | - Andrew Green
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre, University of Gothenburg, 41119 Gothenburg, Sweden
| | - Bridget A Fernandez
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada
| | - Frederico Duque
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal; University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Richard Delorme
- FondaMental Foundation, 94010 Créteil, France; Human Genetics and Cognitive Functions Unit, Institut Pasteur, 75015 Paris, France; Centre National de la Recherche Scientifique URA 2182 (Genes, Synapses, and Cognition), Institut Pasteur, 75015 Paris, France; Department of Child and Adolescent Psychiatry, Robert Debré Hospital, Assistance Publique - Hôpitaux de Paris, 75019 Paris, France
| | - Geraldine Dawson
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Pauline Chaste
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; FondaMental Foundation, 94010 Créteil, France
| | - Cátia Café
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal
| | - Sean Brennan
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Thomas Bourgeron
- FondaMental Foundation, 94010 Créteil, France; Human Genetics and Cognitive Functions Unit, Institut Pasteur, 75015 Paris, France; Centre National de la Recherche Scientifique URA 2182 (Genes, Synapses, and Cognition), Institut Pasteur, 75015 Paris, France; University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Patrick F Bolton
- Institute of Psychiatry, King's College London, London SE5 8AF, UK; South London & Maudsley Biomedical Research Centre for Mental Health, London SE5 8AF, UK
| | - Sven Bölte
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University of Frankfurt, 60528 Frankfurt, Germany
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Gillian Baird
- Paediatric Neurodisability, King's Health Partners, King's College London, London WC2R 2LS, UK
| | - Anthony J Bailey
- Department of Psychiatry, University of Oxford and Warneford Hospital, Oxford OX3 7JX, UK
| | - Evdokia Anagnostou
- Bloorview Research Institute, University of Toronto, Toronto, ON M4G 1R8, Canada
| | - Joana Almeida
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal
| | - Ellen M Wijsman
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Veronica J Vieland
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Astrid M Vicente
- Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; Center for Biodiversity, Functional, & Integrative Genomics, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal
| | - Gerard D Schellenberg
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Margaret Pericak-Vance
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Andrew D Paterson
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Dalla Lana School of Public Health, Toronto, ON M5T 3M7, Canada
| | - Jeremy R Parr
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Guiomar Oliveira
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal; University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - John I Nurnberger
- Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics and Program in Medical Neuroscience, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Anthony P Monaco
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Office of the President, Tufts University, Medford, MA 02155, USA
| | - Elena Maestrini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Sabine M Klauck
- Division of Molecular Genome Analysis, German Cancer Research Center (Deutsches Krebsforschungszentrum), 69120 Heidelberg, Germany
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan L Haines
- Vanderbilt Brain Institute, Center for Human Genetics Research, and Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Daniel H Geschwind
- Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Goethe University, 60528 Frankfurt am Main, Germany
| | - Susan E Folstein
- Division of Child and Adolescent Psychiatry, Department of Psychiatry, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Sean Ennis
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Hilary Coon
- Utah Autism Research Program, Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Agatino Battaglia
- Stella Maris Clinical Research Institute for Child and Adolescent Neuropsychiatry, 56128 Calambrone, Pisa, Italy
| | - Peter Szatmari
- Department of Psychiatry and Behavioural Neurosciences, Offord Centre for Child Studies, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - James S Sutcliffe
- Vanderbilt Brain Institute, Center for Human Genetics Research, and Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Joachim Hallmayer
- Department of Psychiatry, Stanford University Medical School, Stanford, CA 94305, USA
| | - Michael Gill
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Louise Gallagher
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Catalina Betancur
- Institut National de la Santé et de la Recherche Médicale U1130, 75005 Paris, France; Centre National de la Recherche Scientifique UMR 8246, 75005 Paris, France; Neuroscience Paris Seine, Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 75005 Paris, France.
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A1, Canada.
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Werling DM, Lowe JK, Luo R, Cantor RM, Geschwind DH. Replication of linkage at chromosome 20p13 and identification of suggestive sex-differential risk loci for autism spectrum disorder. Mol Autism 2014; 5:13. [PMID: 24533643 PMCID: PMC3942516 DOI: 10.1186/2040-2392-5-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 01/24/2014] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Autism spectrum disorders (ASDs) are male-biased and genetically heterogeneous. While sequencing of sporadic cases has identified de novo risk variants, the heritable genetic contribution and mechanisms driving the male bias are less understood. Here, we aimed to identify familial and sex-differential risk loci in the largest available, uniformly ascertained, densely genotyped sample of multiplex ASD families from the Autism Genetics Resource Exchange (AGRE), and to compare results with earlier findings from AGRE. METHODS From a total sample of 1,008 multiplex families, we performed genome-wide, non-parametric linkage analysis in a discovery sample of 847 families, and separately on subsets of families with only male, affected children (male-only, MO) or with at least one female, affected child (female-containing, FC). Loci showing evidence for suggestive linkage (logarithm of odds ≥2.2) in this discovery sample, or in previous AGRE samples, were re-evaluated in an extension study utilizing all 1,008 available families. For regions with genome-wide significant linkage signal in the discovery stage, those families not included in the corresponding discovery sample were then evaluated for independent replication of linkage. Association testing of common single nucleotide polymorphisms (SNPs) was also performed within suggestive linkage regions. RESULTS We observed an independent replication of previously observed linkage at chromosome 20p13 (P < 0.01), while loci at 6q27 and 8q13.2 showed suggestive linkage in our extended sample. Suggestive sex-differential linkage was observed at 1p31.3 (MO), 8p21.2 (FC), and 8p12 (FC) in our discovery sample, and the MO signal at 1p31.3 was supported in our expanded sample. No sex-differential signals met replication criteria, and no common SNPs were significantly associated with ASD within any identified linkage regions. CONCLUSIONS With few exceptions, analyses of subsets of families from the AGRE cohort identify different risk loci, consistent with extreme locus heterogeneity in ASD. Large samples appear to yield more consistent results, and sex-stratified analyses facilitate the identification of sex-differential risk loci, suggesting that linkage analyses in large cohorts are useful for identifying heritable risk loci. Additional work, such as targeted re-sequencing, is needed to identify the specific variants within these loci that are responsible for increasing ASD risk.
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Affiliation(s)
| | | | | | | | - Daniel H Geschwind
- Neurogenetics Program and Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, 90095 Los Angeles, CA, USA.
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Parikshak NN, Luo R, Zhang A, Won H, Lowe JK, Chandran V, Horvath S, Geschwind DH. Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell 2014; 155:1008-21. [PMID: 24267887 DOI: 10.1016/j.cell.2013.10.031] [Citation(s) in RCA: 693] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/31/2013] [Accepted: 10/03/2013] [Indexed: 01/09/2023]
Abstract
Genetic studies have identified dozens of autism spectrum disorder (ASD) susceptibility genes, raising two critical questions: (1) do these genetic loci converge on specific biological processes, and (2) where does the phenotypic specificity of ASD arise, given its genetic overlap with intellectual disability (ID)? To address this, we mapped ASD and ID risk genes onto coexpression networks representing developmental trajectories and transcriptional profiles representing fetal and adult cortical laminae. ASD genes tightly coalesce in modules that implicate distinct biological functions during human cortical development, including early transcriptional regulation and synaptic development. Bioinformatic analyses suggest that translational regulation by FMRP and transcriptional coregulation by common transcription factors connect these processes. At a circuit level, ASD genes are enriched in superficial cortical layers and glutamatergic projection neurons. Furthermore, we show that the patterns of ASD and ID risk genes are distinct, providing a biological framework for further investigating the pathophysiology of ASD.
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Affiliation(s)
- Neelroop N Parikshak
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program in Neuroscience, University of California, Los Angeles, Los Angeles, CA 90095, USA
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20
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Chaste P, Klei L, Sanders SJ, Murtha MT, Hus V, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Lord C, Mane SM, Martin CL, Martin DM, Morrow EM, Walsh CA, Sutcliffe JS, State MW, Devlin B, Cook EH, Kim SJ. Adjusting head circumference for covariates in autism: clinical correlates of a highly heritable continuous trait. Biol Psychiatry 2013; 74:576-84. [PMID: 23746936 PMCID: PMC3772969 DOI: 10.1016/j.biopsych.2013.04.018] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 03/25/2013] [Accepted: 04/16/2013] [Indexed: 11/29/2022]
Abstract
BACKGROUND Brain development follows a different trajectory in children with autism spectrum disorders (ASD) than in typically developing children. A proxy for neurodevelopment could be head circumference (HC), but studies assessing HC and its clinical correlates in ASD have been inconsistent. This study investigates HC and clinical correlates in the Simons Simplex Collection cohort. METHODS We used a mixed linear model to estimate effects of covariates and the deviation from the expected HC given parental HC (genetic deviation). After excluding individuals with incomplete data, 7225 individuals in 1891 families remained for analysis. We examined the relationship between HC/genetic deviation of HC and clinical parameters. RESULTS Gender, age, height, weight, genetic ancestry, and ASD status were significant predictors of HC (estimate of the ASD effect = .2 cm). HC was approximately normally distributed in probands and unaffected relatives, with only a few outliers. Genetic deviation of HC was also normally distributed, consistent with a random sampling of parental genes. Whereas larger HC than expected was associated with ASD symptom severity and regression, IQ decreased with the absolute value of the genetic deviation of HC. CONCLUSIONS Measured against expected values derived from covariates of ASD subjects, statistical outliers for HC were uncommon. HC is a strongly heritable trait, and population norms for HC would be far more accurate if covariates including genetic ancestry, height, and age were taken into account. The association of diminishing IQ with absolute deviation from predicted HC values suggests HC could reflect subtle underlying brain development and warrants further investigation.
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Affiliation(s)
- Pauline Chaste
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA, FondaMental Foundation, Créteil, France
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Stephan J. Sanders
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA, Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michael T. Murtha
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Vanessa Hus
- Department of Psychology, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer K. Lowe
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - A. Jeremy Willsey
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Daniel Moreno-De-Luca
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Timothy W. Yu
- Division of Genetics, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric Fombonne
- Department of Psychiatry, Oregon Health & Science University, Portland, Oregon, USA
| | - Daniel Geschwind
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Dorothy E. Grice
- Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, USA
| | | | - Catherine Lord
- Center for Autism and the Developing Brain, Weill Cornell Medical College, White Plains, New York, USA
| | | | - Christa Lese Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Donna M. Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Eric M. Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry; and Institute for Brain Science, Brown University, Lab for Molecular Medicine, Providence, Rhode Island, USA, Developmental Disorders Genetics Research Program, Emma Pendleton Bradley Hospital and Department of Psychiatry and Human Behavior, Brown University Medical School, East Providence, Rhode Island, USA
| | - Christopher A. Walsh
- Howard Hughes Medical Institute and Division of Genetics, Children's Hospital Boston, and Neurology and Pediatrics, Harvard Medical School Center for Life Sciences, Boston, Massachusetts, USA
| | - James S. Sutcliffe
- Departments of Molecular Physiology & Biophysics and Psychiatry, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Matthew W. State
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA, Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Edwin H. Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Soo-Jeong Kim
- Center for Integrative Brain Research, Seattle Children's Research Institute & Department of Psychiatry and Behavioral Science, University of Washington, Seattle, WA, USA,Corresponding author Soo-Jeong Kim, M.D., Center for Integrative Brain Research, Seattle Children's Research Institute, 1900 9 Ave, Seattle, WA 98101, USA, , Tel: +12068841275, Fax:+12068841210
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Moreno-De-Luca D, Sanders SJ, Willsey AJ, Mulle JG, Lowe JK, Geschwind DH, State MW, Martin CL, Ledbetter DH. Using large clinical data sets to infer pathogenicity for rare copy number variants in autism cohorts. Mol Psychiatry 2013; 18:1090-5. [PMID: 23044707 PMCID: PMC3720840 DOI: 10.1038/mp.2012.138] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/24/2012] [Accepted: 08/20/2012] [Indexed: 11/16/2022]
Abstract
Copy number variants (CNVs) have a major role in the etiology of autism spectrum disorders (ASD), and several of these have reached statistical significance in case-control analyses. Nevertheless, current ASD cohorts are not large enough to detect very rare CNVs that may be causative or contributory (that is, risk alleles). Here, we use a tiered approach, in which clinically significant CNVs are first identified in large clinical cohorts of neurodevelopmental disorders (including but not specific to ASD), after which these CNVs are then systematically identified within well-characterized ASD cohorts. We focused our initial analysis on 48 recurrent CNVs (segmental duplication-mediated 'hotspots') from 24 loci in 31 516 published clinical cases with neurodevelopmental disorders and 13 696 published controls, which yielded a total of 19 deletion CNVs and 11 duplication CNVs that reached statistical significance. We then investigated the overlap of these 30 CNVs in a combined sample of 3955 well-characterized ASD cases from three published studies. We identified 73 deleterious recurrent CNVs, including 36 deletions from 11 loci and 37 duplications from seven loci, for a frequency of 1 in 54; had we considered the ASD cohorts alone, only 58 CNVs from eight loci (24 deletions from three loci and 34 duplications from five loci) would have reached statistical significance. In conclusion, until there are sufficiently large ASD research cohorts with enough power to detect very rare causative or contributory CNVs, data from larger clinical cohorts can be used to infer the likely clinical significance of CNVs in ASD.
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Affiliation(s)
- D Moreno-De-Luca
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA,Programs in Neurogenetics and Human Genetics and Genomics, Child Study Center and Departments of Psychiatry and Genetics, Yale University School of Medicine, New Haven, CT, USA,Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 315, Atlanta, GA 30322, USAE-mail:
| | - S J Sanders
- Programs in Neurogenetics and Human Genetics and Genomics, Child Study Center and Departments of Psychiatry and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - A J Willsey
- Programs in Neurogenetics and Human Genetics and Genomics, Child Study Center and Departments of Psychiatry and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - J G Mulle
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - J K Lowe
- Neurogenetics Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - D H Geschwind
- Neurogenetics Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - M W State
- Programs in Neurogenetics and Human Genetics and Genomics, Child Study Center and Departments of Psychiatry and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - C L Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - D H Ledbetter
- Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA. E-mail:
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22
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Klei L, Sanders SJ, Murtha MT, Hus V, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Lord C, Mane SM, Martin CL, Martin DM, Morrow EM, Walsh CA, Melhem NM, Chaste P, Sutcliffe JS, State MW, Cook EH, Roeder K, Devlin B. Common genetic variants, acting additively, are a major source of risk for autism. Mol Autism 2012; 3:9. [PMID: 23067556 PMCID: PMC3579743 DOI: 10.1186/2040-2392-3-9] [Citation(s) in RCA: 279] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 10/04/2012] [Indexed: 11/10/2022] Open
Abstract
Background Autism spectrum disorders (ASD) are early onset neurodevelopmental syndromes typified by impairments in reciprocal social interaction and communication, accompanied by restricted and repetitive behaviors. While rare and especially de novo genetic variation are known to affect liability, whether common genetic polymorphism plays a substantial role is an open question and the relative contribution of genes and environment is contentious. It is probable that the relative contributions of rare and common variation, as well as environment, differs between ASD families having only a single affected individual (simplex) versus multiplex families who have two or more affected individuals. Methods By using quantitative genetics techniques and the contrast of ASD subjects to controls, we estimate what portion of liability can be explained by additive genetic effects, known as narrow-sense heritability. We evaluate relatives of ASD subjects using the same methods to evaluate the assumptions of the additive model and partition families by simplex/multiplex status to determine how heritability changes with status. Results By analyzing common variation throughout the genome, we show that common genetic polymorphism exerts substantial additive genetic effects on ASD liability and that simplex/multiplex family status has an impact on the identified composition of that risk. As a fraction of the total variation in liability, the estimated narrow-sense heritability exceeds 60% for ASD individuals from multiplex families and is approximately 40% for simplex families. By analyzing parents, unaffected siblings and alleles not transmitted from parents to their affected children, we conclude that the data for simplex ASD families follow the expectation for additive models closely. The data from multiplex families deviate somewhat from an additive model, possibly due to parental assortative mating. Conclusions Our results, when viewed in the context of results from genome-wide association studies, demonstrate that a myriad of common variants of very small effect impacts ASD liability.
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Affiliation(s)
- Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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23
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Luo R, Sanders SJ, Tian Y, Voineagu I, Huang N, Chu SH, Klei L, Cai C, Ou J, Lowe JK, Hurles ME, Devlin B, State MW, Geschwind DH. Genome-wide transcriptome profiling reveals the functional impact of rare de novo and recurrent CNVs in autism spectrum disorders. Am J Hum Genet 2012; 91:38-55. [PMID: 22726847 DOI: 10.1016/j.ajhg.2012.05.011] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 04/06/2012] [Accepted: 05/08/2012] [Indexed: 12/15/2022] Open
Abstract
Copy-number variants (CNVs) are a major contributor to the pathophysiology of autism spectrum disorders (ASDs), but the functional impact of CNVs remains largely unexplored. Because brain tissue is not available from most samples, we interrogated gene expression in lymphoblasts from 244 families with discordant siblings in the Simons Simplex Collection in order to identify potentially pathogenic variation. Our results reveal that the overall frequency of significantly misexpressed genes (which we refer to here as outliers) identified in probands and unaffected siblings does not differ. However, in probands, but not their unaffected siblings, the group of outlier genes is significantly enriched in neural-related pathways, including neuropeptide signaling, synaptogenesis, and cell adhesion. We demonstrate that outlier genes cluster within the most pathogenic CNVs (rare de novo CNVs) and can be used for the prioritization of rare CNVs of potentially unknown significance. Several nonrecurrent CNVs with significant gene-expression alterations are identified (these include deletions in chromosomal regions 3q27, 3p13, and 3p26 and duplications at 2p15), suggesting that these are potential candidate ASD loci. In addition, we identify distinct expression changes in 16p11.2 microdeletions, 16p11.2 microduplications, and 7q11.23 duplications, and we show that specific genes within the 16p CNV interval correlate with differences in head circumference, an ASD-relevant phenotype. This study provides evidence that pathogenic structural variants have a functional impact via transcriptome alterations in ASDs at a genome-wide level and demonstrates the utility of integrating gene expression with mutation data for the prioritization of genes disrupted by potentially pathogenic mutations.
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Affiliation(s)
- Rui Luo
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, 90095, USA
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Konopka G, Wexler E, Rosen E, Mukamel Z, Osborn GE, Chen L, Lu D, Gao F, Gao K, Lowe JK, Geschwind DH. Modeling the functional genomics of autism using human neurons. Mol Psychiatry 2012; 17:202-14. [PMID: 21647150 PMCID: PMC3170664 DOI: 10.1038/mp.2011.60] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human neural progenitors from a variety of sources present new opportunities to model aspects of human neuropsychiatric disease in vitro. Such in vitro models provide the advantages of a human genetic background combined with rapid and easy manipulation, making them highly useful adjuncts to animal models. Here, we examined whether a human neuronal culture system could be utilized to assess the transcriptional program involved in human neural differentiation and to model some of the molecular features of a neurodevelopmental disorder, such as autism. Primary normal human neuronal progenitors (NHNPs) were differentiated into a post-mitotic neuronal state through addition of specific growth factors and whole-genome gene expression was examined throughout a time course of neuronal differentiation. After 4 weeks of differentiation, a significant number of genes associated with autism spectrum disorders (ASDs) are either induced or repressed. This includes the ASD susceptibility gene neurexin 1, which showed a distinct pattern from neurexin 3 in vitro, and which we validated in vivo in fetal human brain. Using weighted gene co-expression network analysis, we visualized the network structure of transcriptional regulation, demonstrating via this unbiased analysis that a significant number of ASD candidate genes are coordinately regulated during the differentiation process. As NHNPs are genetically tractable and manipulable, they can be used to study both the effects of mutations in multiple ASD candidate genes on neuronal differentiation and gene expression in combination with the effects of potential therapeutic molecules. These data also provide a step towards better understanding of the signaling pathways disrupted in ASD.
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Gusev A, Kenny EE, Lowe JK, Salit J, Saxena R, Kathiresan S, Altshuler DM, Friedman JM, Breslow JL, Pe'er I. DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation. Am J Hum Genet 2011; 88:706-717. [PMID: 21620352 DOI: 10.1016/j.ajhg.2011.04.023] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 04/13/2011] [Accepted: 04/26/2011] [Indexed: 02/01/2023] Open
Abstract
Rare variants affecting phenotype pose a unique challenge for human genetics. Although genome-wide association studies have successfully detected many common causal variants, they are underpowered in identifying disease variants that are too rare or population-specific to be imputed from a general reference panel and thus are poorly represented on commercial SNP arrays. We set out to overcome these challenges and detect association between disease and rare alleles using SNP arrays by relying on long stretches of genomic sharing that are identical by descent. We have developed an algorithm, DASH, which builds upon pairwise identical-by-descent shared segments to infer clusters of individuals likely to be sharing a single haplotype. DASH constructs a graph with nodes representing individuals and links on the basis of such segments spanning a locus and uses an iterative minimum cut algorithm to identify densely connected components. We have applied DASH to simulated data and diverse GWAS data sets by constructing haplotype clusters and testing them for association. In simulations we show this approach to be significantly more powerful than single-marker testing in an isolated population that is from Kosrae, Federated States of Micronesia and has abundant IBD, and we provide orthogonal information for rare, recent variants in the outbred Wellcome Trust Case-Control Consortium (WTCCC) data. In both cohorts, we identified a number of haplotype associations, five such loci in the WTCCC data and ten in the isolated, that were conditionally significant beyond any individual nearby markers. We have replicated one of these loci in an independent European cohort and identified putative structural changes in low-pass whole-genome sequence of the cluster carriers.
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Affiliation(s)
- Alexander Gusev
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Eimear E Kenny
- Department of Computer Science, Columbia University, New York, NY 10027, USA; Medical Sciences and Human Genetics, Rockefeller University, New York, NY 10065, USA
| | - Jennifer K Lowe
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jaqueline Salit
- Medical Sciences and Human Genetics, Rockefeller University, New York, NY 10065, USA
| | - Richa Saxena
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Cardiovascular Disease Prevention Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - David M Altshuler
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Center for Human Genetic Research and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey M Friedman
- Medical Sciences and Human Genetics, Rockefeller University, New York, NY 10065, USA
| | - Jan L Breslow
- Medical Sciences and Human Genetics, Rockefeller University, New York, NY 10065, USA
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY 10027, USA.
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Voineagu I, Wang X, Johnston P, Lowe JK, Tian Y, Horvath S, Mill J, Cantor RM, Blencowe BJ, Geschwind DH. Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature 2011; 474:380-4. [PMID: 21614001 PMCID: PMC3607626 DOI: 10.1038/nature10110] [Citation(s) in RCA: 1289] [Impact Index Per Article: 99.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2010] [Accepted: 04/13/2011] [Indexed: 02/07/2023]
Abstract
Autism spectrum disorder (ASD) is a common, highly heritable neuro-developmental condition characterized by marked genetic heterogeneity1–3. Thus, a fundamental question is whether autism represents an etiologically heterogeneous disorder in which the myriad genetic or environmental risk factors perturb common underlying molecular pathways in the brain4. Here, we demonstrate consistent differences in transcriptome organization between autistic and normal brain by gene co-expression network analysis. Remarkably, regional patterns of gene expression that typically distinguish frontal and temporal cortex are significantly attenuated in the ASD brain, suggesting abnormalities in cortical patterning. We further identify discrete modules of co-expressed genes associated with autism: a neuronal module enriched for known autism susceptibility genes, including the neuronal specific splicing factor A2BP1/FOX1, and a module enriched for immune genes and glial markers. Using high-throughput RNA-sequencing we demonstrate dysregulated splicing of A2BP1-dependent alternative exons in ASD brain. Moreover, using a published autism GWAS dataset, we show that the neuronal module is enriched for genetically associated variants, providing independent support for the causal involvement of these genes in autism. In contrast, the immune-glial module showed no enrichment for autism GWAS signals, indicating a non-genetic etiology for this process. Collectively, our results provide strong evidence for convergent molecular abnormalities in ASD, and implicate transcriptional and splicing dysregulation as underlying mechanisms of neuronal dysfunction in this disorder.
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Affiliation(s)
- Irina Voineagu
- Program in Neurogenetics and Neurobehavioral Genetics, Department of Neurology and Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90095-1769, USA
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Kenny EE, Kim M, Gusev A, Lowe JK, Salit J, Smith JG, Kovvali S, Kang HM, Newton-Cheh C, Daly MJ, Stoffel M, Altshuler DM, Friedman JM, Eskin E, Breslow JL, Pe'er I. Increased power of mixed models facilitates association mapping of 10 loci for metabolic traits in an isolated population. Hum Mol Genet 2010; 20:827-39. [PMID: 21118897 DOI: 10.1093/hmg/ddq510] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The potential benefits of using population isolates in genetic mapping, such as reduced genetic, phenotypic and environmental heterogeneity, are offset by the challenges posed by the large amounts of direct and cryptic relatedness in these populations confounding basic assumptions of independence. We have evaluated four representative specialized methods for association testing in the presence of relatedness; (i) within-family (ii) within- and between-family and (iii) mixed-models methods, using simulated traits for 2906 subjects with known genome-wide genotype data from an extremely isolated population, the Island of Kosrae, Federated States of Micronesia. We report that mixed models optimally extract association information from such samples, demonstrating 88% power to rank the true variant as among the top 10 genome-wide with 56% achieving genome-wide significance, a >80% improvement over the other methods, and demonstrate that population isolates have similar power to non-isolate populations for observing variants of known effects. We then used the mixed-model method to reanalyze data for 17 published phenotypes relating to metabolic traits and electrocardiographic measures, along with another 8 previously unreported. We replicate nine genome-wide significant associations with known loci of plasma cholesterol, high-density lipoprotein, low-density lipoprotein, triglycerides, thyroid stimulating hormone, homocysteine, C-reactive protein and uric acid, with only one detected in the previous analysis of the same traits. Further, we leveraged shared identity-by-descent genetic segments in the region of the uric acid locus to fine-map the signal, refining the known locus by a factor of 4. Finally, we report a novel associations for height (rs17629022, P< 2.1 × 10⁻⁸).
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Affiliation(s)
- Eimear E Kenny
- Department of Computer Science, Columbia University, 505 Computer Science Building, 1214 Amsterdam Ave.: Mailcode 0401, New York, NY 10027-7003, USA
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Bonnen PE, Lowe JK, Altshuler DM, Breslow JL, Stoffel M, Friedman JM, Pe'er I. European admixture on the Micronesian island of Kosrae: lessons from complete genetic information. Eur J Hum Genet 2010; 18:309-16. [PMID: 19844264 PMCID: PMC2987223 DOI: 10.1038/ejhg.2009.180] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 08/11/2009] [Accepted: 09/11/2009] [Indexed: 01/16/2023] Open
Abstract
The architecture of natural variation present in a contemporary population is a result of multiple population genetic forces, including population bottleneck and expansion, selection, drift, and admixture. We seek to untangle the contribution of admixture to genetic diversity on the Micronesian island of Kosrae. Toward this goal, we used a complete genetic approach by combining a dense genome-wide map of 100,000 single-nucleotide polymorphisms (SNPs) with data from uniparental markers from the mitochondrial genome and the nonrecombining portion of the Y chromosome. These markers were typed in approximately 3200 individuals from Kosrae, representing 80% of the adult population of the island. We developed novel software that uses SNP data to delineate ancestry for individual segments of the genome. Through this analysis, we determined that 39% of Kosraens have some European ancestry. However, the vast majority of admixed individuals (77%) have European alleles spanning less than 10% of their genomes. Data from uniparental markers show most of this admixture to be male, introduced in the late nineteenth century. Furthermore, pedigree analysis shows that the majority of European admixture on Kosrae is because of the contribution of one individual. This approach shows the benefit of combining information from autosomal and uniparental polymorphisms and provides new methodology for determining ancestry in a population.
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Affiliation(s)
- Penelope E Bonnen
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
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Smith JG, Lowe JK, Kovvali S, Maller JB, Salit J, Daly MJ, Stoffel M, Altshuler DM, Friedman JM, Breslow JL, Newton-Cheh C. Genome-wide association study of electrocardiographic conduction measures in an isolated founder population: Kosrae. Heart Rhythm 2009; 6:634-41. [PMID: 19389651 DOI: 10.1016/j.hrthm.2009.02.022] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 02/11/2009] [Indexed: 12/19/2022]
Abstract
BACKGROUND Cardiac conduction, as assessed by electrocardiographic PR interval and QRS duration, is an important electrophysiological trait and a determinant of arrhythmia risk. OBJECTIVE We sought to identify common genetic determinants of these measures. METHODS We examined 1604 individuals from the island of Kosrae, Federated States of Micronesia, an isolated founder population. We adjusted for covariates and estimated the heritability of quantitative electrocardiographic QRS duration and PR interval and, secondarily, its subcomponents, P-wave duration and PR segment. Finally, we performed a genome-wide association study (GWAS) in a subset of 1262 individuals genotyped using the Affymetrix GeneChip Human Mapping 500K microarray. RESULTS The heritability of PR interval was 34% (standard error [SE] 5%, P = 4 x 10(-18)); of PR segment, 31% (SE 6%, P = 3.2 x 10(-13)); and of P-wave duration, 17% (SE 5%, P = 5.8 x 10(-6)), but the heritablility of QRS duration was only 3% (SE 4%, P = .20). Hence, GWAS was performed only for the PR interval and its subcomponents. A total of 338,049 single nucleotide polymorphisms (SNPs) passed quality filters. For the PR interval, the most significantly associated SNPs were located in and downstream of the alpha-subunit of the cardiac voltage-gated sodium channel gene SCN5A, with a 4.8 ms (SE 1.0) or 0.23 standard deviation increase in adjusted PR interval for each minor allele copy of rs7638909 (P = 1.6 x 10(-6), minor allele frequency 0.40). These SNPs were also associated with P-wave duration (P = 1.5 x 10(-4)) and PR segment (P = .01) but not with QRS duration (P > or =.22). CONCLUSIONS The PR interval and its subcomponents showed substantial heritability in a South Pacific islander population and were associated with common genetic variation in SCN5A.
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Affiliation(s)
- J Gustav Smith
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe'er I. Whole population, genome-wide mapping of hidden relatedness. Genome Res 2008; 19:318-26. [PMID: 18971310 DOI: 10.1101/gr.081398.108] [Citation(s) in RCA: 308] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. Unlike methods with comparable objectives, GERMLINE scales linearly with the number of samples, enabling analysis of whole-genome data in large cohorts. Our approach is based on a dictionary of haplotypes that is used to efficiently discover short exact matches between individuals. We then expand these matches using dynamic programming to identify long, nearly identical segmental sharing that is indicative of relatedness. We use GERMLINE to comprehensively survey hidden relatedness both in the HapMap as well as in a densely typed island population of 3000 individuals. We verify that GERMLINE is in concordance with other methods when they can process the data, and also facilitates analysis of larger scale studies. We bolster these results by demonstrating novel applications of precise analysis of hidden relatedness for (1) identification and resolution of phasing errors and (2) exposing polymorphic deletions that are otherwise challenging to detect. This finding is supported by concordance of detected deletions with other evidence from independent databases and statistical analyses of fluorescence intensity not used by GERMLINE.
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Affiliation(s)
- Alexander Gusev
- Department of Computer Science, Columbia University, New York, New York 10027, USA.
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Burkhardt R, Kenny EE, Lowe JK, Birkeland A, Josowitz R, Noel M, Salit J, Maller JB, Pe'er I, Daly MJ, Altshuler D, Stoffel M, Friedman JM, Breslow JL. Common SNPs in HMGCR in micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13. Arterioscler Thromb Vasc Biol 2008; 28:2078-84. [PMID: 18802019 DOI: 10.1161/atvbaha.108.172288] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
UNLABELLED Background- Variation in LDL-cholesterol (LDL-C) among individuals is a complex genetic trait involving multiple genes and gene-environment interactions. METHODS AND RESULTS In a genome-wide association study (GWAS) to identify genetic variants influencing LDL-C in an isolated population from Kosrae, we observed associations for SNPs in the gene encoding 3hydroxy-3-methylglutaryl (HMG)-coenzyme A (CoA) reductase (HMGCR). Three of these SNPs (rs7703051, rs12654264, and rs3846663) met the statistical threshold of genome-wide significance when combined with data from the Diabetes Genetics Initiative GWAS. We followed up the association results and identified a functional SNP in intron13 (rs3846662), which was in linkage disequilibrium with the SNPs of genome-wide significance and affected alternative splicing of HMGCR mRNA. In vitro studies in human lymphoblastoid cells demonstrated that homozygosity for the rs3846662 minor allele was associated with up to 2.2-fold lower expression of alternatively spliced HMGCR mRNA lacking exon13, and minigene transfection assays confirmed that allele status at rs3846662 directly modulated alternative splicing of HMGCR exon13 (42.9+/-3.9 versus 63.7+/-1.0%Deltaexon13/total HMGCR mRNA, P=0.02). Further, the alternative splice variant could not restore HMGCR activity when expressed in HMGCR deficient UT-2 cells. CONCLUSIONS We identified variants in HMGCR that are associated with LDL-C across populations and affect alternative splicing of HMGCR exon13.
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Affiliation(s)
- Ralph Burkhardt
- Laboratory of Biochemical Genetics and Metabolism, The Rockefeller University, New York, NY 10065, USA
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Abstract
The conceptual framework which underlies many studies of purine and pyrimidine metabolism in intact cells has been critically evaluated. The model that is implicit in many such studies is the single, partially purified enzyme. This paper gives examples both of instances in which the extrapolation of results of enzymes studies to intact cells has been successful and of instances in which enzymes behave differently in the intact cell than in cell extracts. Pitfalls in the extrapolation of results of enzyme studies to intact cells concern (a) metabolic pathways, (b) intracellular enzyme activities, (c) enzyme regulation, and (d) intracellular metabolite concentrations. Examples are also given of situations in which perturbations in one aspect of purine or pyrimidine metabolism lead to changes in other aspects, often distant in the network of reactions.
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Kukekova AV, Nelson J, Kuchtey RW, Lowe JK, Johnson JL, Ostrander EA, Aguirre GD, Acland GM. Linkage mapping of canine rod cone dysplasia type 2 (rcd2) to CFA7, the canine orthologue of human 1q32. Invest Ophthalmol Vis Sci 2006; 47:1210-5. [PMID: 16505060 DOI: 10.1167/iovs.05-0861] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To map the canine rcd2 retinal degeneration locus. Rod-cone dysplasia type 2 (rcd2), an early-onset autosomal recessive form of progressive retinal atrophy (PRA), is phenotypically similar to early-onset forms of retinitis pigmentosa collectively termed Leber congenital amaurosis and segregates naturally in the collie breed of dog. Multiple genes have previously been evaluated as candidates for rcd2, but all have been excluded. METHODS A set of informative experimental pedigrees segregating the rcd2 phenotype was produced. A genome-wide scan of these pedigrees using a set of 241 markers was undertaken. To refine the localized homology between canine and human maps, an RH map of the identified rcd2 region was built using a 3000 cR panel. A positional candidate gene strategy was then undertaken to begin to evaluate potentially causative genes. RESULTS A locus responsible for the rcd2 phenotype was mapped to CFA7 in a region corresponding to human chromosome 1, region q32.1-q32.2. Maximum linkage was observed between rcd2 and marker FH3972 (theta = 0.02; lod = 25.53), and the critical region was flanked by markers FH2226 and FH3972. As CRB1 is the closest gene on human chromosome 1q known to cause retinal degeneration, canine gene-specific markers for CRB1 were developed, and this gene was excluded as a positional candidate for rcd2. CONCLUSIONS The rcd2 locus represents a novel retinal degeneration gene. It is anticipated that when identified, this gene will offer new insights into retinal developmental and degenerative processes, and new opportunities for exploring experimental therapies.
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Affiliation(s)
- Anna V Kukekova
- James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
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Bonnen PE, Pe'er I, Plenge RM, Salit J, Lowe JK, Shapero MH, Lifton RP, Breslow JL, Daly MJ, Reich DE, Jones KW, Stoffel M, Altshuler D, Friedman JM. Evaluating potential for whole-genome studies in Kosrae, an isolated population in Micronesia. Nat Genet 2006; 38:214-7. [PMID: 16429162 DOI: 10.1038/ng1712] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2005] [Accepted: 11/17/2005] [Indexed: 11/09/2022]
Abstract
Whole-genome association studies are predicted to be especially powerful in isolated populations owing to increased linkage disequilibrium (LD) and decreased allelic diversity, but this possibility has not been empirically tested. We compared genome-wide data on 113,240 SNPs typed on 30 trios from the Pacific island of Kosrae to the same markers typed in the 270 samples from the International HapMap Project. The extent of LD is longer and haplotype diversity is lower in Kosrae than in the HapMap populations. More than 98% of Kosraen haplotypes are present in HapMap populations, indicating that HapMap will be useful for genetic studies on Kosrae. The long-range LD around common alleles and limited diversity result in improved efficiency in genetic studies in this population and augments the power to detect association of 'hidden SNPs'.
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Affiliation(s)
- Penelope E Bonnen
- Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
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Lowe JK, Guyon R, Cox ML, Mitchell DC, Lonkar AL, Lingaas F, André C, Galibert F, Ostrander EA, Murphy KE. Radiation hybrid mapping of the canine type I and type IV collagen gene subfamilies. Funct Integr Genomics 2003; 3:112-6. [PMID: 12687409 DOI: 10.1007/s10142-003-0082-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2002] [Accepted: 02/10/2003] [Indexed: 10/26/2022]
Abstract
We are interested in the collagen gene superfamily and its involvement in hereditary diseases of the human and domestic dog. Presented here is radiation hybrid mapping of the type I and type IV collagen gene subfamilies on the most recent version of the canine map. The col1A1 gene was mapped to chromosome 9, col1A2 was mapped to chromosome 14, col4A1 and col4A2 were mapped to chromosome 22 and col4A3 and col4A4 were mapped to chromosome 25. The col4A5 and col4A6 genes, while linked to one another, are not linked in the present version of the canine map but likely are present on the X chromosome. These data provide an insight into the molecular evolution of these subfamilies and increase the number of mapped genes in discrete regions of the canine genome.
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Affiliation(s)
- Jennifer K Lowe
- Department of Molecular and Cellular Biology, University of Washington, Seattle, WA 98115, USA
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Abstract
Collie eye anomaly (cea) is a hereditary ocular disorder affecting development of the choroid and sclera segregating in several breeds of dog, including rough, smooth, and Border collies and Australian shepherds. The disease is reminiscent of the choroidal hypoplasia phenotype observed in humans in conjunction with craniofacial or renal abnormalities. In dogs, however, the clinical phenotype can vary significantly; many dogs exhibit no obvious clinical consequences and retain apparently normal vision throughout life, while severely affected animals develop secondary retinal detachment, intraocular hemorrhage, and blindness. We report genetic studies establishing that the primary cea phenotype, choroidal hypoplasia, segregates as an autosomal recessive trait with nearly 100% penetrance. We further report linkage mapping of the primary cea locus to a 3.9-cM region of canine chromosome 37 (LOD = 22.17 at theta = 0.076), in a region corresponding to human chromosome 2q35. These results suggest the presence of a developmental regulatory gene important in ocular embryogenesis, with potential implications for other disorders of ocular vascularization.
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Affiliation(s)
- Jennifer K Lowe
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, D4-100, Seattle, WA 98109-1024, USA
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Guyon R, Lorentzen TD, Hitte C, Kim L, Cadieu E, Parker HG, Quignon P, Lowe JK, Renier C, Gelfenbeyn B, Vignaux F, DeFrance HB, Gloux S, Mahairas GG, André C, Galibert F, Ostrander EA. A 1-Mb resolution radiation hybrid map of the canine genome. Proc Natl Acad Sci U S A 2003; 100:5296-301. [PMID: 12700351 PMCID: PMC154339 DOI: 10.1073/pnas.0831002100] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2002] [Accepted: 02/19/2003] [Indexed: 11/18/2022] Open
Abstract
The purebred dog population consists of >300 partially inbred genetic isolates or breeds. Restriction of gene flow between breeds, together with strong selection for traits, has led to the establishment of a unique resource for dissecting the genetic basis of simple and complex mammalian traits. Toward this end, we present a comprehensive radiation hybrid map of the canine genome composed of 3,270 markers including 1,596 microsatellite-based markers, 900 cloned gene sequences and ESTs, 668 canine-specific bacterial artificial chromosome (BAC) ends, and 106 sequence-tagged sites. The map was constructed by using the RHDF5000-2 whole-genome radiation hybrid panel and computed by using MULTIMAP and TSP/CONCORDE. The 3,270 markers map to 3,021 unique positions and define an average intermarker distance corresponding to 1 Mb. We also define a minimal screening set of 325 highly informative well spaced markers, to be used in the initiation of genome-wide scans. The well defined synteny between the dog and human genomes, established in part as a function of this work by the identification of 85 conserved fragments, will allow follow-up of initial findings of linkage by selection of candidate genes from the human genome sequence. This work continues to define the canine system as the method of choice in the pursuit of the genes causing mammalian variation and disease.
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Affiliation(s)
- Richard Guyon
- Unité Mixte de Recherche 6061, Centre National de la Recherche Scientifique, Génétique et Développement, Faculté de Médecine, 35043 Rennes Cédex, France
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38
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Hitte C, Lorentzen TD, Guyon R, Kim L, Cadieu E, Parker HG, Quignon P, Lowe JK, Gelfenbeyn B, Andre C, Ostrander EA, Galibert F. Comparison of MultiMap and TSP/CONCORDE for constructing radiation hybrid maps. J Hered 2003; 94:9-13. [PMID: 12692156 DOI: 10.1093/jhered/esg012] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Radiation hybrid (RH) map construction allows investigators to locate both type I and type II markers on a given genome map. The process is composed of two steps. The first consists of determining the pattern distribution of a set of markers within the different cell lines of an RH panel. This is mainly done by polymerase chain reaction (PCR) amplification and gel electrophoresis, and results in a series of numbers indicating the presence or the absence of each marker in each cell line. The second step consists of a comparison of these numbers, using various algorithms, to group and then order markers. Because different algorithms may provide (slightly) different orders, we have compared the merits of the MultiMap and TSP/CONCORDE packages using a data set of information currently under analysis for construction of the canine genome RH map.
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Affiliation(s)
- C Hitte
- UMR6061, CNRS, Université de Rennes1, 2 av. Pr. Léon Bernard 35043 Rennes Cedex, France
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Sidjanin DJ, Lowe JK, McElwee JL, Milne BS, Phippen TM, Sargan DR, Aguirre GD, Acland GM, Ostrander EA. Canine CNGB3 mutations establish cone degeneration as orthologous to the human achromatopsia locus ACHM3. Hum Mol Genet 2002; 11:1823-33. [PMID: 12140185 DOI: 10.1093/hmg/11.16.1823] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cone degeneration (cd ) is an autosomal recessive canine disease that occurs naturally in the Alaskan Malamute and German Shorthaired Pointer breeds. It is phenotypically similar to human achromatopsia, a heterogeneous autosomal recessive disorder associated with three distinct loci. Both the canine disease and its human counterparts are characterized by day-blindness and absence of retinal cone function in adults. We report linkage of the canine cd locus to marker C29.002 on canine chromosome 29 at recombination fraction theta = 0.0 with a maximum LOD score of 24.68 in a series of informative outbred pedigrees derived from cd-affected Alaskan Malamutes. Conserved gene order between CFA29 and the long arm of human chromosome 8 argued for homology between the cd locus and the human achromatopsia locus, ACHM3, at 8q21-22. The canine homolog of the cyclic nucleotide-gated channel beta-subunit gene (CNGB3), responsible for the human ACHM3 disease phenotype, was mapped within the zero-recombination interval for the cd locus. A deletion removing all exons of canine CNGB3 was identified in cd-affected Alaskan Malamute-derived dogs. A missense mutation in exon 6 (D262N, nucleotide 784) within a conserved region of the same gene was detected in German Shorthaired Pointers affected with an allelic disorder. Identification of these canine disorders as homologs of human ACHM3 underscores the power of recent developments in canine genomics, and provides a valuable system for exploring disease mechanisms and evaluating potential therapeutic measures in disorders of cone photoreceptors.
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Affiliation(s)
- Duska J Sidjanin
- Center for Canine Genetics and Reproduction, James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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Credille KM, Venta PJ, Breen M, Lowe JK, Murphy KE, Ostrander EA, Galibert F, Dunstan RW. DNA sequence and physical mapping of the canine transglutaminase 1 gene. Cytogenet Cell Genet 2001; 93:73-6. [PMID: 11474183 DOI: 10.1159/000056952] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The transglutaminase 1 gene (TGM1) encodes an enzyme necessary for cross-linking the structural proteins that form the cornified envelope, an essential component of the outermost layer of the skin, the stratum corneum. Reported here is the complete coding region of canine TGM1, its chromosome localization, and its map position in the integrated canine linkage-radiation hybrid map. Canine TGM1 consists of 2,448 nucleotides distributed over 15 exons. The nucleotide sequence has 90% identity to human TGM1. The deduced canine TGM1 protein is 816 amino acids long and is 92% identical to human TGM1. Using fluorescence in situ hybridization, we localized canine TGM1 to dog (Canis familiaris) chromosome 8 (CFA 8q). Canine TGM1 localized to CFA 8 on the integrated linkage-radiation hybrid map in the interval FH2149-MYH7. Characterizing the coding region of canine TGM1 is a first step in examining the role of this enzyme in normal and defective cornification in the dog.
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Affiliation(s)
- K M Credille
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843-4467, USA.
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Miller AB, Lowe JK, Ostrander EA, Galibert F, Murphy KE. Cloning, sequence analysis and radiation hybrid mapping of a mammalian KRT2p gene. Funct Integr Genomics 2001; 1:305-11. [PMID: 11793249 DOI: 10.1007/s101420100038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2001] [Accepted: 05/14/2001] [Indexed: 11/25/2022]
Abstract
We report here on the cloning, characterization and radiation hybrid mapping of the canine basic keratin gene KRT2p. The gene spans 8.3 kb, consists of nine exons and eight introns, and is characterized by the typical features of both basic keratins and keratins in general, including glycine-rich head and tail domains, which flank an alpha-helical rod domain of approximately 310 amino acids. Comparisons of sequence and structure reveal that canine KRT2p is strikingly similar to human KRT2p. Alignment of the predicted amino acid sequences for human and dog reveals greater than 80% identity. In the rod domain, the amino acid identity exceeds 90%. We note, however, that canine KRT2p encodes a protein 21 residues longer than human K2p due to the insertion of a glycine repeat motif, GG(G)X, in the head and tail domains of the canine gene. This is the first report of the nearly complete genome sequence for KRT2p of any organism. Radiation hybrid mapping of canine KRT2p to chromosome 27 of the dog is also reported.
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Affiliation(s)
- A B Miller
- Department of Microbiology and Molecular Cell Sciences, The University of Memphis, Memphis, TN 38152, USA
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Li R, Faraco JH, Lin L, Lin X, Hinton L, Rogers W, Lowe JK, Ostrander EA, Mignot E. Physical and radiation hybrid mapping of canine chromosome 12, in a region corresponding to human chromosome 6p12-q12. Genomics 2001; 73:299-315. [PMID: 11350122 DOI: 10.1006/geno.2000.6487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The positional cloning of the hypocretin receptor 2, the gene for autosomal recessive canine narcolepsy, has led to the development of a physical map spanning a large portion of canine chromosome 12 (CFA12), in a region corresponding to human chromosome 6p12-q13. More than 40 expressed sequence tags (ESTs) were used in homology search experiments, together with chromosome walking, to build both physical and radiation hybrid maps of the CFA12 13-21 region. The resulting map of bacterial artificial chromosome ends, ESTs, and microsatellite markers represents the longest continuous high-density map of the dog genome reported to date. These data further establish the dog as a system for studying disease genes of interest to human populations and highlight feasible approaches for positional cloning of disease genes in organisms where genomic resources are limited.
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Affiliation(s)
- R Li
- Room P-114, Stanford Center for Narcolepsy Research, 1201 Welch Road, Stanford, California 94305-5485, USA
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Sijbesma RP, Beijer FH, Brunsveld L, Folmer BJ, Hirschberg JH, Lange RF, Lowe JK, Meijer EW. Reversible polymers formed from self-complementary monomers using quadruple hydrogen bonding. Science 1997; 278:1601-4. [PMID: 9374454 DOI: 10.1126/science.278.5343.1601] [Citation(s) in RCA: 1582] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Units of 2-ureido-4-pyrimidone that dimerize strongly in a self-complementary array of four cooperative hydrogen bonds were used as the associating end group in reversible self-assembling polymer systems. The unidirectional design of the binding sites prevents uncontrolled multidirectional association or gelation. Linear polymers and reversible networks were formed from monomers with two and three binding sites, respectively. The thermal and environmental control over lifetime and bond strength makes many properties, such as viscosity, chain length, and composition, tunable in a way not accessible to traditional polymers. Hence, polymer networks with thermodynamically controlled architectures can be formed, for use in, for example, coatings and hot melts, where a reversible, strongly temperature-dependent rheology is highly advantageous.
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Affiliation(s)
- R P Sijbesma
- Laboratory of Organic Chemistry, Eindhoven University of Technology, Post Office Box 513, 5600 MB Eindhoven, Netherlands
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Snyder FF, Chudley AE, MacLeod PM, Carter RJ, Fung E, Lowe JK. Partial deficiency of hypoxanthine-guanine phosphoribosyltransferase with reduced affinity for PP-ribose-P in four related males with gout. Hum Genet 1984; 67:18-22. [PMID: 6204922 DOI: 10.1007/bf00270552] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A family is described in which four affected males, spanning two generations, have hyperuricemia and gout accompanied by hematuria but are without severe neurologic involvement. The affected males were found to have markedly reduced levels of erythrocytic hypoxanthine-guanine phosphoribosyltransferase (HGPRT) activity; these were 5-12% with hypoxanthine and 0.5-3% with guanine as compared to controls. Erythrocytic adenine phosphoribosyltransferase (APRT) was approximately three-fold elevated in the affected individuals. The residual HGPRT activity in affected males enabled characterization of some of the properties of this mutation. The apparent Michaelis constants (km) for both hypoxanthine and guanine were essentially unchanged, whereas the km for PP-ribose-P was approximately 10-20-fold elevated for all four affected males. The enzyme was more sensitive to product inhibition by IMP and GMP than controls, and exhibited greater thermal lability at 65 degrees C than found with control lysates.
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Lowe JK, Gowans B, Brox L. Deoxyadenosine metabolism and toxicity in cultured L5178Y cells. Cancer Res 1977; 37:3013-7. [PMID: 301772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The growth of cultured L5178Y cells is inhibited by relatively low concentrations fo deoxyadenosine in the presence of deoxycoformycin, an inhibitor of adenosine deaminase. Cell viability is reduced, presumably as a consequence of the induced state of unbalanced growth which is characterized by inhibition in DNA synthesis, accumulation of cells in G1 or early S phase, a continuation in RNA synthesis, and increasing cell volume. The intracellular concentrations of purine and pyrimidine ribonucleoside phosphates remain essentially unchanged. The significant changes in the intracellular deoxynucleoside triphosphate pools are an increase in deoxyadenosine triphosphate and a decrease in deoxycytidine triphosphate.
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Cass CE, Lowe JK, Manchak JM, Henderson JF. Biological effects of inhibition of guanine nucleotide synthesis by mycophenolic acid in cultured neuroblastoma cells. Cancer Res 1977; 37:3314-20. [PMID: 195725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mycophenolic acid, an inhibitor of inosinate dehydrogenase, had cytostatic and cytotoxic effects on cultured neuroblastoma cells. Proliferation was inhibited by 50% when cells were incubated with 0.07 micrometerM mycophenolic acid, and cell viability was reduced by 83% when cells were treated with 10 micrometerM mycophenolic acid for 24 hr. Treatment of monolayer cultures with mycophenolic acid reduced intracellular concentrations of guanosine triphosphate by 70% within 3 hr, whereas cytidine triphosphate and uridine triphosphate concentrations were significantly elevated, and adenosine triphosphate concentrations were increased only slightly. Reduction of cellular guanine nucleotides had differential effects on rates of macromolecular synthesis: incorporation of radioactive thymidine into acid-insoluble material was inhibited by mycophenolic acid to a much greater extent than was that of adenosine and leucine. Although proliferation of neuroblastoma cells was inhibited, differentiation, as judged by formation of neuronlike processes in serum-free medium, was unaffected by decreased intracellular concentrations of guanosine triphosphate.
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Lowe JK, Brox L, Henderson JF. Consequences of inhibition of guanine nucleotide synthesis by mycophenolic acid and virazole. Cancer Res 1977; 37:736-43. [PMID: 837373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mycophenolic acid and virazole are inhibitors of inosinate dehydrogenase and produce growth inhibition and loss of viability in cultured murine lymphoma L5178Y cells. Treatment with 1 muM mycophenolic acid produced the following changes in concentrations of acid-soluble nucleotides: (a) guanosine triphosphate decreased to less than 10% of control within 2 hr; (b) uridine triphosphate and cytidine triphosphate concentrations increased markedly; (c) adenosine triphosphate did not change; (d) deoxyguanosine triphosphate decreased; and (e) thymidine triphosphate increased. DNA synthesis was inhibited by 90% within 2 hr, whereas the incorporation of adenosine into RNA and of leucine into protein were much less affected. Virazole (100 muM) produces similar effects. These biochemical effects of mycophenolic acid, as well as its effects on cell growth, can be prevented by addition of guanylate to the medium. Mycophenolic acid treatment also appears to cause breakdown of high-molecular-weight DNA.
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Grindey GB, Lowe JK, Divekar AY, Hakala MT. Potentiation by guanine nucleosides of the growth-inhibitory effects of adenosine analogs on L1210 and sarcoma 180 cells in culture. Cancer Res 1976; 36:379-83. [PMID: 944090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The growth-inhibitory effect of 6-methylmercaptopurine riboside (MMPR) against leukemia L1210 cells in culture was dramatically potentiated by the addition of guanine nucleosides to the medium. In the presence of either deoxyguanosine or guanosine, the concentration of MMPR that caused 50% inhibition of growth was 35 times lower than in the absence of these nucleosides. Similar potentiation was also observed against Sarcoma 180 cells in culture by guanosine. The metabolic basis of this synergism was approached in a study of the incorporation of [14C]glycine into 5'-phosphoribosyl-N-formylglycinamide in Sarcoma 180 cells. The results show that the site of inhibition resulting in synergism is an early step in purine biosynthesis, probably phosphoribosyl pyrophosphate amidotransferase (EC 2.4.2.14). In the L1210 cell system, the addition of hypoxanthine to the medium prevented the potentiation of MMPR by guanine nucleosides supporting the conclusion that the site of the synergistic interaction involves purine biosynthesis de novo. While hypoxanthine partially reversed the growth-inhibitory effects of MMPR, an even higher degree of protection was observed in the presence of both uridine and hypoxanthine, suggesting that MMPR may have additional sites of action concerned with pyrimidine metabolism.
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