1
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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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2
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Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, Gonzalez LE, Mandell JD, Mane SM, Murtha MT, Sullivan CA, Walker MF, Waqar Z, Wei L, Willsey AJ, Yamrom B, Lee YH, Grabowska E, Dalkic E, Wang Z, Marks S, Andrews P, Leotta A, Kendall J, Hakker I, Rosenbaum J, Ma B, Rodgers L, Troge J, Narzisi G, Yoon S, Schatz MC, Ye K, McCombie WR, Shendure J, Eichler EE, State MW, Wigler M. The contribution of de novo coding mutations to autism spectrum disorder. Nature 2014; 515:216-21. [PMID: 25363768 PMCID: PMC4313871 DOI: 10.1038/nature13908] [Citation(s) in RCA: 1663] [Impact Index Per Article: 166.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/03/2014] [Indexed: 12/20/2022]
Abstract
Whole exome sequencing has proven to be a powerful tool for understanding the genetic architecture of human disease. Here we apply it to more than 2,500 simplex families, each having a child with an autistic spectrum disorder. By comparing affected to unaffected siblings, we show that 13% of de novo missense mutations and 43% of de novo likely gene-disrupting (LGD) mutations contribute to 12% and 9% of diagnoses, respectively. Including copy number variants, coding de novo mutations contribute to about 30% of all simplex and 45% of female diagnoses. Almost all LGD mutations occur opposite wild-type alleles. LGD targets in affected females significantly overlap the targets in males of lower intelligence quotient (IQ), but neither overlaps significantly with targets in males of higher IQ. We estimate that LGD mutation in about 400 genes can contribute to the joint class of affected females and males of lower IQ, with an overlapping and similar number of genes vulnerable to contributory missense mutation. LGD targets in the joint class overlap with published targets for intellectual disability and schizophrenia, and are enriched for chromatin modifiers, FMRP-associated genes and embryonically expressed genes. Most of the significance for the latter comes from affected females.
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Affiliation(s)
- Ivan Iossifov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Brian J O'Roak
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Molecular &Medical Genetics, Oregon Health &Science University, Portland, Oregon 97208, USA
| | - Stephan J Sanders
- 1] Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA [2] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael Ronemus
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Niklas Krumm
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Dan Levy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Holly A Stessman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Kali T Witherspoon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Laura Vives
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Karynne E Patterson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Bryan Paeper
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Jeanselle Dea
- Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Shan Dong
- 1] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA [2] Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Luis E Gonzalez
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Jeffrey D Mandell
- Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Shrikant M Mane
- Yale Center for Genomic Analysis, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael T Murtha
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Catherine A Sullivan
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael F Walker
- Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Zainulabedin Waqar
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Liping Wei
- 1] Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China [2] National Institute of Biological Sciences, Beijing 102206, China
| | - A Jeremy Willsey
- 1] Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA [2] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Boris Yamrom
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Yoon-ha Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ewa Grabowska
- 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] New York Genome Center, New York, New York 10013, USA
| | - Ertugrul Dalkic
- 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] Department of Medical Biology, Bulent Ecevit University School of Medicine, 67600 Zonguldak, Turkey
| | - Zihua Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Steven Marks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Peter Andrews
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Anthony Leotta
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jude Kendall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Inessa Hakker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Julie Rosenbaum
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Beicong Ma
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Linda Rodgers
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jennifer Troge
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Giuseppe Narzisi
- 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] New York Genome Center, New York, New York 10013, USA
| | - Seungtai Yoon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Kenny Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Evan E Eichler
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, Seattle, Washington 98195, USA
| | - Matthew W State
- 1] Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA [2] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA [3] Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA [4] Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael Wigler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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3
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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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4
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Willsey AJ, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, Ercan-Sencicek AG, Gockley J, Gupta AR, Han W, He X, Hoffman EJ, Klei L, Lei J, Liu W, Liu L, Lu C, Xu X, Zhu Y, Mane SM, Lein ES, Wei L, Noonan JP, Roeder K, Devlin B, Sestan N, State MW. Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell 2014; 155:997-1007. [PMID: 24267886 DOI: 10.1016/j.cell.2013.10.020] [Citation(s) in RCA: 623] [Impact Index Per Article: 62.3] [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: 05/17/2013] [Revised: 08/02/2013] [Accepted: 10/07/2013] [Indexed: 01/08/2023]
Abstract
Autism spectrum disorder (ASD) is a complex developmental syndrome of unknown etiology. Recent studies employing exome- and genome-wide sequencing have identified nine high-confidence ASD (hcASD) genes. Working from the hypothesis that ASD-associated mutations in these biologically pleiotropic genes will disrupt intersecting developmental processes to contribute to a common phenotype, we have attempted to identify time periods, brain regions, and cell types in which these genes converge. We have constructed coexpression networks based on the hcASD "seed" genes, leveraging a rich expression data set encompassing multiple human brain regions across human development and into adulthood. By assessing enrichment of an independent set of probable ASD (pASD) genes, derived from the same sequencing studies, we demonstrate a key point of convergence in midfetal layer 5/6 cortical projection neurons. This approach informs when, where, and in what cell types mutations in these specific genes may be productively studied to clarify ASD pathophysiology.
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Affiliation(s)
- A Jeremy Willsey
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
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5
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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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6
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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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7
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Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, Ercan-Sencicek AG, DiLullo NM, Parikshak NN, Stein JL, Walker MF, Ober GT, Teran NA, Song Y, El-Fishawy P, Murtha RC, Choi M, Overton JD, Bjornson RD, Carriero NJ, Meyer KA, Bilguvar K, Mane SM, Sestan N, Lifton RP, Günel M, Roeder K, Geschwind DH, Devlin B, State MW. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 2012; 485:237-41. [PMID: 22495306 DOI: 10.1038/nature10945] [Citation(s) in RCA: 1434] [Impact Index Per Article: 119.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 02/14/2012] [Indexed: 12/14/2022]
Abstract
Multiple studies have confirmed the contribution of rare de novo copy number variations to the risk for autism spectrum disorders. But whereas de novo single nucleotide variants have been identified in affected individuals, their contribution to risk has yet to be clarified. Specifically, the frequency and distribution of these mutations have not been well characterized in matched unaffected controls, and such data are vital to the interpretation of de novo coding mutations observed in probands. Here we show, using whole-exome sequencing of 928 individuals, including 200 phenotypically discordant sibling pairs, that highly disruptive (nonsense and splice-site) de novo mutations in brain-expressed genes are associated with autism spectrum disorders and carry large effects. On the basis of mutation rates in unaffected individuals, we demonstrate that multiple independent de novo single nucleotide variants in the same gene among unrelated probands reliably identifies risk alleles, providing a clear path forward for gene discovery. Among a total of 279 identified de novo coding mutations, there is a single instance in probands, and none in siblings, in which two independent nonsense variants disrupt the same gene, SCN2A (sodium channel, voltage-gated, type II, α subunit), a result that is highly unlikely by chance.
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Affiliation(s)
- Stephan J Sanders
- Program on Neurogenetics, Child Study Center, Department of Psychiatry, Yale University School of Medicine, 230 South Frontage Road, New Haven, Connecticut 06520, USA
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8
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Celestino-Soper PBS, Shaw CA, Sanders SJ, Li J, Murtha MT, Ercan-Sencicek AG, Davis L, Thomson S, Gambin T, Chinault AC, Ou Z, German JR, Milosavljevic A, Sutcliffe JS, Cook EH, Stankiewicz P, State MW, Beaudet AL. Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE. Hum Mol Genet 2011; 20:4360-70. [PMID: 21865298 DOI: 10.1093/hmg/ddr363] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Autism is a neurodevelopmental disorder with increasing evidence of heterogeneous genetic etiology including de novo and inherited copy number variants (CNVs). We performed array comparative genomic hybridization using a custom Agilent 1 M oligonucleotide array intended to cover 197 332 unique exons in RefSeq genes; 98% were covered by at least one probe and 95% were covered by three or more probes with the focus on detecting relatively small CNVs that would implicate a single protein-coding gene. The study group included 99 trios from the Simons Simplex Collection. The analysis identified and validated 55 potentially pathogenic CNVs, categorized as de novo autosomal heterozygous, inherited homozygous autosomal, complex autosomal and hemizygous deletions on the X chromosome of probands. Twenty percent (11 of 55) of these CNV calls were rare when compared with the Database of Genomic Variants. Thirty-six percent (20 of 55) of the CNVs were also detected in the same samples in an independent analysis using the 1 M Illumina single-nucleotide polymorphism array. Findings of note included a common and sometimes homozygous 61 bp exonic deletion in SLC38A10, three CNVs found in lymphoblast-derived DNA but not present in whole-blood derived DNA and, most importantly, in a male proband, an exonic deletion of the TMLHE (trimethyllysine hydroxylase epsilon) that encodes the first enzyme in the biosynthesis of carnitine. Data for CNVs present in lymphoblasts but absent in fresh blood DNA suggest that these represent clonal outgrowth of individual B cells with pre-existing somatic mutations rather than artifacts arising in cell culture. GEO accession number GSE23765 (http://www.ncbi.nlm.nih.gov/geo/, date last accessed on 30 August 2011). Genboree accession: http://genboree.org/java-bin/gbrowser.jsp?refSeqId=1868&entryPointId=chr17&from=53496072&to=53694382&isPublic=yes, date last accessed on 30 August 2011.
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9
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Imielinski M, Baldassano RN, Griffiths A, Russell RK, Annese V, Dubinsky M, Kugathasan S, Bradfield JP, Walters TD, Sleiman P, Kim CE, Muise A, Wang K, Glessner JT, Saeed S, Zhang H, Frackelton EC, Hou C, Flory JH, Otieno G, Chiavacci RM, Grundmeier R, Castro M, Latiano A, Dallapiccola B, Stempak J, Abrams DJ, Taylor K, McGovern D, Silber G, Wrobel I, Quiros A, Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmuda MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ, Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Gut I, Heath S, Laukens D, Mni M, Rutgeerts P, Van Gossum A, Zelenika D, Franchimont D, Hugot JP, de Vos M, Vermeire S, Louis E, Cardon LR, Anderson CA, Drummond H, Nimmo E, Ahmad T, Prescott NJ, Onnie CM, Fisher SA, Marchini J, Ghori J, Bumpstead S, Gwillam R, Tremelling M, Delukas P, Mansfield J, Jewell D, Satsangi J, Mathew CG, Parkes M, Georges M, Daly MJ, Heyman MB, Ferry GD, Kirschner B, Lee J, Essers J, Grand R, Stephens M, Levine A, Piccoli D, Van Limbergen J, Cucchiara S, Monos DS, Guthery SL, Denson L, Wilson DC, Grant SFA, Daly M, Silverberg MS, Satsangi J, Hakonarson H. Common variants at five new loci associated with early-onset inflammatory bowel disease. Nat Genet 2009; 41:1335-40. [PMID: 19915574 DOI: 10.1038/ng.489] [Citation(s) in RCA: 379] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 10/22/2009] [Indexed: 12/13/2022]
Abstract
The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis are common causes of morbidity in children and young adults in the western world. Here we report the results of a genome-wide association study in early-onset IBD involving 3,426 affected individuals and 11,963 genetically matched controls recruited through international collaborations in Europe and North America, thereby extending the results from a previous study of 1,011 individuals with early-onset IBD. We have identified five new regions associated with early-onset IBD susceptibility, including 16p11 near the cytokine gene IL27 (rs8049439, P = 2.41 x 10(-9)), 22q12 (rs2412973, P = 1.55 x 10(-9)), 10q22 (rs1250550, P = 5.63 x 10(-9)), 2q37 (rs4676410, P = 3.64 x 10(-8)) and 19q13.11 (rs10500264, P = 4.26 x 10(-10)). Our scan also detected associations at 23 of 32 loci previously implicated in adult-onset Crohn's disease and at 8 of 17 loci implicated in adult-onset ulcerative colitis, highlighting the close pathogenetic relationship between early- and adult-onset IBD.
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Affiliation(s)
- Marcin Imielinski
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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10
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Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmada MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ, Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Gut I, Heath S, Laukens D, Mni M, Rutgeerts P, Van Gossum A, Zelenika D, Franchimont D, Hugot JP, de Vos M, Vermeire S, Louis E, Cardon LR, Anderson CA, Drummond H, Nimmo E, Ahmad T, Prescott NJ, Onnie CM, Fisher SA, Marchini J, Ghori J, Bumpstead S, Gwilliam R, Tremelling M, Deloukas P, Mansfield J, Jewell D, Satsangi J, Mathew CG, Parkes M, Georges M, Daly MJ. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet 2008; 40:955-62. [PMID: 18587394 PMCID: PMC2574810 DOI: 10.1038/ng.175] [Citation(s) in RCA: 1984] [Impact Index Per Article: 124.0] [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] [Received: 02/01/2008] [Accepted: 05/02/2008] [Indexed: 02/07/2023]
Abstract
Several risk factors for Crohn's disease have been identified in recent genome-wide association studies. To advance gene discovery further, we combined data from three studies on Crohn's disease (a total of 3,230 cases and 4,829 controls) and carried out replication in 3,664 independent cases with a mixture of population-based and family-based controls. The results strongly confirm 11 previously reported loci and provide genome-wide significant evidence for 21 additional loci, including the regions containing STAT3, JAK2, ICOSLG, CDKAL1 and ITLN1. The expanded molecular understanding of the basis of this disease offers promise for informed therapeutic development.
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Affiliation(s)
- Jeffrey C Barrett
- Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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11
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Shimkets RA, Lowe DG, Tai JT, Sehl P, Jin H, Yang R, Predki PF, Rothberg BE, Murtha MT, Roth ME, Shenoy SG, Windemuth A, Simpson JW, Simons JF, Daley MP, Gold SA, McKenna MP, Hillan K, Went GT, Rothberg JM. Gene expression analysis by transcript profiling coupled to a gene database query. Nat Biotechnol 1999; 17:798-803. [PMID: 10429247 DOI: 10.1038/11743] [Citation(s) in RCA: 139] [Impact Index Per Article: 5.6] [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: 11/09/2022]
Abstract
We describe an mRNA profiling technique for determining differential gene expression that utilizes, but does not require, prior knowledge of gene sequences. This method permits high-throughput reproducible detection of most expressed sequences with a sensitivity of greater than 1 part in 100,000. Gene identification by database query of a restriction endonuclease fingerprint, confirmed by competitive PCR using gene-specific oligonucleotides, facilitates gene discovery by minimizing isolation procedures. This process, called GeneCalling, was validated by analysis of the gene expression profiles of normal and hypertrophic rat hearts following in vivo pressure overload.
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Affiliation(s)
- R A Shimkets
- CuraGen Corporation, 555 Long Wharf Drive, New Haven, CT 06511, USA.
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12
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Lin X, Swaroop A, Vaccarino FM, Murtha MT, Haas M, Ji X, Ruddle FH, Leckman JF. Characterization and sequence analysis of the human homeobox-containing gene GBX2. Genomics 1996; 31:335-42. [PMID: 8838315 DOI: 10.1006/geno.1996.0056] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [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: 02/02/2023]
Abstract
Polymerase chain reaction (PCR) was used to amplify portion of homeobox genes present in a human 11-week fetal brain cDNA library. One of these PCR products was determined by sequencing to be the Gastrulation and brain specific-2 gene (GBX2). Screening this human fetal brain cDNA library with probes specific for GBX2 led to the identification of a 2151-bp cDNA clone. The nucleotide sequence of the cDNA clone encodes for a protein of 347 amino acid residues. The amino acid sequence of the GBX2 homeodomain is identical (100%) to the that of homologous gene, Gbx2, expressed in the developing mouse embryo and virtually identical (97%) to a gene expressed in the developing chicken embryo, CHox7. The 5' end of the GBX2 gene contains a CpG island in the untranslated region and a trinucleotide (CCG)8 repeat in the coding region. The amino-terminal end of the GBX2 protein is proline-rich, with 30 proline residues in one stretch of 120 amino acids. A single 2.2-kb transcript was detected by Northern analysis in the developing human CNS as well as in other tissues. The human genomic clone for GBX2 was also isolated, characterized, and mapped to 2q36(d)-q37 by somatic cell hybrid analysis and fluorescence in situ hybridization. These studies provide a framework for designing future experiments that are needed to determine the functional significance of this gene in CNS development.
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Affiliation(s)
- X Lin
- Department of Biology, Yale University, New Haven, Connecticut 06510, USA
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13
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Affiliation(s)
- F H Ruddle
- Department of Biology, Yale University, New Haven, Connecticut 06520-8103
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14
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Ruddle FH, Bentley KL, Murtha MT, Risch N. Gene loss and gain in the evolution of the vertebrates. Dev Suppl 1994:155-161. [PMID: 7579516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Homeobox cluster genes (Hox genes) are highly conserved and can be usefully employed to study phyletic relationships and the process of evolution itself. A phylogenetic survey of Hox genes shows an increase in gene number in some more recently evolved forms, particularly in vertebrates. The gene increase has occurred through a two-step process involving first, gene expansion to form a cluster, and second, cluster duplication to form multiple clusters. We also describe data that suggests that non-Hox genes may be preferrentially associated with the Hox clusters and raise the possibility that this association may have an adaptive biological function. Hox gene loss may also play a role in evolution. Hox gene loss is well substantiated in the vertebrates, and we identify additional possible instances of gene loss in the echinoderms and urochordates based on PCR surveys. We point out the possible adaptive role of gene loss in evolution, and urge the extension of gene mapping studies to relevant species as a means of its substantiation.
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Affiliation(s)
- F H Ruddle
- Department of Biology, Yale University, New Haven, CT, USA
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15
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Abstract
Homeobox cluster genes (Hox genes) are highly conserved and can be usefully employed to study phyletic relationships and the process of evolution itself. A phylogenetic survey of Hox genes shows an increase in gene number in some more recently evolved forms, particularly in vertebrates. The gene increase has occurred through a two-step process involving first, gene expansion to form a cluster, and second, cluster duplication to form multiple clusters. We also describe data that suggests that non-Hox genes may be preferrentially associated with the Hox clusters and raise the possibility that this association may have an adaptive biological function. Hox gene loss may also play a role in evolution. Hox gene loss is well substantiated in the vertebrates, and we identify additional possible instances of gene loss in the echinoderms and urochordates based on PCR surveys. We point out the possible adaptive role of gene loss in evolution, and urge the extension of gene mapping studies to relevant species as a means of its substantiation.
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Affiliation(s)
- Frank H. Ruddle
- Department of Biology, Yale University, New Haven, CT, USA
- Department of Genetics, Yale University Medical School, New Haven CT, USA
| | | | | | - Neil Risch
- Department of Epidemiology and Public Health, Yale University Medical School, New Haven, CT, USA
- Department of Genetics, Yale University Medical School, New Haven CT, USA
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16
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Abstract
Homeobox genes encode DNA-binding transcription regulators that participate in the formation of embryonic pattern or contribute to cell-type specificity during metazoan development. Homeobox genes that regulate axial patterning and segmental identity (Hox/HOM genes) share a conserved clustered genomic organization. Mammals have four clusters that have likely arisen from the duplication of a single ancestral cluster. The number of Hox-type genes in other deuterostomes was estimated by using a polymerase chain reaction sampling method. Increased Hox gene complements are associated with the appearance of chordate and vertebrate characters. Our data suggest the presence of one Hox cluster in the acorn worm, a hemichordate; two Hox clusters in amphioxus, a cephalochordate; and three in the lamprey, a primitive vertebrate.
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Affiliation(s)
- J W Pendleton
- Department of Biology, Yale University, New Haven, CT 06511-8112
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17
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Abstract
The importance of the Hox/HOM class of homeobox genes in early anterior-posterior pattern formation and the conserved genomic organization of this gene family provides an interesting study in genome evolution. The Platyhelminthes (flatworms) are a basal metazoan group with a simple bilateral body plan. We used the polymerase chain reaction (PCR) to detect Hox/HOM-class homeobox genes from species representing two classes of flatworms. Seven planarian and five trematode Hox/HOM-class homeoboxes were found. The sequences of the genes are consistent with the presence of one Hox/HOM-type cluster in the flatworms. Further analysis of this putative cluster may be expected to provide outgroup information for studying the evolution of the Hox/HOM clusters in the higher metazoa.
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Affiliation(s)
- J L Bartels
- Department of Biology, Yale University, New Haven, Connecticut 06511
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18
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Abstract
A newly identified homeobox gene designated Dbx has been mapped to mouse Chromosome (Chr) 7. This gene is expressed in a restricted manner in developing mouse brain and spinal cord and has amino acid sequence similarities with members of the homeobox gene family such as Drosophila H2.0 and mouse Hlx. Using a fragment of the Dbx cDNA as a probe, a PstI restriction fragment length polymorphism was used to determine genotypes of 144 progeny from an interspecific backcross. Segregation analysis revealed linkage of Dbx with six prepositioned reference loci on mouse Chr 7. No recombination was observed between Dbx and Odc-rs6, indicating that Dbx lies approximately 25 cM distal to the Chr 7 centromere in a region that has conserved linkage relationships with regions of human Chrs 11 and 19.
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19
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Lu S, Bogarad LD, Murtha MT, Ruddle FH. Expression pattern of a murine homeobox gene, Dbx, displays extreme spatial restriction in embryonic forebrain and spinal cord. Proc Natl Acad Sci U S A 1992; 89:8053-7. [PMID: 1355604 PMCID: PMC49854 DOI: 10.1073/pnas.89.17.8053] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.8] [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] [Indexed: 02/07/2023] Open
Abstract
Homeobox genes specify regional identity during development. A homeobox sequence that we have named Dbx was isolated from 13.5-day embryonic mouse telencephalon cDNA. The Dbx homeodomain shows highest sequence homology to Drosophila H2.0 and chicken CHox E. We report here the expression pattern of Dbx during mouse embryogenesis. In situ hybridization analyses indicate that Dbx is expressed exclusively within the embryonic central nervous system in a highly restricted manner. Dbx transcripts are detected within a region of the prospective cerebral cortex of the midgestation telencephalon. Dbx is also expressed in the diencephalon as well as in two thin continuous columns of neuroblasts within the hindbrain and spinal cord. This expression is limited to regions of active mitosis. Dbx may act to specify subsets of neuroblasts during the development of the central nervous system.
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Affiliation(s)
- S Lu
- Department of Biology, Yale University, New Haven, CT 06511
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20
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Abstract
The homeobox genes encode a family of DNA-binding regulatory proteins whose function and genomic organization make them an important model system for the study of development and differentiation. Oligonucleotide primers corresponding to highly conserved regions of Antennapediaclass homeodomains were designed to detect and identify homeobox sequences in populations of DNA or RNA by means of the polymerase chain reaction (PCR). Here we present a survey of sequences detected by PCR using an initial set of primers (HoxA and HoxB) based on an early nucleotide consensus for vertebrate Antennapedia-class homeodomains. Several novel sequences are reported from both mouse genomic DNA and RNA from the developing mouse telencephalon. Forebrain-derived clones are similar to the chicken CHox7, Drosophila H2.0, and mouse Hlx genes. PCR also proved to be a rapid method for identifying homeobox sequences from diverse metazoan species. Cloning of three Antennapedia-related sequences from cnidarians provides evidence of ancient roles for homeobox genes early in metazoan evolution.
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Affiliation(s)
- M T Murtha
- Department of Biology, Yale University, New Haven, CT 06511
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21
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Abstract
The Gld gene of Drosophila melanogaster is transiently expressed during every stage of development. The temporal pattern of Gld expression is highly correlated with that of ecdysteroids. Exogeneous treatment of third instar larvae with 20-hydroxyecdysone induces the accumulation of Gld mRNA in the hypoderm and anterior spiracular gland cells. During metamorphosis Gld is expressed in a variety of tissues derived from the ectoderm. In the developing reproductive tract, Gld mRNA accumulates in the female spermathecae and oviduct and in the male ejaculatory duct and ejaculatory bulb. These four organs are derived from closely related cell lineages in the genital imaginal disc. Since the expression of Gld is not required for the development of these reproductive structures, this spatial pattern of expression is most likely a fortuitous consequence of a shared regulatory factor in this cell lineage. At the adult stage a high level of the Gld mRNA is only observed in the male ejaculatory duct.
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Affiliation(s)
- D L Cox-Foster
- Department of Molecular Biology, Vanderbilt University, Nashville, Tennessee 37235
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22
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Abstract
The temporal patterns of glucose dehydrogenase (Gld) and alcohol dehydrogenase (Adh) expression in Drosophila are correlated positively and negatively, respectively, with ecdysterone titers during the late third instar. In mutant l(3)ecdysone-1ts (ecd-1) larvae, the normal peak of Gld mRNA late in the third instar is not expressed. Conversely, the normal decrease in Adh mRNA at this stage fails to occur in ecd-1. These two abnormal patterns can be reversed by treatment with exogenous ecdysterone. Premature exposure of wild type mid-third instar larvae to ecdysterone also results in the rapid accumulation of Gld mRNA and signals the repression of Adh mRNA. The observed decrease in Adh mRNA expression is accompanied by a transient switch in promoter usage from proximal to distal transcription start sites, which normally occurs later in the third instar.
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Affiliation(s)
- M T Murtha
- Department of Molecular Biology, Vanderbilt University, Nashville, Tennessee 37235
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