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Amish SJ, Bernall S, DeHaan P, Miller M, O’Rourke S, Boyer MC, Muhlfeld C, Lodmell A, Leary RF, Luikart G. Rapid SNP genotyping, sex identification, and hybrid-detection in threatened bull trout. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01289-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Genis D, Ortega-Cubero S, San Nicolás H, Corral J, Gardenyes J, de Jorge L, López E, Campos B, Lorenzo E, Tonda R, Beltran S, Negre M, Obón M, Beltran B, Fàbregas L, Alemany B, Márquez F, Ramió-Torrentà L, Gich J, Volpini V, Pastor P. Heterozygous STUB1 mutation causes familial ataxia with cognitive affective syndrome (SCA48). Neurology 2018; 91:e1988-e1998. [PMID: 30381368 DOI: 10.1212/wnl.0000000000006550] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 08/06/2018] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE To describe a new spinocerebellar ataxia (SCA48) characterized by early cerebellar cognitive-affective syndrome (CCAS) and late-onset SCA. METHODS This is a descriptive study of a family that has been followed for more than a decade with periodic neurologic and neuropsychological examinations, MRI, brain SPECT perfusion, and genetic analysis. Whole exome sequencing was performed in 3 affected and 1 unaffected family member and subsequently validated by linkage analysis of chromosome 16p13.3. RESULTS Six patients fully developed cognitive-affective and complete motor cerebellar syndrome associated with vermian and hemispheric cerebellar atrophy, suggesting a continuum from a dysexecutive syndrome slowly evolving to a complete and severe CCAS with late truncal ataxia. Three presymptomatic patients showed focal cerebellar atrophy in the vermian, paravermian, and the medial part of cerebellar lobes VI and VII, suggesting that cerebellar atrophy preceded the ataxia, and that the neurodegeneration begins in cerebellar areas related to cognition and emotion, spreading later to the whole cerebellum. Among the candidate variants, only the frameshift heterozygous c.823_824delCT STUB1 (p.L275Dfs*16) pathogenic variant cosegregated with the disease. The p.L275Dfs*16 heterozygous STUB1 pathogenic variant leads to neurodegeneration and atrophy in cognition- and emotion-related cerebellar areas and reinforces the importance of STUB1 in maintaining cognitive cerebellar function. CONCLUSIONS We report a heterozygous STUB1 pathogenic genetic variant causing dominant cerebellar ataxia. Since recessive mutations in STUB1 gene have been previously associated with SCAR16, these findings suggest a previously undescribed SCA locus (SCA48; MIM# 618093).
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Affiliation(s)
- David Genis
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Sara Ortega-Cubero
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Hector San Nicolás
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Jordi Corral
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Josep Gardenyes
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Laura de Jorge
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Eva López
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Berta Campos
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Elena Lorenzo
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Raúl Tonda
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Sergi Beltran
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Montserrat Negre
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - María Obón
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Brigitte Beltran
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Laura Fàbregas
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Berta Alemany
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Fabián Márquez
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Lluís Ramió-Torrentà
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Jordi Gich
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Víctor Volpini
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Pau Pastor
- From the Unit of Ataxias, Spastic Paraparesis, and Rare Neurological Diseases (D.G., B.A.) and Neuropsychology Unit (J.G.), Neurology Service (F.M., L.R.-T.), Nuclear Medicine Unit (M.N.), Genetic Unit, Laboratori Clinic Territorial de Girona (M.O.), and MRI Center, Institute of Diagnostic Imaging (IDI), and Radiology Department (B.B.), University Hospital "Dr. Josep Trueta," Hospital de Santa Caterina, Parc Hospitalari Martí i Julià; Group of Investigation in Neurodegeneration and Neuroinflammation (D.G., B.A., F.M., L.R.-T., J.G.), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IDIBGI), Girona; Medical Sciences Department (B.A., L.R.-T.), University of Girona; Neurogenetics Laboratory, Division of Neurosciences (S.O.-C., E. Lorenzo, P.P.), Center for Applied Medical Research, University of Navarra, Pamplona; Department of Neurology and Neurosurgery (S.O.-C., H.S.N.), Hospital Universitario de Burgos (HUBU); CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (S.O.-C., E. Lorenzo, P.P.), Instituto de Salud Carlos III, Madrid; Molecular Diagnostic Centre for Hereditary Diseases (CDGM) (J.C., J.G., L.d.J., E. López, B.C., V.V.), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona; Centro Nacional de Análisis Genómico (CNAG-CRG) (R.T., S.B.), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF) (R.T., S.B.), Barcelona; National Bioinformatics Institute (R.T.), Madrid; Clinical Psychology (L.F.), Hospital de Dia de Malalties Neurodegeneratives, Hospital de Santa Caterina, Parc Hospitalari Martí i Julià, Girona; and Movement Disorders Unit, Department of Neurology (P.P.), University Hospital Mutua de Terrassa, Barcelona, Spain.
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Fountain ED, Kang JK, Tempel DJ, Palsbøll PJ, Pauli JN, Zachariah Peery M. Genomics meets applied ecology: Characterizing habitat quality for sloths in a tropical agroecosystem. Mol Ecol 2017; 27:41-53. [DOI: 10.1111/mec.14388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/11/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Emily D. Fountain
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI USA
| | - Jung koo Kang
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI USA
- Marine Evolution and Conservation Groningen Institute of Evolutionary Life Sciences University of Groningen Groningen The Netherlands
- Center of Quantitative Sciences in Biomedicine Department of Mathematics North Carolina State University Raleigh NC USA
| | - Douglas J. Tempel
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI USA
| | - Per J. Palsbøll
- Marine Evolution and Conservation Groningen Institute of Evolutionary Life Sciences University of Groningen Groningen The Netherlands
| | - Jonathan N. Pauli
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI USA
| | - M. Zachariah Peery
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI USA
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Detecting Pedigree Relationship Errors. Methods Mol Biol 2017. [PMID: 28980240 DOI: 10.1007/978-1-4939-7274-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Pedigree relationship errors often occur in family data collected for genetic studies, and unidentified errors can lead to either increased false positives or decreased power in both linkage and association analyses. Here, we review several allele sharing as well as likelihood-based statistics that were proposed to efficiently extract genealogical information from available genome-wide marker data, and the software package PREST that implements these methods. We provide the detailed analytical steps involved using two application examples, and we discuss various practical issues, including result interpretation.
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Riddle MA, Maher BS, Wang Y, Grados M, Bienvenu OJ, Goes FS, Cullen B, Murphy DL, Rauch SL, Greenberg BD, Knowles JA, McCracken JT, Pinto A, Piacentini J, Pauls DL, Rasmussen SA, Shugart YY, Nestadt G, Samuels J. OBSESSIVE-COMPULSIVE PERSONALITY DISORDER: EVIDENCE FOR TWO DIMENSIONS. Depress Anxiety 2016; 33:128-35. [PMID: 26594839 DOI: 10.1002/da.22452] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 09/23/2015] [Accepted: 10/18/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND To determine possible dimensions that underlie obsessive-compulsive personality disorder (OCPD) and to investigate their clinical correlates, familiality, and genetic linkage. METHODS Participants were selected from 844 adults assessed with the Structured Instrument for the Diagnosis of DSM-IV Personality Disorders (SIDP) in the OCD Collaborative Genetics Study (OCGS) that targeted families with obsessive-compulsive disorder (OCD) affected sibling pairs. We conducted an exploratory factor analysis, which included the eight SIDP-derived DSM-IV OCPD traits and the indecision trait from the DSM-III, assessed clinical correlates, and estimated sib-sib correlations to evaluate familiality of the factors. Using MERLIN and MINX, we performed genome-wide quantitative trait locus (QTL) linkage analysis to test for allele sharing among individuals. RESULTS Two factors were identified: Factor 1: order/control (perfectionism, excessive devotion to work, overconscientiousness, reluctance to delegate, and rigidity); and Factor 2: hoarding/indecision (inability to discard and indecisiveness). Factor 1 score was associated with poor insight, whereas Factor 2 score was associated with task incompletion. A significant sib-sib correlation was found for Factor 2 (rICC = .354, P < .0001) but not Factor 1 (rICC = .129, P = .084). The linkage findings were different for the two factors. When Factor 2 was analyzed as a quantitative trait, a strong signal was detected on chromosome 10 at marker d10s1221: KAC LOD = 2.83, P = .0002; and marker d10s1225: KAC LOD = 1.35, P = .006. CONCLUSIONS The results indicate two factors of OCPD, order/control and hoarding/indecision. The hoarding/indecision factor is familial and shows modest linkage to a region on chromosome 10.
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Affiliation(s)
- Mark A Riddle
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Brion S Maher
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Ying Wang
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marco Grados
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - O Joseph Bienvenu
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bernadette Cullen
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Dennis L Murphy
- Laboratory of Clinical Science, National Institute of Mental Health, National Institute of Health, Bethesda, Maryland
| | - Scott L Rauch
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Boston, Massachusetts
| | - Benjamin D Greenberg
- Department of Psychiatry and Human Behavior, Brown Medical School, Butler Hospital, Providence, Rhode Island
| | - James A Knowles
- Department of Psychiatry, University of Southern California School of Medicine, Los Angeles, California
| | - James T McCracken
- Department of Psychiatry and Biobehavioral Sciences, School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Anthony Pinto
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York State Psychiatric Institute, New York City, New York
| | - John Piacentini
- Department of Psychiatry and Biobehavioral Sciences, School of Medicine, University of California Los Angeles, Los Angeles, California
| | - David L Pauls
- Department of Psychiatry, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Steven A Rasmussen
- Department of Psychiatry and Human Behavior, Brown Medical School, Butler Hospital, Providence, Rhode Island
| | - Yin Yao Shugart
- Unit of Statistical Genomics, Division of Intramural Research, National Institute of Mental Health, National Institute of Health, Bethesda, Maryland
| | - Gerald Nestadt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jack Samuels
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Samuels J, Shugart YY, Wang Y, Grados MA, Bienvenu OJ, Pinto A, Rauch SL, Greenberg BD, Knowles JA, Fyer AJ, Piacentini J, Pauls DL, Cullen B, Rasmussen SA, Stewart SE, Geller DA, Maher BS, Goes FS, Murphy DL, McCracken JT, Riddle MA, Nestadt G. Clinical correlates and genetic linkage of social and communication difficulties in families with obsessive-compulsive disorder: Results from the OCD Collaborative Genetics Study. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:326-36. [PMID: 24798771 DOI: 10.1002/ajmg.b.32235] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 04/11/2014] [Indexed: 11/09/2022]
Abstract
Some individuals with obsessive-compulsive disorder (OCD) have autistic-like traits, including deficits in social and communication behaviors (pragmatics). The objective of this study was to determine if pragmatic impairment aggregates in OCD families and discriminates a clinically and genetically distinct subtype of OCD. We conducted clinical examinations on, and collected DNA samples from, 706 individuals with OCD in 221 multiply affected OCD families. Using the Pragmatic Rating Scale (PRS), we compared the prevalence of pragmatic impairment in OCD-affected relatives of probands with and without pragmatic impairment. We also compared clinical features of OCD-affected individuals in families having at least one, versus no, individual with pragmatic impairment, and assessed for linkage to OCD in the two groups of families. The odds of pragmatic impairment were substantially greater in OCD-affected relatives of probands with pragmatic impairment. Individuals in high-PRS families had greater odds of separation anxiety disorder and social phobia, and a greater number of schizotypal personality traits. In high-PRS families, there was suggestive linkage to OCD on chromosome 12 at marker D12S1064 and on chromosome X at marker DXS7132 whereas, in low-PRS families, there was suggestive linkage to chromosome 3 at marker D3S2398. Pragmatic impairment aggregates in OCD families. Separation anxiety disorder, social phobia, and schizotypal personality traits are part of a clinical spectrum associated with pragmatic impairment in these families. Specific regions of chromosomes 12 and X are linked to OCD in high-PRS families. Thus, pragmatic impairment may distinguish a clinically and genetically homogeneous subtype of OCD.
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Affiliation(s)
- Jack Samuels
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
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7
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Miller NH, Justice CM, Marosy B, Swindle K, Kim Y, Roy-Gagnon MH, Sung H, Behneman D, Doheny KF, Pugh E, Wilson AF. Intra-familial tests of association between familial idiopathic scoliosis and linked regions on 9q31.3-q34.3 and 16p12.3-q22.2. Hum Hered 2012; 74:36-44. [PMID: 23154503 PMCID: PMC4123546 DOI: 10.1159/000343751] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 09/07/2012] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Custom genotyping of markers in families with familial idiopathic scoliosis were used to fine-map candidate regions on chromosomes 9 and 16 in order to identify candidate genes that contribute to this disorder and prioritize them for next-generation sequence analysis. METHODS Candidate regions on 9q and 16p-16q, previously identified as linked to familial idiopathic scoliosis in a study of 202 families, were genotyped with a high-density map of single nucleotide polymorphisms. Tests of linkage for fine-mapping and intra-familial tests of association, including tiled regression, were performed on scoliosis as both a qualitative and quantitative trait. RESULTS AND CONCLUSIONS Nominally significant linkage results were found for markers in both candidate regions. Results from intra-familial tests of association and tiled regression corroborated the linkage findings and identified possible candidate genes suitable for follow-up with next-generation sequencing in these same families. Candidate genes that met our prioritization criteria included FAM129B and CERCAM on chromosome 9 and SYT1, GNAO1, and CDH3 on chromosome 16.
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Affiliation(s)
- Nancy H Miller
- Department of Orthopaedic Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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8
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Shugart YY, Wang Y. Identification of genotype errors. Methods Mol Biol 2012; 850:11-24. [PMID: 22307691 DOI: 10.1007/978-1-61779-555-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
It has been documented that there exist some errors in most large genotype datasets and that an error rate of 1-2% is adequate to lead to the distortion of map distance as well as a false conclusion of linkage (Abecasis et al. Eur J Hum Genet 9(2):130-134, 2001), therefore one needs to ensure that the data are as clean as possible. On the other hand, the process of data cleaning is tedious and demands efforts and experience. O'Connell and Weeks implemented four error-checking algorithms in computer software called PedCheck. In this chapter, the four algorithms implemented in PedCheck are discussed with a focus on the genotype-elimination method. Furthermore, an example for four levels of error checking permitted by PedCheck is provided with the required input files. In addition, alternative algorithms implemented in other statistical computing programs are also briefly discussed.
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Affiliation(s)
- Yin Y Shugart
- Unit of Statistical Genomics, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
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Abstract
Pedigree relationship errors often occur in family data collected for genetic studies, and unidentified errors can lead to either increased false positives or decreased power in both linkage and association analyses. Here we review several allele sharing, as well as likelihood-based statistics, that were proposed to efficiently extract genealogical information from available genome-wide marker data, and the software package PREST that implements these methods. We provide detailed analytical steps involved using two application examples, and we discuss various practical issues including results interpretation.
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Affiliation(s)
- Lei Sun
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
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10
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Cropp CD, Simpson CL, Wahlfors T, Ha N, George A, Jones MS, Harper U, Ponciano-Jackson D, Green TA, Tammela TLJ, Bailey-Wilson J, Schleutker J. Genome-wide linkage scan for prostate cancer susceptibility in Finland: evidence for a novel locus on 2q37.3 and confirmation of signal on 17q21-q22. Int J Cancer 2011; 129:2400-7. [PMID: 21207418 DOI: 10.1002/ijc.25906] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 11/20/2010] [Accepted: 12/10/2010] [Indexed: 12/31/2022]
Abstract
Genome-wide linkage studies have been used to localize rare and highly penetrant prostate cancer (PRCA) susceptibility genes. Linkage studies performed in different ethnic backgrounds and populations have been somewhat disparate, resulting in multiple, often irreproducible signals because of genetic heterogeneity and high sporadic background of the disease. Our first genome-wide linkage study and subsequent fine-mapping study of Finnish hereditary prostate cancer (HPC) families gave evidence of linkage to one region. Here, we conducted subsequent scans with microsatellites and SNPs in a total of 69 Finnish HPC families. GENEHUNTER-PLUS was used for parametric and nonparametric analyses. Our microsatellite genome-wide linkage study provided evidence of linkage to 17q12-q23, with a heterogeneity LOD (HLOD) score of 3.14 in a total of 54 of the 69 families. Genome-wide SNP analysis of 59 of the 69 families gave a highest HLOD score of 3.40 at 2q37.3 under a dominant high penetrance model. Analyzing all 69 families by combining microsatellite and SNP maps also yielded HLOD scores of > 3.3 in two regions (2q37.3 and 17q12-q21.3). These significant linkage peaks on chromosome 2 and 17 confirm previous linkage evidence of a locus on 17q from other populations and provide a basis for continued research into genetic factors involved in PRCA. Fine-mapping analysis of these regions is ongoing and candidate genes at linked loci are currently under analysis.
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Affiliation(s)
- Cheryl D Cropp
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
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Abstract
Genetic markers are widely used to determine the parentage of individuals in studies of mating systems, reproductive success, dispersals, quantitative genetic parameters and in the management of conservation populations. These markers are, however, imperfect for parentage analyses because of the presence of genotyping errors and undetectable alleles, which may cause incompatible genotypes (mismatches) between parents and offspring and thus result in false exclusions of true parentage. Highly polymorphic markers widely used in parentage analyses, such as microsatellites, are especially prone to genotyping errors. In this investigation, I derived the probabilities of excluding a random (related) individual from parentage and the probabilities of Mendelian-inconsistent errors (mismatches) and Mendelian-consistent errors (which do not cause mismatches) in parent-offspring dyads, when a marker having null alleles, allelic dropouts and false alleles is used in a parentage analysis. These probabilities are useful in evaluating the impact of various types of genotyping errors on the information content of a set of markers in and thus the power of a parentage analysis, in determining the threshold number of genetic mismatches that is appropriate for a parentage exclusion analysis and in estimating the rates of genotyping errors and frequencies of null alleles from observed mismatches between known parent-offspring dyads. These applications are demonstrated by numerical examples using both hypothetical and empirical data sets and discussed in the context of practical parentage exclusion analyses.
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Affiliation(s)
- Jinliang Wang
- Institute of Zoology, Zoological Society of London, London NW1 4RY, UK.
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12
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Combined linkage and linkage disequilibrium analysis of a motor speech phenotype within families ascertained for autism risk loci. J Neurodev Disord 2010; 2:210-223. [PMID: 21125004 PMCID: PMC2974936 DOI: 10.1007/s11689-010-9063-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 09/10/2010] [Indexed: 01/08/2023] Open
Abstract
Using behavioral and genetic information from the Autism Genetics Resource Exchange (AGRE) data set we developed phenotypes and investigated linkage and association for individuals with and without Autism Spectrum Disorders (ASD) who exhibit expressive language behaviors consistent with a motor speech disorder. Speech and language variables from Autism Diagnostic Interview-Revised (ADI-R) were used to develop a motor speech phenotype associated with non-verbal or unintelligible verbal behaviors (NVMSD:ALL) and a related phenotype restricted to individuals without significant comprehension difficulties (NVMSD:C). Using Affymetrix 5.0 data, the PPL framework was employed to assess the strength of evidence for or against trait-marker linkage and linkage disequilibrium (LD) across the genome. Ingenuity Pathway Analysis (IPA) was then utilized to identify potential genes for further investigation. We identified several linkage peaks based on two related language-speech phenotypes consistent with a potential motor speech disorder: chromosomes 1q24.2, 3q25.31, 4q22.3, 5p12, 5q33.1, 17p12, 17q11.2, and 17q22 for NVMSD:ALL and 4p15.2 and 21q22.2 for NVMSD:C. While no compelling evidence of association was obtained under those peaks, we identified several potential genes of interest using IPA. CONCLUSION: Several linkage peaks were identified based on two motor speech phenotypes. In the absence of evidence of association under these peaks, we suggest genes for further investigation based on their biological functions. Given that autism spectrum disorders are complex with a wide range of behaviors and a large number of underlying genes, these speech phenotypes may belong to a group of several that should be considered when developing narrow, well-defined, phenotypes in the attempt to reduce genetic heterogeneity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11689-010-9063-2) contains supplementary material, which is available to authorized users.
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Marosy B, Justice CM, Vu C, Zorn A, Nzegwu N, Wilson AF, Miller NH. Identification of susceptibility loci for scoliosis in FIS families with triple curves. Am J Med Genet A 2010; 152A:846-55. [PMID: 20358593 DOI: 10.1002/ajmg.a.33222] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The triple curve pattern (three lateral curvatures of equal severity) has been recognized as a distinct and unique clinical subtype of scoliosis. As part of a large study of familial idiopathic scoliosis (FIS), a subset of five families with a triple curve pattern (at least one member of each family having a triple curve) was evaluated to determine if this curve pattern was linked to any of the markers previously genotyped as part of the STRP-based previous linkage screen. Model independent linkage analysis (SIBPAL, v4.5) of the initial genomic screen identified candidate regions on chromosomes 6 and 10 when FIS was analyzed both as qualitative and quantitative traits in single- and multipoint linkage analyses. Additional fine mapping analyses of this subgroup with SNPs corroborated the findings in these regions (P < 0.001). These regions have been previously linked to FIS, however, this is the first time these regions have been implicated in a clinically well-defined subgroup and may suggest a unique genetic etiology for the formation of a triple curve.
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Affiliation(s)
- Beth Marosy
- Department of Orthopaedic Surgery, Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Katki HA, Sanders CL, Graubard BI, Bergen AW. Using DNA fingerprints to infer familial relationships within NHANES III households. J Am Stat Assoc 2010; 105:552-563. [PMID: 20664713 DOI: 10.1198/jasa.2010.ap09258] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Developing, targeting, and evaluating genomic strategies for population-based disease prevention require population-based data. In response to this urgent need, genotyping has been conducted within the Third National Health and Nutrition Examination (NHANES III), the nationally-representative household-interview health survey in the U.S. However, before these genetic analyses can occur, family relationships within households must be accurately ascertained. Unfortunately, reported family relationships within NHANES III households based on questionnaire data are incomplete and inconclusive with regards to actual biological relatedness of family members. We inferred family relationships within households using DNA fingerprints (Identifiler(R)) that contain the DNA loci used by law enforcement agencies for forensic identification of individuals. However, performance of these loci for relationship inference is not well understood. We evaluated two competing statistical methods for relationship inference on pairs of household members: an exact likelihood ratio relying on allele frequencies to an Identical By State (IBS) likelihood ratio that only requires matching alleles. We modified these methods to account for genotyping errors and population substructure. The two methods usually agree on the rankings of the most likely relationships. However, the IBS method underestimates the likelihood ratio by not accounting for the informativeness of matching rare alleles. The likelihood ratio is sensitive to estimates of population substructure, and parent-child relationships are sensitive to the specified genotyping error rate. These loci were unable to distinguish second-degree relationships and cousins from being unrelated. The genetic data is also useful for verifying reported relationships and identifying data quality issues. An important by-product is the first explicitly nationally-representative estimates of allele frequencies at these ubiquitous forensic loci.
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Affiliation(s)
- Hormuzd A Katki
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, 6120 Executive Blvd. Room 8014 Rockville, MD 20852, U.S.A
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15
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Wojciechowski R, Bailey-Wilson JE, Stambolian D. Association of matrix metalloproteinase gene polymorphisms with refractive error in Amish and Ashkenazi families. Invest Ophthalmol Vis Sci 2010; 51:4989-95. [PMID: 20484597 DOI: 10.1167/iovs.10-5474] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) are involved in scleral extracellular matrix remodeling and have shown differential expression in experimental myopia. The genetic association of refractive error and polymorphisms in MMP and TIMP genes in Old Order Amish (AMISH) and Ashkenazi Jewish (ASHK) families was investigated. METHODS Individuals from 55 AMISH and 63 ASHK families participated in the study. Ascertainment was designed to enrich the families for myopia; the mean spherical equivalent (MSE) refractive error (SD) was -1.61 (2.72) D in the AMISH, and -3.56 (3.32) D in the ASHK. One hundred forty-six common haplotype tagging SNPs covering 14 MMP and 4 TIMP genes were genotyped in 358 AMISH and 535 ASHK participants. Association analyses of MSE and the spherical component of refraction (SPH) were performed separately for the AMISH and the ASHK. Bonferroni-corrected significance thresholds and local false discovery rates were used to account for multiple testing. RESULTS After they were filtered for quality-control, 127 SNPs were included in the analyses. No polymorphisms showed statistically significant association to refraction in the ASHK (minimum P = 0.0132). In AMISH, two SNPs showed evidence of association with refractive phenotypes: rs1939008 (P = 0.00016 for SPH); and rs9928731 (P = 0.00026 for SPH). These markers were each estimated to explain <5% of the variance of SPH in the AMISH sample. CONCLUSIONS Statistically significant genetic associations of ocular refraction to polymorphisms near MMP1 and within MMP2 were identified in the AMISH but not among the ASHK families. The results suggest that the MMP1 and MMP2 genes are involved in refractive variation in the AMISH. Genetic and/or environmental heterogeneity most likely contribute to differences in association results between ethnic groups.
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Affiliation(s)
- Robert Wojciechowski
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland 21224, USA.
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Abstract
STUDY DESIGN Statistical analysis of genomic screening and fine mapping data. OBJECTIVE The goals of this study were to analyze a region on chromosome 17 and to identify specific genetic determinants within this region linked to familial idiopathic scoliosis (FIS) in a subgroup of families in which affected males have undergone surgery. SUMMARY OF BACKGROUND DATA The high prevalence and variability of FIS is indicative of genetic heterogeneity. To localize genes related to scoliosis, identification of groups of families with common clinical characteristics is a strategy that reduces genetic heterogeneity. Two independent studies have implicated a region on chromosome 17 as related to FIS. METHODS With approval of the Institutional Review Board, the initial study population consisted of 202 families (1198 individuals), each of which had 2 or more affected individuals; 17 of those families had an affected male who had surgery. Individuals underwent genomic screening and subsequent fine mapping. Results were obtained using model-independent linkage analysis, with scoliosis set as a qualitative and as a quantitative trait, as implemented in SIBPAL (S.A.G.E., v4.5). The level of significance was set at P < or = 0.05. RESULTS The initial study population had significant results at markers d17s975 and d17s2196. Analyses of a subgroup of families with males having undergone surgery using a customized single nucleotide polymorphism panel resulted in increased significance of this region. CONCLUSION The data confirm a previously reported genetic locus on chromosome 17 as statistically significant in the etiology of FIS within a subgroup of families in which an affected male had spinal surgery.
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17
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Cheng CY, Lee KE, Duggal P, Moore EL, Wilson AF, Klein R, Bailey-Wilson JE, Klein BEK. Genome-wide linkage analysis of multiple metabolic factors: evidence of genetic heterogeneity. Obesity (Silver Spring) 2010; 18:146-52. [PMID: 19444228 PMCID: PMC2866100 DOI: 10.1038/oby.2009.142] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The metabolic syndrome is a highly complex disease and has become one of the major public-health challenges worldwide. We sought to identify genetic loci with potential influence on multiple metabolic factors in a white population in Beaver Dam, Wisconsin, and to explore the possibility of genetic heterogeneity by family history of diabetes (FHD). Three metabolic factors were generated using principal-component factor analysis, and they represented: (i) glycemia, (ii) blood pressure, and (iii) combined (BMI, high-density lipoprotein (HDL) cholesterol, and serum uric acid) factors. Multipoint model-free linkage analysis of these factors with 385 microsatellite markers was performed on 1,055 sib-pairs, using Haseman-Elston regression. Genome-wide suggestive evidence of linkage was found at 30 cM on chromosome 22q (empirical P (P(e)) = 0.0002) for the glycemia factor, at 188-191 cM on chromosome 1q (P(e) = 0.0007) for the blood pressure factor, and at 82 cM on chromosome 17q (P(e) = 0.0007) for the combined factor. Subset analyses of the families by FHD showed evidence of genetic heterogeneity, with divergent linkage signals in the subsets on at least four chromosomes. We found evidence of genetic heterogeneity by FHD for the three metabolic factors. The results also confirmed findings of previous studies that mapped components of the metabolic syndrome to a chromosome 1q region.
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Affiliation(s)
- Ching-Yu Cheng
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, USA
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Li X, Mei L, Yang K, Rotter JI, Guo X. Identifying association under a previous linkage peak on chromosome 16 for body mass index using cross-sectional and longitudinal data of the Framingham Heart Study. BMC Proc 2009; 3 Suppl 7:S101. [PMID: 20017965 PMCID: PMC2795872 DOI: 10.1186/1753-6561-3-s7-s101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We performed association analysis under a previous linkage peak on chromosome 16 with genome-wide single-nucleotide polymorphism (SNP) data to identify genetic variants underlying body mass index (BMI). Data from all subjects with baseline measures and a subgroup who had complete data at four selected time points from the Framingham Heart Study were analyzed. The cross-sectional measures include BMI at baseline for all subjects, as well as BMI at selected time points for the subgroup. The longitudinal measure is the within-subject mean of BMI for the subgroup at the four time points. Association analysis was first performed using PLINK after dividing large pedigrees into nuclear families. We then followed up the identified regions by variance-components methods as implemented in SOLAR using the extended pedigrees. The strongest evidence for associations were observed at 52.3 Mbp (PLINK p = 0.00002, QTLD p = 0.005), on the FTO gene, and at 48.1 Mbp (PLINK p = 0.002, QTLD p = 0.0006) on chromosome 16, which are directly under the previous identified linkage peak. This association was consistently observed for all samples at baseline, and for the subgroup at time point 2, 3, 4 and MEAN, both by PLINK and SOLAR. In addition, another SNP/region at 46.7 Mbp on same chromosome was found to be associated with several BMI measures in the subgroup. Fine-mapping with more markers provided further evidence for SNP association with BMI in the same region (at 52.4 Mbp, QTLD p = 0.0003). These results suggest the existence of genes/DNA variations in these regions that contribute to BMI variation.
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Affiliation(s)
- Xiaohui Li
- Medical Genetics Institute, Cedars-Sinai Medical Center, 8635 West Third Street, Suite 1150, Los Angeles, California 90048 USA.
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Pergadia ML, Agrawal A, Loukola A, Montgomery GW, Broms U, Saccone SF, Wang JC, Todorov AA, Heikkilä K, Statham DJ, Henders AK, Campbell MJ, Rice JP, Todd RD, Heath AC, Goate AM, Peltonen L, Kaprio J, Martin NG, Madden PAF. Genetic linkage findings for DSM-IV nicotine withdrawal in two populations. Am J Med Genet B Neuropsychiatr Genet 2009; 150B:950-9. [PMID: 19180564 PMCID: PMC2995916 DOI: 10.1002/ajmg.b.30924] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nicotine withdrawal (NW) is both an important contributor to difficulty quitting cigarettes and because of mood-related withdrawal symptoms a problem of particular relevance to psychiatry. Twin-studies suggest that genetic factors influence NW (heritability = 45%). Only one previous linkage study has published findings on NW [Swan et al. (2006); Am J Med Genet Part B 141B:354-360; LOD = 2.7; Chr. 6 at 159 cM]. As part of an international consortium, genome-wide scans (using over 360 autosomal microsatellite markers) and telephone diagnostic interviews were conducted on 289 Australian (AUS) and 161 Finnish (FIN, combined (COMB) N = 450 families) families ascertained from twin registries through index-cases with a lifetime history of cigarette smoking. The statistical approach used an affected-sib-pair design (at least two adult full siblings reported a history of DSM-IV NW) and conducted the linkage analyses using MERLIN. Linkage signals with LOD scores >1.5 were found on two chromosomes: 6 (FIN: LOD = 1.93 at 75 cM) and 11 at two different locations (FIN: LOD = 3.55 at 17 cM, and AUS: LOD = 1.68 with a COMB: LOD = 2.30 at 123 cM). The multipoint LOD score of 3.55 on chromosome 11p15 in FIN met genomewide significance (P = 0.013 with 1,000 simulations). At least four strong candidate genes lie within or near this peak on chromosome 11: DRD4, TPH, TH, and CHRNA10. Other studies have reported that chromosome 11 may harbor genes associated with various aspects of smoking behavior. This study adds to that literature by highlighting evidence for NW.
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Affiliation(s)
- Michele L Pergadia
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, Missouri 63110, USA.
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Fine-mapping of candidate region in Amish and Ashkenazi families confirms linkage of refractive error to a QTL on 1p34-p36. Mol Vis 2009; 15:1398-406. [PMID: 19626131 PMCID: PMC2713730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 07/14/2009] [Indexed: 11/17/2022] Open
Abstract
PURPOSE A previous genome-wide study in Orthodox Ashkenazi Jewish pedigrees showed significant linkage of ocular refraction to a Quantitative Trait Locus (QTL) on 1p34-36.1. We carried out a fine-mapping study of this region in Orthodox Ashkenazi Jewish (ASHK) and Old Order Amish (OOA) families to confirm linkage and narrow the candidate region. METHODS Families were recruited from ASHK and OOA American communities. The samples included: 402 individuals in 53 OOA families; and 596 members in 68 ASHK families. Families were ascertained to contain multiple myopic individuals. Genotyping of 1,367 SNPs was carried out within a 35cM (approximately 23.9 Mb) candidate QTL region on 1p34-36. Multipoint variance components (VC) and regression-based (REG) linkage analyses were carried out separately in OOA and ASHK groups, and in a combined analysis that included all families. RESULTS Evidence of linkage of refractive error was found in both OOA (VC LOD=3.45, REG LOD=3.38 at approximately 59 cM) and ASHK families (VC LOD=3.12, REG LOD=4.263 at ~66 cM). Combined analyses showed three highly significant linkage peaks, separated by approximately 11cM (or 10 Mb), within the candidate region. CONCLUSION In a fine-mapping linkage study of OOA and ASHK families, we have confirmed linkage of refractive error to a QTL on 1p. The area of linkage has been narrowed down to a gene-rich region at 1p34.2-35.1 containing ~124 genes.
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Zhang H, Stern H. Inferences for genotyping error rate in ancestry identification from simple sequence repeat marker profiles. JOURNAL OF AGRICULTURAL, BIOLOGICAL, AND ENVIRONMENTAL STATISTICS 2009. [DOI: 10.1198/jabes.2009.0011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Wojciechowski R, Stambolian D, Ciner E, Ibay G, Holmes TN, Bailey-Wilson JE. Genomewide linkage scans for ocular refraction and meta-analysis of four populations in the Myopia Family Study. Invest Ophthalmol Vis Sci 2009; 50:2024-32. [PMID: 19151385 PMCID: PMC2885973 DOI: 10.1167/iovs.08-2848] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Genomewide linkage scans were performed in Caucasian (CAUC) and Old Order Amish (OOA) families to identify genomic regions containing genes responsible for refractive error control. We also performed a meta-analysis by combining these results with our previous linkage results from Ashkenazi Jewish (ASHK) and African American (AFRAM) families. METHODS Two hundred seventy-one CAUC and 411 OOA participants (36 and 61 families, respectively) were recruited to participate in the Myopia Family Study. Recruitment criteria were designed to enrich the sample for multiplex myopic families. Genomewide, model-free, multipoint linkage analyses were performed separately for each population by using >370 microsatellite markers. Empirical significance levels were determined via gene-dropping simulations. A meta-analysis was performed by combining linkage results from the CAUC, OOA, AFRAM, and ASHK samples, and results were compared to previously reported loci for myopia and refraction. RESULTS Suggestive evidence of linkage was found at 12q24 (LOD = 4.583, P = 0.00037) and 4q21 (LOD = 2.72, P = 0.0028) in the CAUC sample and at 5qter (LOD = 3.271, P = 0.0014) in the OOA. Meta-analysis linkage results were largely driven by population-specific signals from ASHK and AFRAM families. The meta-analysis showed suggestive evidence of linkage to 4q21-22 (meta-P = 0.00214) adjacent to the previously reported MYP9 and MYP11 loci. CONCLUSIONS The results showed suggestive evidence of linkage of ocular refraction to 12q24 and 4q21 in CAUC and to 5qter in OOA families. The meta-analysis supports the view that several genes play a role in refractive development across populations. In MFS families, four broad genomic regions (on 1p, 4q, 7p, and 12q) most likely contain genes that influence ocular refraction.
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Affiliation(s)
- Robert Wojciechowski
- Inherited Disease Research Branch, National Human Genome Research Institute, Baltimore, Maryland 21231, USA.
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Ciner E, Ibay G, Wojciechowski R, Dana D, Holmes TN, Bailey-Wilson JE, Stambolian D. Genome-wide scan of African-American and white families for linkage to myopia. Am J Ophthalmol 2009; 147:512-517.e2. [PMID: 19026404 DOI: 10.1016/j.ajo.2008.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 09/02/2008] [Accepted: 09/03/2008] [Indexed: 11/24/2022]
Abstract
PURPOSE To identify myopia susceptibility genes influencing common myopia in 94 African-American and 36 White families. DESIGN A prospective study of families with myopia consisting of a minimum of two individuals affected with myopia. METHODS Extended families consisting of at least two siblings affected with myopia were ascertained. A genome-wide linkage scan using 387 markers was conducted by the Center for Inherited Disease Research. Linkage analyses were conducted with parametric and nonparametric methods. Model-free linkage analysis was performed maximizing over penetrance and over dominance (that is, fitting a wide range of both dominant and recessive models). RESULTS Under the model-free analysis, the maximum two point heterogeneity logarithm of the odds score (MALOD) was 2.87 at D6S1009 in the White cohort and the maximum multipoint MALOD was 2.42 at D12S373-D12S1042 in the same cohort. The nonparametric linkage (NPL) maximum multipoint at D6S1035 had a P value of .005. An overall multipoint NPL score was obtained by combining NPL scores from both populations. The highest combined NPL score was observed at D20S478 with a significant P value of .008. Suggestive evidence of linkage in the White cohort mapped to a previously mapped locus on chromosome 11 at D11S1981 (NPL = 2.14; P = .02). CONCLUSIONS Suggestive evidence of linkage to myopia in both African Americans and Whites was seen on chromosome 20 and became more significant when the scores were combined for both groups. The locus on chromosome 11 independently confirms a report by Hammond and associates mapping a myopia quantitative trait locus to this region.
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Abstract
SUMMARY We present a software package for pedigree reconstruction in natural populations using co-dominant genomic markers such as microsatellites and single nucleotide polymorphisms (SNPs). If available, the algorithm makes use of prior information such as known relationships (sub-pedigrees) or the age and sex of individuals. Statistical confidence is estimated by Markov Chain Monte Carlo (MCMC) sampling. The accuracy of the algorithm is demonstrated for simulated data as well as an empirical dataset with known pedigree. The parentage inference is robust even in the presence of genotyping errors. AVAILABILITY The C source code of FRANz can be obtained under the GPL from http://www.bioinf.uni-leipzig.de/Software/FRANz/.
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Affiliation(s)
- Markus Riester
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
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Teo YY, Fry AE, Sanjoaquin MA, Pederson B, Small KS, Rockett KA, Kwiatkowski DP, Clark TG. Assessing genuine parents-offspring trios for genetic association studies. Hum Hered 2008; 67:26-37. [PMID: 18931507 PMCID: PMC3000594 DOI: 10.1159/000164396] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Accepted: 12/20/2007] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Family-based association tests such as the transmission disequilibrium test (TDT) are dependent on the successful ascertainment of true nuclear family trios. Relationship misspecification inevitably occurs in a proportion of trios collected for genotyping which undetected can lead to a loss of power and increased Type I error due to biases in over-transmission of common alleles. Here, we introduce a method for evaluating the authenticity of nuclear family trios. METHODS Operating in a Bayesian framework, our approach assesses the extent of pedigree inconsistent genotype configurations in the presence of genotyping errors. Unlike other approaches, our method: (i) utilizes information from three individuals collectively (the whole trio) rather than consider two independent pairwise relationships; (ii) down-weighs SNPs with poor performance; (iii) does not require the user to pre-define a rate of genotyping error, which is often unknown to the user and seldom fixed across the different SNPs considered which available methods unrealistically assumed. RESULTS Simulation studies and comparisons with a real set of data showed that our approach is more likely to correctly identify the presence of true and misspecified trios compared to available software, accurately infers the extent of relationship misspecification in a trio and accurately estimates the genotyping error rates. CONCLUSIONS Assessing relationship misspecification depends on the fidelity of the genotype data used. Available algorithms are not optimised for genotyping technology with varying rates of errors across the markers. Through our comparison studies, our approach is shown to outperform available methods for assessing relationship misspecifications.
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Affiliation(s)
- Yik Y Teo
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
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26
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Ciner E, Wojciechowski R, Ibay G, Bailey-Wilson JE, Stambolian D. Genomewide scan of ocular refraction in African-American families shows significant linkage to chromosome 7p15. Genet Epidemiol 2008; 32:454-63. [PMID: 18293391 DOI: 10.1002/gepi.20318] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Refractive development is influenced by environmental and genetic factors. Genetic studies have identified several regions of linkage to ocular refraction, but none have been carried out in African-derived populations. We performed quantitative trait locus linkage analyses in African-American (AA) families to identify genomic regions responsible for refraction. We recruited 493 AA individuals in 96 families to participate in the Myopia Family Study. Genotyping of 387 microsatellite markers was performed on 398 participants. The mean refraction among genotyped individuals was -2.87 D (SD=3.58) and myopia of at least 1 D was present in 267 (68%) participants. Multipoint, regression-based, linkage analyses were carried out on a logarithmic transformation of ocular refraction using the statistical package MERLIN-REGRESS. Empirical significance levels were determined via 4,898 whole-genome gene-dropping simulations. Linkage analyses were repeated after clustering families into two subgroups based on admixture proportions as determined by the software package STRUCTURE. Genomewide significant linkage was seen at 47 cM on chromosome 7 (logarithm of the odds ratio (LOD)=5.87, P=0.00005). In addition, three regions on chromosomes 2p, 3p and 10p showed suggestive evidence of linkage (LOD>2, P<0.005) for ocular refraction. We mapped the first quantitative trait locus for ocular refraction in an AA population to chr.7p15. Two previous studies in European-derived families reported some evidence of linkage to a nearby region, suggesting that this region may contain polymorphisms that mediate refraction across populations. The genomic region under our linkage peak spans approximately 17 Mb and contains approximately 170 genes. Further refinement of this region will be pursued in future studies.
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Affiliation(s)
- Elise Ciner
- The Eye Institute of the Pennsylvania College of Optometry, Philadelphia, Pennsylvania, USA
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Revazova ES, Turovets NA, Kochetkova OD, Agapova LS, Sebastian JL, Pryzhkova MV, Smolnikova VIU, Kuzmichev LN, Janus JD. HLA homozygous stem cell lines derived from human parthenogenetic blastocysts. CLONING AND STEM CELLS 2008; 10:11-24. [PMID: 18092905 DOI: 10.1089/clo.2007.0063] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Individual HLA homozygous parthenogenetic human stem cell (hpSC-Hhom) lines have the potential for cell-based therapy in a significant number of individuals, provided the HLA haplotype is prevalent. We report the successful derivation of four stable hpSC-Hhom lines from both HLA homozygous and HLA heterozygous donors. Of these, the hpSC-Hhom-4 line carries the HLA haplotype found most commonly within the U.S. population, and is shared by different racial groups. These hpSC-Hhom lines demonstrate typical human embryonic stem cell morphology, expressing appropriate stem cell markers and possessing high levels of alkaline phosphatase and telomerase activity. Additionally, injection of these cell lines into immunodeficient animals leads to teratoma formation. G-banded karyotyping demonstrates a normal 46,XX karyotype in lines hpSC-Hhom-1 and hpSC-Hhom-4, and chromosomal anomalies in lines hpSC-Hhom-2 and hpSC-Hhom-3, both derived from the same donor. HLA genotyping of all four hpSC-Hhom lines demonstrates that they are HLA homozygous. Furthermore, in the case of HLA heterozygous donors, the hpSC-Hhom lines inherit the haplotype from only one of the donor's parents. Single-nucleotide polymorphism (SNP) data analysis suggests that hpSC-Hhom lines derived from HLA heterozygous oocyte donors are homozygous throughout the genome as assessed by SNP analysis. The protocol used for deriving these HLA homozygous stem cell lines minimizes the use of animal-derived components, which makes them more appealing for potential clinical application.
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Affiliation(s)
- E S Revazova
- International Stem Cell Corporation, Oceanside, California 92056, USA
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28
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Revazova ES, Turovets NA, Kochetkova OD, Kindarova LB, Kuzmichev LN, Janus JD, Pryzhkova MV. Patient-specific stem cell lines derived from human parthenogenetic blastocysts. CLONING AND STEM CELLS 2008; 9:432-49. [PMID: 17594198 DOI: 10.1089/clo.2007.0033] [Citation(s) in RCA: 199] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Parthenogenetic activation of human oocytes may be one way to produce histocompatible cells for cell-based therapy. We report the successful derivation of six pluripotent human embryonic stem cell (hESC) lines from blastocysts of parthenogenetic origin. The parthenogenetic human embryonic stem cells (phESC) demonstrate typical hESC morphology, express appropriate markers, and possess high levels of alkaline phosphatase and telomerase activity. The phESC lines have a normal 46, XX karyotype, except one cell line, and have been cultured from between 21 to 35 passages. The phESC lines form embryoid bodies in suspension culture and teratomas after injection to immunodeficient animals and give differentiated derivatives of all three embryonic germ layers. DNA profiling of all six phESC lines demonstrates that they are MHC matched with the oocyte donors. The study of imprinted genes demonstrated further evidence of the parthenogenetic origin of the phESC lines. Our research has resulted in a protocol for the production of human parthenogenetic embryos and the derivation of stem cell lines from them, which minimizes the presence of animal-derived components, making the derived phESC lines more suitable for potential clinical use.
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Affiliation(s)
- E S Revazova
- Lifeline Cell Technology, Walkersville, Maryland, USA
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Abstract
Model-free linkage methods are based on identifying regions of the genome in which patterns of allele sharing among family members correspond to patterns of phenotype correlation among family members. Two general classes of model-free linkage methods are discussed in this chapter, relative pair methods designed primarily for analysis of discrete traits and variance component methods designed primarily for analysis of quantitative traits. These methods have been used to identify numerous genes influencing complex human phenotypes and remain viable approaches to gene localization in the twenty-first century.
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Affiliation(s)
- Laura Almasy
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78245, USA
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30
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Engert JC, Lemire M, Faith J, Brisson D, Fujiwara TM, Roslin NM, Brewer CG, Montpetit A, Darmond-Zwaig C, Renaud Y, Doré C, Bailey SD, Verner A, Tremblay G, St-Pierre J, Bétard C, Platko J, Rioux JD, Morgan K, Hudson TJ, Gaudet D. Identification of a chromosome 8p locus for early-onset coronary heart disease in a French Canadian population. Eur J Hum Genet 2007; 16:105-14. [PMID: 17805225 DOI: 10.1038/sj.ejhg.5201920] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Susceptibility to coronary heart disease (CHD) has long been known to exhibit familial aggregation, with heritability estimated to be greater than 50%. The French Canadian population of the Saguenay-Lac Saint-Jean region of Quebec, Canada is descended from a founder population that settled this region 300-400 years ago and this may provide increased power to detect genes contributing to complex traits such as CHD. Probands with early-onset CHD, defined by angiographically determined coronary stenosis, and their relatives were recruited from this population (average sibship size of 6.4). Linkage analysis was performed following a genome-wide microsatellite marker scan on 42 families with 284 individuals. Nonparametric linkage (NPL) analysis provided suggestive evidence for a CHD susceptibility locus on chromosome 8 with an NPL score of 3.14 (P=0.001) at D8S1106. Linkage to this locus was verified by fine mapping in an enlarged sample of 50 families with 320 individuals. This analysis provided evidence of linkage at D8S552 (NPL score=3.53, P=0.0003), a marker that maps to the same location as D8S1106. Candidate genes in this region, including macrophage scavenger receptor 1, farnesyl-diphosphate farnesyltransferase 1, fibrinogen-like 1, and GATA-binding protein 4, were resequenced in all coding exons in both affected and unaffected individuals. Association studies with variants in these and five other genes did not identify a disease-associated mutation. In conclusion, a genome-wide scan and additional fine mapping provide evidence for a locus on chromosome 8 that contributes to CHD in a French Canadian population.
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Affiliation(s)
- James C Engert
- McGill University Health Centre, Montréal, Québec, Canada.
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31
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Saccone SF, Pergadia ML, Loukola A, Broms U, Montgomery GW, Wang JC, Agrawal A, Dick DM, Heath AC, Todorov AA, Maunu H, Heikkila K, Morley KI, Rice JP, Todd RD, Kaprio J, Peltonen L, Martin NG, Goate AM, Madden PAF. Genetic linkage to chromosome 22q12 for a heavy-smoking quantitative trait in two independent samples. Am J Hum Genet 2007; 80:856-66. [PMID: 17436240 PMCID: PMC1852734 DOI: 10.1086/513703] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Accepted: 02/07/2007] [Indexed: 11/03/2022] Open
Abstract
We conducted a genomewide linkage screen of a simple heavy-smoking quantitative trait, the maximum number of cigarettes smoked in a 24-h period, using two independent samples: 289 Australian and 155 Finnish nuclear multiplex families, all of which were of European ancestry and were targeted for DNA analysis by use of probands with a heavy-smoking phenotype. We analyzed the trait, using a regression of identity-by-descent allele sharing on the sum and difference of the trait values for relative pairs. Suggestive linkage was detected on chromosome 22 at 27-29 cM in each sample, with a LOD score of 5.98 at 26.96 cM in the combined sample. After additional markers were used to localize the signal, the LOD score was 5.21 at 25.46 cM. To assess the statistical significance of the LOD score in the combined sample, 1,000 simulated genomewide screens were conducted, resulting in an empirical P value of .006 for the LOD score of 5.21. This linkage signal is driven mainly by the microsatellite marker D22S315 (22.59 cM), which had a single-point LOD score of 5.41 in the combined sample and an empirical P value <.001 from 1,000 simulated genomewide screens. This marker is located within an intron of the gene ADRBK2, encoding the beta-adrenergic receptor kinase 2. Fine mapping of this linkage region may reveal variants contributing to heaviness of smoking, which will lead to a better understanding of the genetic mechanisms underlying nicotine dependence.
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Affiliation(s)
- Scott F Saccone
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.
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32
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Klein AP, de Andrade M, Hruban RH, Bondy M, Schwartz AG, Gallinger S, Lynch HT, Syngal S, Rabe KG, Goggins MG, Petersen GM. Linkage analysis of chromosome 4 in families with familial pancreatic cancer. Cancer Biol Ther 2007; 6:320-3. [PMID: 17312386 PMCID: PMC3144722 DOI: 10.4161/cbt.6.3.3721] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Approximately 10% of pancreatic ductal adenocarcinomas have a familial basis. While a small portion of this familial clustering can be explained by inherited mutations in known genes (BRCA2, p16/CDKN2A, PRSS1, and STK11), the genetic basis for the majority of this familial clustering remains unknown. In addition, a pancreatic cancer susceptibility locus has been reported to be linked to chromosome 4q32-34 in a single family having a high penetrance of early-onset pancreatic ductal adenocarcinoma and pancreatic insufficiency. The goal of this study is to determine if linkage to chromosome 4q exists in our series of well-characterized families with idiopathic familial pancreatic cancer enrolled in the Pancreatic Cancer Genetic Epidemiology Consortium (PACGENE). METHODS Parametric and nonparametric linkage analyses were performed using 21 microsatellite markers on chromosome 4 on affected individuals with pancreatic cancer from 42 familial pancreatic cancer kindreds. RESULTS Markov Chain Monte Carlo parametric and nonparametric linkage analyses using SIMWALK2 as well as nonparametric linkage analysis using MERLIN did not provide strong evidence of linkage in this region (LOD < 1.0). Only one family provided a multipoint LOD score of >0.5 adjacent to the reported region. CONCLUSIONS Our results do not support linkage to the 4q32-34 region in the majority of our familial pancreatic cancer kindreds. However, because multiple pancreatic cancer susceptibility genes are likely to exist, it is possible that a subset of the families in this study may be linked to this region.
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Affiliation(s)
- Alison P Klein
- The Sol Goldman Pancreatic Research Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland 21231, USA.
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Duggal P, Klein AP, Lee KE, Klein R, Klein BEK, Bailey-Wilson JE. Identification of novel genetic loci for intraocular pressure: a genomewide scan of the Beaver Dam Eye Study. ACTA ACUST UNITED AC 2007; 125:74-9. [PMID: 17210855 PMCID: PMC2528864 DOI: 10.1001/archopht.125.1.74] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
OBJECTIVE To identify genetic loci that control intraocular pressure (IOP). METHODS We performed a genomewide scan of IOP, using 486 pedigrees ascertained through a population-based cohort, the Beaver Dam Eye Study. Linkage analysis was performed using the modified Haseman-Elston regression models and variance components linkage analysis. RESULTS Seven regions of interest were identified on chromosomes 2, 5, 6, 7, 12, 15, and 19. The novel linkage region on chromosome 19p had an empirical multipoint P value of 6.1 x 10(-5). Two of the regions (2 and 19) were especially interesting since each has been identified as a potential linkage region for blood pressure. CONCLUSIONS The results of this genomewide scan provide evidence that a quantitative trait locus may influence elevated IOP and may colocalize with blood pressure loci. These loci may control systemic pressure reflected in the eye and vascular system. CLINICAL RELEVANCE Glaucoma is a leading cause of blindness in the world, and the identification of genes that contribute to this disease is essential. Elevated IOP is a principal risk factor for primary open-angle glaucoma and an intriguing quantitative trait that may strongly influence the development of disease.
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Affiliation(s)
- Priya Duggal
- Statistical Genetics Section, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA.
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Baffoe-Bonnie AB, Kittles RA, Gillanders E, Ou L, George A, Robbins C, Ahaghotu C, Bennett J, Boykin W, Hoke G, Mason T, Pettaway C, Vijayakumar S, Weinrich S, Jones MP, Gildea D, Riedesel E, Albertus J, Moses T, Lockwood E, Klaric M, Faruque M, Royal C, Trent JM, Berg K, Collins FS, Furbert-Harris PM, Bailey-Wilson JE, Dunston GM, Powell I, Carpten JD. Genome-wide linkage of 77 families from the African American Hereditary Prostate Cancer study (AAHPC). Prostate 2007; 67:22-31. [PMID: 17031815 DOI: 10.1002/pros.20456] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND The African American Hereditary Prostate Cancer (AAHPC) Study was designed to recruit families with early-onset disease fulfilling criteria of >or=4 affected. METHODS We present a approximately 10 cM genome-wide linkage (GWL) analysis on 77 families including 254 affected and 274 unaffected genotyped. RESULTS Linkage analysis revealed three chromosomal regions with GENEHUNTER multipoint HLOD scores >or=1.3 for all 77 families at 11q22, 17p11, and Xq21. One family yielded genome-wide significant evidence of linkage (LOD = 3.5) to the 17p11 region with seven other families >or=2.3 in this region. Twenty-nine families with no-male-to-male (MM) transmission gave a peak HLOD of 1.62 (alpha = 0.33) at the Xq21 locus. Two novel peaks >or=0.91 for the 16 families with '>6 affected' occurred at 2p21 and 22q12. CONCLUSIONS These chromosomal regions in the genome warrant further follow-up based on the hypothesis of multiple susceptibility genes with modest effects, or several major genes segregating in small subsets of families.
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Fyer AJ, Hamilton SP, Durner M, Haghighi F, Heiman GA, Costa R, Evgrafov O, Adams P, de Leon AB, Taveras N, Klein DF, Hodge SE, Weissman MM, Knowles JA. A third-pass genome scan in panic disorder: evidence for multiple susceptibility loci. Biol Psychiatry 2006; 60:388-401. [PMID: 16919526 DOI: 10.1016/j.biopsych.2006.04.018] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Revised: 04/24/2006] [Accepted: 04/25/2006] [Indexed: 01/20/2023]
Abstract
BACKGROUND Panic disorder (PD) is a common illness with a definite but "complex" genetic contribution and estimated heritability of 30-46%. METHODS We report a genome scan in 120 multiplex PD pedigrees consisting of 1591 individuals of whom 992 were genotyped with 371 markers at an average spacing of 9cM. Parametric two-point, multipoint, and nonparametric analyses were performed using three PD models (Broad, Intermediate, Narrow) and allowing for homogeneity or heterogeneity. The two-point analyses were also performed allowing for independent male and female recombination fractions (theta). Genome-wide significance was empirically evaluated using simulations of this dataset. RESULTS Evidence for linkage reached genome-wide significance in one region on chromosome 15q (near GABA-A receptor subunit genes) and was suggestive at loci on 2p, 2q and 9p using an averaged theta. Analyses allowing for sex-specific theta's were consistent except that support at one locus on 2q increased to genome-wide significance and an additional region of suggestive linkage on 12q was identified. However, differences in male and female recombination fractions predicted by the sex-specific approach were not consistent with current physical maps. CONCLUSIONS These data provide evidence for chromosomal regions on 15q and 2q that may be important in genetic susceptibility to panic disorder. Although we are encouraged by the findings of analyses using sex-specific recombination fractions, we also note that further understanding of this analytic strategy will be important.
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Affiliation(s)
- Abby J Fyer
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University and New York State Psychiatric Institute, New York, New York 10032, USA.
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36
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Shugart YY, Samuels J, Willour VL, Grados MA, Greenberg BD, Knowles JA, McCracken JT, Rauch SL, Murphy DL, Wang Y, Pinto A, Fyer AJ, Piacentini J, Pauls DL, Cullen B, Page J, Rasmussen SA, Bienvenu OJ, Hoehn-Saric R, Valle D, Liang KY, Riddle MA, Nestadt G. Genomewide linkage scan for obsessive-compulsive disorder: evidence for susceptibility loci on chromosomes 3q, 7p, 1q, 15q, and 6q. Mol Psychiatry 2006; 11:763-70. [PMID: 16755275 DOI: 10.1038/sj.mp.4001847] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Obsessive-compulsive disorder (OCD) is the tenth most disabling medical condition worldwide. Twin and family studies implicate a genetic etiology for this disorder, although specific genes have yet to be identified. Here, we present the first large-scale model-free linkage analysis of both extended and nuclear families using both 'broad' (definite and probable diagnoses) and 'narrow' (definite only) definitions of OCD. We conducted a genome-scan analysis of 219 families collected as part of the OCD Collaborative Genetics Study. Suggestive linkage signals were revealed by multipoint analysis on chromosomes 3q27-28 (P=0.0003), 6q (P=0.003), 7p (P=0.001), 1q (P=0.003), and 15q (P=0.006). Using the 'broad' OCD definition, we observed the strongest evidence for linkage on chromosome 3q27-28. The maximum overall Kong and Cox LODall score (2.67) occurred at D3S1262 and D3S2398, and simulation based P-values for these two signals were 0.0003 and 0.0004, respectively, although for both signals, the simulation-based genome-wide significance levels were 0.055. Covariate-linkage analyses implicated a possible role of gene(s) on chromosome 1 in increasing the risk for an earlier onset form of OCD. We are currently pursuing fine mapping in the five regions giving suggestive signals, with a particular focus on 3q27-28. Given probable etiologic heterogeneity in OCD, mapping gene(s) involved in the disorder may be enhanced by replication studies, large-scale family-based linkage studies, and the application of novel statistical methods.
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MESH Headings
- Chromosomes, Human
- Chromosomes, Human, Pair 1
- Chromosomes, Human, Pair 15
- Chromosomes, Human, Pair 3
- Chromosomes, Human, Pair 6
- Chromosomes, Human, Pair 7
- Family Health
- Genetic Predisposition to Disease
- Genome, Human
- Genomics
- Humans
- Lod Score
- Obsessive-Compulsive Disorder/genetics
- Phenotype
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Affiliation(s)
- Y Y Shugart
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD 21287, USA.
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Alden KJ, Marosy B, Nzegwu N, Justice CM, Wilson AF, Miller NH. Idiopathic scoliosis: identification of candidate regions on chromosome 19p13. Spine (Phila Pa 1976) 2006; 31:1815-9. [PMID: 16845357 DOI: 10.1097/01.brs.0000227264.23603.dc] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
STUDY DESIGN We performed genomic screening, statistical linkage analysis, and fine mapping of 202 families with at least 2 individuals with idiopathic scoliosis. OBJECTIVE To identify regions on chromosome 19p13 statistically linked to the phenotypic expression of idiopathic scoliosis. SUMMARY OF BACKGROUND DATA Idiopathic scoliosis is a common structural curvature of the spine affecting otherwise healthy children. Presently, no clear consensus exists regarding the underlying abnormality or genetic determinants of this disease. METHODS Model-independent linkage analysis of qualitative and quantitative traits related to scoliosis was used to screen genotyping data from 391 markers in 202 families (1198 individuals). Subsets of families with probands having a curve > or = 30 degrees were dichotomized based on the most likely mode of inheritance for each family (autosomal dominant or X-linked dominant). Fine mapping was performed to show linkage to candidate regions on chromosome 19. RESULTS When the threshold of disease was set at a curvature of > or = 30 degrees, qualitative linkage analysis revealed significant results at 2 successive markers on chromosome 19. CONCLUSION The data confirm a previously reported genetic locus on chromosome 19 as potentially significant in the etiology of idiopathic scoliosis.
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Affiliation(s)
- Kris J Alden
- Department of Orthopaedic Surgery, Johns Hopkins University, Baltimore, MD, USA
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Miller NH, Marosy B, Justice CM, Novak SM, Tang EY, Boyce P, Pettengil J, Doheny KF, Pugh EW, Wilson AF. Linkage analysis of genetic loci for kyphoscoliosis on chromosomes 5p13, 13q13.3, and 13q32. Am J Med Genet A 2006; 140:1059-68. [PMID: 16596674 DOI: 10.1002/ajmg.a.31211] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Kyphoscoliosis, a three-dimensional deformity of spinal growth, is characterized by a curvature in the coronal plane (scoliosis) in conjunction with thoracic kyphosis in excess of the normal range in the sagittal plane. We identified kyphoscoliosis within members of seven families (53 individuals) originally ascertained as part of a large collaborative study of familial idiopathic scoliosis. Model-independent linkage analysis of a genome-wide microsatellite screen identified areas suggestive of linkage on chromosomes 2q22, 5p13, 13q, and 17q11. Single-point and multipoint analyses of an additional 25 flanking microsatellite markers corroborated linkage to these regions, with areas on chromosomes 5p13, 13q13, and 13q32 being the most significant (P < 0.005). Analyses of single nucleotide polymorphism (SNP) markers in the candidate region on chromosome 5 narrowed the region to approximately 3.5 Mb (P < 0.05), with the most significant P values (P < 0.01) occurring in approximately a 1.3-Mb region. Candidate loci in this region include IRX1, IRX2, and IRX4 of the Iroquois Homeobox protein family. On chromosome 13, single-point and multipoint analyses resulted in multiple SNPs having P values < 0.05 within five candidate genes: Osteoblast-specific factor 2 or periostin, forkhead box O1A, A-kinase anchor protein 11, TBC1 domain family member 4, and glypican 5, thus supporting the potential relevance of this region in the pathogenesis of kyphoscoliosis.
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Affiliation(s)
- Nancy H Miller
- Department of Orthopaedic Surgery, Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.
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Li X, Quiñones MJ, Wang D, Bulnes-Enriquez I, Jimenez X, De La Rosa R, Aurea GL, Taylor KD, Hsueh WA, Rotter JI, Yang H. Genetic effects on obesity assessed by bivariate genome scan: the Mexican-American coronary artery disease study. Obesity (Silver Spring) 2006; 14:1192-200. [PMID: 16899800 DOI: 10.1038/oby.2006.136] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To identify the genetic determinants of obesity using univariate and bivariate models in a genome scan. RESEARCH METHODS AND PROCEDURES We evaluated the genetic and environmental effects and performed a genome-wide linkage analysis of obesity-related traits in 478 subjects from 105 Mexican-American nuclear families ascertained through a proband with documented coronary artery disease. The available obesity traits include BMI, body surface area (BSA), waist-to-hip ratio (WHR), and trunk fat mass as percentage of body weight. Heritability estimates and multipoint linkage analysis were performed using a variance components procedure implemented in SOLAR software. RESULTS The heritability estimates were 0.62 for BMI, 0.73 for BSA, 0.40 for WHR, and 0.38 for trunk fat mass as percentage of body weight. Using a bivariate genetic model, we observed significant genetic correlations between BMI and other obesity-related traits (all p < 0.01). Evidence for univariate linkage was observed at 252 to approximately 267 cM on chromosome 2 for three obesity-related traits (except for WHR) and at 163 to approximately 167 cM on chromosome 5 for BMI and BSA, with the maximum logarithm of the odds ratio score of 3.12 (empirical p value, 0.002) for BSA on chromosome 2. Use of the bivariate linkage model yielded an additional peak (logarithm of the odds ratio = 3.25, empirical p value, 0.002) at 25 cM on chromosome 7 for the pair of BMI and BSA. DISCUSSION The evidence for linkage on chromosomes 2q36-37 and 5q36 is supported both by univariate and bivariate analysis, and an additional linkage peak at 7p15 was identified by the bivariate model. This suggests that use of the bivariate model provides additional information to identify linkage of genes responsible for obesity-related traits.
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Affiliation(s)
- Xiaohui Li
- Genetic Epidemiology, Medical Genetic Institute, Steven Spielberg Pediatric Research Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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Marosy B, Justice CM, Nzegwu N, Kumar G, Wilson AF, Miller NH. Lack of association between the aggrecan gene and familial idiopathic scoliosis. Spine (Phila Pa 1976) 2006; 31:1420-5. [PMID: 16741449 DOI: 10.1097/01.brs.0000219944.18223.52] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
STUDY DESIGN A study was conducted to determine the potential association between a specific aggrecan gene polymorphism and familial idiopathic scoliosis (FIS). OBJECTIVES To determine the allelic distribution of the exon 12 polymorphism within a sample of families with FIS. SUMMARY OF BACKGROUND DATA FIS is a structural curvature of the spine where the underlying genetic etiology has not been established. The aggrecan locus has been linked to multiple skeletal disorders. A polymorphism, within the aggrecan gene, was previously reported to be associated with curve severity in individuals with scoliosis. METHODS Fifty-eight families with FIS were genotyped for the aggrecan exon 12 polymorphism using a polymerase chain reaction method. Model-independent sib-pair linkage analyses and tests of association were performed to analyze the genetic effects of the exon 12 polymorphism. RESULTS Linkage analyses of a genomic screen performed on a subgroup of 48 families with a most likely to be X-linked dominant mode of inheritance of FIS showed marginally significant results on chromosome 15q25-26 (P < 0.05). The overall distribution of the alleles was consistent with previously reported literature; no evidence of association and marginal significance of linkage was found between the polymorphism and FIS or the degree of lateral curvature. CONCLUSIONS Despite the negative association reported here, further investigation of the gene and its potential association to FIS is required.
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Affiliation(s)
- Beth Marosy
- Johns Hopkins University, Baltimore, MD, USA.
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Wojciechowski R, Moy C, Ciner E, Ibay G, Reider L, Bailey-Wilson JE, Stambolian D. Genomewide scan in Ashkenazi Jewish families demonstrates evidence of linkage of ocular refraction to a QTL on chromosome 1p36. Hum Genet 2006; 119:389-99. [PMID: 16501916 PMCID: PMC3123998 DOI: 10.1007/s00439-006-0153-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Accepted: 01/29/2006] [Indexed: 11/24/2022]
Abstract
UNLABELLED The development of refractive error is mediated by both environmental and genetic factors. We performed regression-based quantitative trait locus (QTL) linkage analysis on Ashkenazi Jewish families to identify regions in the genome responsible for ocular refraction. We measured refractive error on individuals in 49 multi-generational American families of Ashkenazi Jewish descent. The average family size was 11.1 individuals and was composed of 2.7 generations. Recruitment criteria specified that each family contain at least two myopic members. The mean spherical equivalent refractive error in the sample was -3.46D (SD=3.29) and 87% of individuals were myopic. Microsatellite genotyping with 387 markers was performed on 411 individuals. We performed multipoint regression-based linkage analysis for ocular refraction and a log transformation of the trait using the statistical package Merlin-Regress. Empirical genomewide significance levels were estimated through gene-dropping simulations by generating random genotypes at each of the 387 markers in 200 replicates of our pedigrees. Maximum LOD scores of 9.5 for ocular refraction and 8.7 for log-transformed refraction (LTR) were observed at 49.1 cM on chromosome 1p36 between markers D1S552 and D1S1622. The empirical genomewide significance levels were P=0.065 for ocular refraction and P<0.005 for LTR, providing strong evidence for linkage of refraction to this locus. The inter-marker region containing the peak spans 11 Mb and contains approximately 189 genes. CONCLUSION We found genomewide significant evidence for linkage of refractive error to a novel QTL on chromosome 1p36 in an Ashkenazi Jewish population.
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Affiliation(s)
- Robert Wojciechowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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Suarez BK, Duan J, Sanders AR, Hinrichs AL, Jin CH, Hou C, Buccola NG, Hale N, Weilbaecher AN, Nertney DA, Olincy A, Green S, Schaffer AW, Smith CJ, Hannah DE, Rice JP, Cox NJ, Martinez M, Mowry BJ, Amin F, Silverman JM, Black DW, Byerley WF, Crowe RR, Freedman R, Cloninger CR, Levinson DF, Gejman PV. Genomewide linkage scan of 409 European-ancestry and African American families with schizophrenia: suggestive evidence of linkage at 8p23.3-p21.2 and 11p13.1-q14.1 in the combined sample. Am J Hum Genet 2006; 78:315-33. [PMID: 16400611 PMCID: PMC1380238 DOI: 10.1086/500272] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Accepted: 12/06/2005] [Indexed: 01/02/2023] Open
Abstract
We report the clinical characteristics of a schizophrenia sample of 409 pedigrees--263 of European ancestry (EA) and 146 of African American ancestry (AA)--together with the results of a genome scan (with a simple tandem repeat polymorphism interval of 9 cM) and follow-up fine mapping. A family was required to have a proband with schizophrenia (SZ) and one or more siblings of the proband with SZ or schizoaffective disorder. Linkage analyses included 403 independent full-sibling affected sibling pairs (ASPs) (279 EA and 124 AA) and 100 all-possible half-sibling ASPs (15 EA and 85 AA). Nonparametric multipoint linkage analysis of all families detected two regions with suggestive evidence of linkage at 8p23.3-q12 and 11p11.2-q22.3 (empirical Z likelihood-ratio score [Z(lr)] threshold >/=2.65) and, in exploratory analyses, two other regions at 4p16.1-p15.32 in AA families and at 5p14.3-q11.2 in EA families. The most significant linkage peak was in chromosome 8p; its signal was mainly driven by the EA families. Z(lr) scores >2.0 in 8p were observed from 30.7 cM to 61.7 cM (Center for Inherited Disease Research map locations). The maximum evidence in the full sample was a multipoint Z(lr) of 3.25 (equivalent Kong-Cox LOD of 2.30) near D8S1771 (at 52 cM); there appeared to be two peaks, both telomeric to neuregulin 1 (NRG1). There is a paracentric inversion common in EA individuals within this region, the effect of which on the linkage evidence remains unknown in this and in other previously analyzed samples. Fine mapping of 8p did not significantly alter the significance or length of the peak. We also performed fine mapping of 4p16.3-p15.2, 5p15.2-q13.3, 10p15.3-p14, 10q25.3-q26.3, and 11p13-q23.3. The highest increase in Z(lr) scores was observed for 5p14.1-q12.1, where the maximum Z(lr) increased from 2.77 initially to 3.80 after fine mapping in the EA families.
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Affiliation(s)
- Brian K. Suarez
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Jubao Duan
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Alan R. Sanders
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Anthony L. Hinrichs
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Carol H. Jin
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Cuiping Hou
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Nancy G. Buccola
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Nancy Hale
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Ann N. Weilbaecher
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Deborah A. Nertney
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Ann Olincy
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Susan Green
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Arthur W. Schaffer
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Christopher J. Smith
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Dominique E. Hannah
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - John P. Rice
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Nancy J. Cox
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Maria Martinez
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Bryan J. Mowry
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Farooq Amin
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Jeremy M. Silverman
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Donald W. Black
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - William F. Byerley
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Raymond R. Crowe
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Robert Freedman
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - C. Robert Cloninger
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Douglas F. Levinson
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
| | - Pablo V. Gejman
- Departments of Psychiatry and Genetics, Washington University, St. Louis; Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, Evanston Northwestern Healthcare and Feinberg School of Medicine, Northwestern University, Evanston, IL; School of Nursing, Louisiana State University Health Sciences Center, New Orleans; Mental Health Clinical Research Center and Department of Psychiatry, University of Iowa College of Medicine, Iowa City; Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, and Department of Medicine, University of Chicago, Chicago; Queensland Centre for Schizophrenia Mental Health Research, The Park, Centre for Mental Health, Wacol, Australia; Department of Psychiatry, University of Queensland, Brisbane; Department of Psychiatry and Colorado Psychiatric Health, University of Colorado School of Medicine, Denver; Atlanta VA Medical Center and Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta; Department of Psychiatry, Mount Sinai School of Medicine, New York; Méthodologie Statistique et Epidémiologie Génétique des Maladies Multifactorielles, Institut National de la Recherche et de la Santé Médicale, Evry, France; Baylor College of Medicine, Houston; Department of Psychiatry, University of California at Irvine, Irvine; Department of Psychiatry, University of California–San Francisco, San Francisco; and Department of Psychiatry, University of Pennsylvania, Philadelphia
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Zhang H, Stern H. Assessment of ancestry probabilities in the presence of genotyping errors. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:472-82. [PMID: 16307226 DOI: 10.1007/s00122-005-0148-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Accepted: 10/21/2005] [Indexed: 05/05/2023]
Abstract
This paper extends an approach for estimating the ancestry probability, the probability that an inbred line is an ancestor of a given hybrid, to account for genotyping errors. The effect of such errors on ancestry probability estimates is evaluated through simulation. The simulation study shows that if misclassification is ignored, then ancestry probabilities may be slightly overestimated. The sensitivity of ancestry probability calculations to the assumed genotyping error rate is also assessed.
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Affiliation(s)
- Hongmei Zhang
- Department of Mathematics and Statistics, The University of West Florida, Pensacola, FL 32514, USA.
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Faraone SV, Skol AD, Tsuang DW, Young KA, Haverstock SL, Prabhudesai S, Mena F, Menon AS, Leong L, Sautter F, Baldwin C, Bingham S, Weiss D, Collins J, Keith T, Vanden Eng JL, Boehnke M, Tsuang MT, Schellenberg GD. Genome scan of schizophrenia families in a large Veterans Affairs Cooperative Study sample: evidence for linkage to 18p11.32 and for racial heterogeneity on chromosomes 6 and 14. Am J Med Genet B Neuropsychiatr Genet 2005; 139B:91-100. [PMID: 16152571 DOI: 10.1002/ajmg.b.30213] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genome-wide linkage analyses of schizophrenia have identified several regions that may harbor schizophrenia susceptibility genes but, given the complex etiology of the disorder, it is unlikely that all susceptibility regions have been detected. We report results from a genome scan of 166 schizophrenia families collected through the Department of Veterans Affairs Cooperative Studies Program. Our definition of affection status included schizophrenia and schizoaffective disorder, depressed type and we defined families as European American (EA) and African American (AA) based on the probands' and parents' races based on data collected by interviewing the probands. We also assessed evidence for racial heterogeneity in the regions most suggestive of linkage. The maximum LOD score across the genome was 2.96 for chromosome 18, at 0.5 cM in the combined race sample. Both racial groups showed LOD scores greater than 1.0 for chromosome 18. The empirical P-value associated with that LOD score is 0.04 assuming a single genome scan for the combined sample with race narrowly defined, and 0.06 for the combined sample allowing for broad and narrow definitions of race. The empirical P-value of observing a LOD score as large as 2.96 in the combined sample, and of at least 1.0 in each racial group, allowing for narrow and broad racial definitions, is 0.04. Evidence for the second and third largest linkage signals come solely from the AA sample on chromosomes 6 (LOD = 2.11 at 33.2 cM) and 14 (LOD = 2.13 at 51.0). The linkage evidence differed between the AA and EA samples (chromosome 6 P-value = 0.007 and chromosome 14 P-value = 0.004).
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Affiliation(s)
- S V Faraone
- Genetics Research Program and Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
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Lambert D, Middle F, Hamshere ML, Segurado R, Raybould R, Corvin A, Green E, O'Mahony E, Nikolov I, Mulcahy T, Haque S, Bort S, Bennett P, Norton N, Owen MJ, Kirov G, Lendon C, Jones L, Jones I, Holmans P, Gill M, Craddock N. Stage 2 of the Wellcome Trust UK-Irish bipolar affective disorder sibling-pair genome screen: evidence for linkage on chromosomes 6q16-q21, 4q12-q21, 9p21, 10p14-p12 and 18q22. Mol Psychiatry 2005; 10:831-41. [PMID: 15940300 DOI: 10.1038/sj.mp.4001684] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Bipolar affective disorder (BPAD) is a common psychiatric disorder with complex genetic aetiology. We have undertaken a genome-wide scan in one of the largest samples of bipolar affected sibling pairs (ASPs) using a two-stage approach combining sample splitting and marker grid tightening. In this second stage analysis, we have examined 17 regions that achieved a nominally significant maximum likelihood LOD score (MLS) threshold of 0.74 (or 1.18 for the X-chromosome) in stage one. The second stage has added 135 ASP families to bring the total stage 2 sample to 395 ASPs. In total, 494 microsatellite markers have been used to screen the human genome at a density of 10 cM in the first stage sample (260 ASPs) and 5 cM in the second stage. Under the broad diagnostic model, two markers gave LOD scores exceeding 3 with two-point analysis: D4S392 (LOD=3.30) and D10S197 (LOD=3.18). Multipoint analysis demonstrated suggestive evidence of linkage between BPAD and chromosomal regions 6q16-q21 (MLS=2.61) and 4q12-q21 (MLS=2.38). 6q16-q21 is of particular interest because our data, together with those from two recent genome scans, make this the best supported linkage region in BPAD. Further, our data show evidence of a gender effect at this locus with increased sharing predominantly within the male-male pairs. Our scan also provides support for linkage (MLS> or =1.5) at several other regions that have been implicated in meta-analyses of bipolar disorder and/or schizophrenia including 9p21, 10p14-p12 and 18q22.
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MESH Headings
- Bipolar Disorder/genetics
- Chromosome Mapping
- Chromosomes, Human, Pair 10
- Chromosomes, Human, Pair 18
- Chromosomes, Human, Pair 4
- Chromosomes, Human, Pair 6
- Chromosomes, Human, Pair 9
- Female
- Genetic Markers
- Genetic Testing
- Genome, Human
- Humans
- Lod Score
- Male
- Parents
- Pedigree
- Siblings
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Affiliation(s)
- D Lambert
- Department of Genetics, Trinity College Dublin, Dublin, Republic of Ireland
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Stambolian D, Ciner EB, Reider LC, Moy C, Dana D, Owens R, Schlifka M, Holmes T, Ibay G, Bailey-Wilson JE. Genome-wide scan for myopia in the Old Order Amish. Am J Ophthalmol 2005; 140:469-76. [PMID: 16084785 DOI: 10.1016/j.ajo.2005.04.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Revised: 04/01/2005] [Accepted: 04/01/2005] [Indexed: 10/25/2022]
Abstract
PURPOSE To identify myopia susceptibility genes influencing common myopia in 34 Old Order Amish families, a genetically well-defined founder population. DESIGN A prospective study of families with myopia consisting of a minimum of two individuals affected with myopia. METHODS Extended families consisting of at least two siblings affected with myopia were ascertained. A genome-wide linkage scan using 387 markers was conducted by the Center for Inherited Disease Research (CIDR). Linkage analyses were conducted with parametric (autosomal dominant, fixed penetrance model) and nonparametric methods. Model-free linkage analysis was also performed maximizing over penetrance and over dominance (that is, fitting a wide range of both dominant and recessive models). RESULTS Under the fixed penetrance model, the maximum two-point heterogeneity LOD score (HLOD) was 1.59 at D20S451 and the maximum multipoint HLOD was 1.92 at D6S1021. The nonparametric maximum multipoint (NPL) at D3S2427 had a P-value of .0005. Under the model-free analysis, multipoint heterogeneity LOD scores of 2.03 were observed on both chromosomes 8 (under a recessive model between D8S1130 and D8S1106) and X (under a recessive model between DXS6800 and DXS6789). Reanalyses of chromosomes 3, 6, 8, 20, and X using the best penetrance models resulted in maximum multipoint HLODs of 1.84 at D3S3053; 1.84 at D3S2427; 2.04 at D8S1130; and 2.34 at DXS6800. CONCLUSIONS The locus on chromosome 8p23 independently confirms a report by Hammond and associates mapping a myopia quantitative trait loci (QTL) to this region.
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Affiliation(s)
- Dwight Stambolian
- Department of Ophthalmology, Stellar Chance Laboratories Rm. 313, University of Pennsylvania, 422 Curie Boulevard, Philadelphia, PA 19104, USA.
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Thomas SC. The estimation of genetic relationships using molecular markers and their efficiency in estimating heritability in natural populations. Philos Trans R Soc Lond B Biol Sci 2005; 360:1457-67. [PMID: 16048788 PMCID: PMC1569511 DOI: 10.1098/rstb.2005.1675] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Molecular marker data collected from natural populations allows information on genetic relationships to be established without referencing an exact pedigree. Numerous methods have been developed to exploit the marker data. These fall into two main categories: method of moment estimators and likelihood estimators. Method of moment estimators are essentially unbiased, but utilise weighting schemes that are only optimal if the analysed pair is unrelated. Thus, they differ in their efficiency at estimating parameters for different relationship categories. Likelihood estimators show smaller mean squared errors but are much more biased. Both types of estimator have been used in variance component analysis to estimate heritability. All marker-based heritability estimators require that adequate levels of the true relationship be present in the population of interest and that adequate amounts of informative marker data are available. I review the different approaches to relationship estimation, with particular attention to optimizing the use of this relationship information in subsequent variance component estimation.
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Cantor RM, Kono N, Duvall JA, Alvarez-Retuerto A, Stone JL, Alarcón M, Nelson SF, Geschwind DH. Replication of autism linkage: fine-mapping peak at 17q21. Am J Hum Genet 2005; 76:1050-6. [PMID: 15877280 PMCID: PMC1196442 DOI: 10.1086/430278] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Accepted: 03/16/2005] [Indexed: 02/01/2023] Open
Abstract
Autism is a heritable but genetically complex disorder characterized by deficits in language and in reciprocal social interactions, combined with repetitive and stereotypic behaviors. As with many genetically complex disorders, numerous genome scans reveal inconsistent results. A genome scan of 345 families from the Autism Genetic Resource Exchange (AGRE) (AGRE_1), gave the strongest evidence of linkage at 17q11-17q21 in families with no affected females. Here, we report a full-genome scan of an independent sample of 91 AGRE families with 109 affected sibling pairs (AGRE_2) that also shows the strongest evidence of linkage to 17q11-17q21 in families with no affected females. Taken together, these samples provide a replication of linkage to this chromosome region that is, to our knowledge, the first such replication in autism. Fine mapping at 2-centimorgan (cM) intervals in the combined sample of families with no affected females reveals a linkage peak at 66.85 cM, which places this locus at 17q21.
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Affiliation(s)
- Rita M Cantor
- Department of Human Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-7088, USA.
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Miller NH, Justice CM, Marosy B, Doheny KF, Pugh E, Zhang J, Dietz HC, Wilson AF. Identification of candidate regions for familial idiopathic scoliosis. Spine (Phila Pa 1976) 2005; 30:1181-7. [PMID: 15897833 DOI: 10.1097/01.brs.0000162282.46160.0a] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
STUDY DESIGN A genomic screen and statistical linkage analysis of 202 families with at least two individuals with idiopathic scoliosis was performed. OBJECTIVES To identify candidate regions or the autosomal loci that may be involved in the expression of familial idiopathic scoliosis. SUMMARY OF BACKGROUND DATA A large sample of families with individuals having idiopathic scoliosis (202 families; 1,198 individuals) was ascertained; diagnoses were based on physical examination and radiographic criteria. METHODS Model-independent linkage analysis of qualitative and quantitative traits (degree of lateral curvature) related to scoliosis was used to screen genotyping data from 391 markers in the 202 families. Subsets of families were determined before genotyping based on the most likely mode of inheritance for each family (autosomal dominant vs. X-linked dominant). Fine mapping results corroborated linkage in the primary candidate regions. RESULTS Candidate regions on chromosomes 6, 9, 16, and 17 were considered to have the strongest evidence for linkage across all subsets considered. CONCLUSION Linkage analyses have identified several candidate regions, a significant step in defining the genetic etiology of this disorder.
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Wang D, Yang H, Quiñones MJ, Bulnes-Enriquez I, Jimenez X, De La Rosa R, Modilevsky T, Yu K, Li Y, Taylor KD, Hsueh WA, Hodis HN, Rotter JI. A Genome-Wide Scan for Carotid Artery Intima-Media Thickness. Stroke 2005; 36:540-5. [PMID: 15692111 DOI: 10.1161/01.str.0000155746.65185.4e] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND AND PURPOSE Carotid artery intima-media thickness (CIMT), a subclinical measure of atherosclerosis, is associated with coronary artery disease (CAD), and stroke. CIMT is also an important predictor of clinical cardiovascular events. To systematically identify the genetic determinants of CIMT, we performed a genome-wide scan using data from 91 2-generation Mexican American families ascertained via a parent with CAD diagnosed. METHODS CIMT was measured in 274 adult offspring (mean age, 34.6 years) using high-resolution B-mode ultrasound; 413 subjects, including adult offspring and their parents, were genotyped using Marshfield screen set 12 (380 microsatellite markers at approximately 10-cM interval). Heritability was estimated using the variance component approach implemented in SOLAR. Linkage analyses were performed using both the sib-pair regression approach and the variance component approach. RESULTS The estimated heritability was 0.68, 0.45, and 0.40 for unadjusted, gender- and age-adjusted, and multivariate-adjusted CIMT, respectively. The strongest evidence of linkage was found on chromosome 2 at D2S2944 (logarithm of the odds [LOD]=3.08). Other suggestive linkages were also found on chromosome 6 at D6S1022 to D6S2410 (LOD=2.21) and chromosome 13 at D13S796 to D13S895 (LOD=1.34). CONCLUSIONS These results show that there is a strong genetic effect on CIMT in these Mexican American CAD families. The linkage peak on chromosome 2 suggests that there is a gene (or genes) at this chromosome location influencing CIMT.
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Affiliation(s)
- Dai Wang
- Medical Genetics Institute, Steven Spielberg Pediatric Research Center, Cedars-Sinai Medical Center, 8700 Beverly Blvd, SSB 378, Los Angeles, Calif 90048, USA.
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