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Yuan X, Xu J, Fang W, Zhao Z, Wang F, Tong Z. The Association Between MGMT Promoter Methylation and Patients with Gastric Cancer: A Meta-Analysis. Genet Test Mol Biomarkers 2017; 21:213-221. [PMID: 28384044 DOI: 10.1089/gtmb.2016.0284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Xiaolong Yuan
- Department of Radiotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Jifei Xu
- Department of Radiotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Weiyang Fang
- Department of Radiotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Zhenfeng Zhao
- Department of Radiotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Fan Wang
- Department of Radiotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Zhuting Tong
- Department of Radiotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
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Abstract
Cardiovascular disease, metabolic syndrome, schizophrenia, diabetes, bipolar disorder, and autism are a few of the numerous complex diseases for which researchers are trying to decipher the genetic composition. One interest of geneticists is to determine the quantitative trait loci (QTLs) that underlie the genetic portion of these diseases and their risk factors. The difficulty for researchers is that the QTLs underlying these diseases are likely to have small to medium effects which will necessitate having large studies in order to have adequate power. Combining information across multiple studies provides a way for researchers to potentially increase power while making the most of existing studies.Here, we will explore some of the methods that are currently being used by geneticists to combine information across multiple genome-wide linkage studies. There are two main types of meta-analyses: (1) those that yield a measure of significance, such as Fisher's p-value method along with its extensions/modifications and the genome search meta-analysis (GSMA) method, and (2) those that yield a measure of a common effect size and the corresponding standard error, such as model-based methods and Bayesian methods. Some of these methods allow for the assessment of heterogeneity. This chapter will conclude with a recommendation for usage.
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Affiliation(s)
- Trecia A Kippola
- Department of Statistics, Oklahoma State University, OK, Stillwater, USA
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3
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Ng MYM, Levinson DF, Faraone SV, Suarez BK, DeLisi LE, Arinami T, Riley B, Paunio T, Pulver AE, Irmansyah, Holmans PA, Escamilla M, Wildenauer DB, Williams NM, Laurent C, Mowry BJ, Brzustowicz LM, Maziade M, Sklar P, Garver DL, Abecasis GR, Lerer B, Fallin MD, Gurling HMD, Gejman PV, Lindholm E, Moises HW, Byerley W, Wijsman EM, Forabosco P, Tsuang MT, Hwu HG, Okazaki Y, Kendler KS, Wormley B, Fanous A, Walsh D, O’Neill FA, Peltonen L, Nestadt G, Lasseter VK, Liang KY, Papadimitriou GM, Dikeos DG, Schwab SG, Owen MJ, O’Donovan MC, Norton N, Hare E, Raventos H, Nicolini H, Albus M, Maier W, Nimgaonkar VL, Terenius L, Mallet J, Jay M, Godard S, Nertney D, Alexander M, Crowe RR, Silverman JM, Bassett AS, Roy MA, Mérette C, Pato CN, Pato MT, Roos JL, Kohn Y, Amann-Zalcenstein D, Kalsi G, McQuillin A, Curtis D, Brynjolfson J, Sigmundsson T, Petursson H, Sanders AR, Duan J, Jazin E, Myles-Worsley M, Karayiorgou M, Lewis CM. Meta-analysis of 32 genome-wide linkage studies of schizophrenia. Mol Psychiatry 2009; 14:774-85. [PMID: 19349958 PMCID: PMC2715392 DOI: 10.1038/mp.2008.135] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Accepted: 11/11/2008] [Indexed: 02/07/2023]
Abstract
A genome scan meta-analysis (GSMA) was carried out on 32 independent genome-wide linkage scan analyses that included 3255 pedigrees with 7413 genotyped cases affected with schizophrenia (SCZ) or related disorders. The primary GSMA divided the autosomes into 120 bins, rank-ordered the bins within each study according to the most positive linkage result in each bin, summed these ranks (weighted for study size) for each bin across studies and determined the empirical probability of a given summed rank (P(SR)) by simulation. Suggestive evidence for linkage was observed in two single bins, on chromosomes 5q (142-168 Mb) and 2q (103-134 Mb). Genome-wide evidence for linkage was detected on chromosome 2q (119-152 Mb) when bin boundaries were shifted to the middle of the previous bins. The primary analysis met empirical criteria for 'aggregate' genome-wide significance, indicating that some or all of 10 bins are likely to contain loci linked to SCZ, including regions of chromosomes 1, 2q, 3q, 4q, 5q, 8p and 10q. In a secondary analysis of 22 studies of European-ancestry samples, suggestive evidence for linkage was observed on chromosome 8p (16-33 Mb). Although the newer genome-wide association methodology has greater power to detect weak associations to single common DNA sequence variants, linkage analysis can detect diverse genetic effects that segregate in families, including multiple rare variants within one locus or several weakly associated loci in the same region. Therefore, the regions supported by this meta-analysis deserve close attention in future studies.
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Affiliation(s)
- MYM Ng
- King’s College London, Department of Medical and Molecular Genetics, London, UK
| | - DF Levinson
- Department of Psychiatry, Stanford University, Stanford, CA, USA
| | - SV Faraone
- Departments of Psychiatry and of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - BK Suarez
- Washington University in St Louis, St Louis, MO, USA
| | - LE DeLisi
- Department of Psychiatry, The New York University Langone Medical Center, New York, NY, USA
- Nathan S Kline Institute for Psychiatric Research, Orangeburg, NY, USA
| | - T Arinami
- Department of Medical Genetics, University of Tsukuba, Tsukuba, Japan
| | - B Riley
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - T Paunio
- National Public Health Institute, Helsinki, Finland
- Department of Psychiatry, Helsinki University Central Hospital, Helsinki, Finland
| | - AE Pulver
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Irmansyah
- Department of Psychiatry, University of Indonesia, Jakarta, Indonesia
| | - PA Holmans
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - M Escamilla
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - DB Wildenauer
- Center for Clinical Research in Neuropsychiatry, School of Psychiatry and Clinical Neurosciences, University of Western Australia, Perth, WA, Australia
| | - NM Williams
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - C Laurent
- Department of Child Psychiatry, Université Pierre et Marie Curie and Hôpital de la Pitiè-Salpêtrière, Paris, France
| | - BJ Mowry
- Queensland Centre for Mental Health Research and University of Queensland, Brisbane, QLD, Australia
| | - LM Brzustowicz
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - M Maziade
- Department of Psychiatry, Laval University & Centre de recherche Université Laval Robert-Giffard, Québec, QC, Canada
| | - P Sklar
- Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - DL Garver
- VA Medical Center, Asheville, NC, USA
| | - GR Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - B Lerer
- Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - MD Fallin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - HMD Gurling
- Department of Mental Health Sciences, University College London, London, UK
| | - PV Gejman
- Center for Psychiatric Genetics, NorthShore University HealthSystem Research Institute and Northwestern University, Evanston, IL, USA
| | - E Lindholm
- Department of Development & Genetics, Uppsala University, Uppsala, Sweden
| | | | - W Byerley
- University of California, San Francisco, CA, USA
| | - EM Wijsman
- Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, USA
| | - P Forabosco
- King’s College London, Department of Medical and Molecular Genetics, London, UK
| | - MT Tsuang
- Center for Behavioral Genomics and Department of Psychiatry, University of California, San Diego, CA, USA
- Harvard Institute of Psychiatric Epidemiology & Genetics, Boston, MA, USA
| | - H-G Hwu
- National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Y Okazaki
- Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan
| | - KS Kendler
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - B Wormley
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - A Fanous
- Washington VA Medical Center, Washington, DC, USA
- Department of Psychiatry, Georgetown University Medical Center, Virginia Commonwealth University, Richmond, VA, USA
| | - D Walsh
- The Health Research Board, Dublin, Ireland
| | - FA O’Neill
- Department of Psychiatry, Queens University, Belfast, Northern Ireland
| | - L Peltonen
- Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
- The Broad Institute, MIT, Boston, MA, USA
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - G Nestadt
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - VK Lasseter
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - KY Liang
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - GM Papadimitriou
- 1st Department of Psychiatry, University of Athens Medical School, and University Mental Health Research Institute, Athens, Greece
| | - DG Dikeos
- 1st Department of Psychiatry, University of Athens Medical School, and University Mental Health Research Institute, Athens, Greece
| | - SG Schwab
- Western Australian Institute for Medical Research, University of Western Australia, Perth, WA, Australia
- School of Psychiatry and Clinical Neurosciences, University of Western Australia, Perth, WA, Australia
- School of Medicine and Pharmacology, University of Western Australia, Perth, WA, Australia
| | - MJ Owen
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - MC O’Donovan
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - N Norton
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - E Hare
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - H Raventos
- School of Biology and CIBCM, University of Costa Rica, San Jose, Costa Rica
| | - H Nicolini
- Carracci Medical Group and Universidad Autonoma de la Ciudad de Mexico, Mexico City, Mexico
| | - M Albus
- State Mental Hospital, Haar, Germany
| | - W Maier
- Department of Psychiatry, University of Bonn, Bonn, Germany
| | - VL Nimgaonkar
- Departments of Psychiatry and Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - L Terenius
- Department of Clinical Neuroscience, Karolinska Hospital, Stockholm, Sweden
| | - J Mallet
- Laboratoire de Génétique Moléculaire de la Neurotransmission et des Processus Neurodégénératifs, Centre National de la Recherche Scientifique, Hôpital de la Pitié Salpêtrière, Paris, France
| | - M Jay
- Department of Child Psychiatry, Université Pierre et Marie Curie and Hôpital de la Pitiè-Salpêtrière, Paris, France
| | - S Godard
- INSERM, Institut de Myologie, Hôpital de la Pitiè-Salpêtrière, Paris, France
| | - D Nertney
- Queensland Centre for Mental Health Research and University of Queensland, Brisbane, QLD, Australia
| | - M Alexander
- Department of Psychiatry, Stanford University, Stanford, CA, USA
| | - RR Crowe
- Department of Psychiatry, The University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - JM Silverman
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
| | - AS Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health and Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - M-A Roy
- Department of Psychiatry, Laval University & Centre de recherche Université Laval Robert-Giffard, Québec, QC, Canada
| | - C Mérette
- Department of Psychiatry, Laval University & Centre de recherche Université Laval Robert-Giffard, Québec, QC, Canada
| | - CN Pato
- Center for Genomic Psychiatry, University of Southern California, Los Angeles, CA, USA
| | - MT Pato
- Center for Genomic Psychiatry, University of Southern California, Los Angeles, CA, USA
| | - J Louw Roos
- Department of Psychiatry, University of Pretoria, Weskoppies Hospital, Pretoria, Republic of South Africa
| | - Y Kohn
- Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - D Amann-Zalcenstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - G Kalsi
- Department of Mental Health Sciences, University College London, London, UK
| | - A McQuillin
- Department of Mental Health Sciences, University College London, London, UK
| | - D Curtis
- Department of Psychological Medicine, St Bartholomew’s and Royal London School of Medicine and Dentistry, London, UK
| | - J Brynjolfson
- Department of Psychiatry, General Hospital, Reykjavik, Iceland
| | - T Sigmundsson
- Department of Psychiatry, General Hospital, Reykjavik, Iceland
| | - H Petursson
- Department of Psychiatry, General Hospital, Reykjavik, Iceland
| | - AR Sanders
- Center for Psychiatric Genetics, NorthShore University HealthSystem Research Institute and Northwestern University, Evanston, IL, USA
| | - J Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem Research Institute and Northwestern University, Evanston, IL, USA
| | - E Jazin
- Department of Development & Genetics, Uppsala University, Uppsala, Sweden
| | - M Myles-Worsley
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - M Karayiorgou
- Departments of Psychiatry and Genetics & Development, Columbia University Medical Center, New York, NY, USA
| | - CM Lewis
- King’s College London, Department of Medical and Molecular Genetics, London, UK
- King’s College London, MRC SGDP Centre, Institute of Psychiatry, London, UK
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4
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Zhou K, Dempfle A, Arcos-Burgos M, Bakker SC, Banaschewski T, Biederman J, Buitelaar J, Castellanos F, Doyle A, Ebstein RP, Ekholm J, Forabosco P, Franke B, Freitag C, Friedel S, Gill M, Hebebrand J, Hinney A, Jacob C, Lesch KP, Loo SK, Lopera F, McCracken JT, McGough JJ, Meyer J, Mick E, Miranda A, Muenke M, Mulas F, Nelson SF, Nguyen T, Oades RD, Ogdie MN, Palacio JD, Pineda D, Reif A, Renner TJ, Roeyers H, Romanos M, Rothenberger A, Schäfer H, Sergeant J, Sinke RJ, Smalley SL, Sonuga-Barke E, Steinhausen HC, van der Meulen E, Walitza S, Warnke A, Lewis CM, Faraone SV, Asherson P. Meta-analysis of genome-wide linkage scans of attention deficit hyperactivity disorder. Am J Med Genet B Neuropsychiatr Genet 2008; 147B:1392-8. [PMID: 18988193 PMCID: PMC2890047 DOI: 10.1002/ajmg.b.30878] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Genetic contribution to the development of attention deficit hyperactivity disorder (ADHD) is well established. Seven independent genome-wide linkage scans have been performed to map loci that increase the risk for ADHD. Although significant linkage signals were identified in some of the studies, there has been limited replications between the various independent datasets. The current study gathered the results from all seven of the ADHD linkage scans and performed a Genome Scan Meta Analysis (GSMA) to identify the genomic region with most consistent linkage evidence across the studies. Genome-wide significant linkage (P(SR) = 0.00034, P(OR) = 0.04) was identified on chromosome 16 between 64 and 83 Mb. In addition there are nine other genomic regions from the GSMA showing nominal or suggestive evidence of linkage. All these linkage results may be informative and focus the search for novel ADHD susceptibility genes.
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Affiliation(s)
- Kaixin Zhou
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - Astrid Dempfle
- Institute of Medical Biometry and Epidemiology, Philipps-University Marburg, Marburg, Germany
| | - Mauricio Arcos-Burgos
- Department of Psychiatry and Behavioral Sciences, Leonard M. Miller School of Medicine, University of Miami, Miami, Florida
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Steven C. Bakker
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tobias Banaschewski
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, University of Heidelberg, Mannheim, Germany
| | - Joseph Biederman
- Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - Jan Buitelaar
- Department of Psychiatry, Radboud University Nijmegen, Donders Centre for Neuroscience, Medical Centre, Nijmegen, The Netherlands
| | | | - Alysa Doyle
- Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Jenny Ekholm
- Department of Human Genetics, UCLA, Los Angeles, California
| | - Paola Forabosco
- Department of Medical and Molecular Genetics, King's College London, London, UK
- Istituto di Genetica delle Popolazioni—CNR, Alghero, Italy
| | - Barbara Franke
- Department of Psychiatry, Radboud University Nijmegen, Donders Centre for Neuroscience, Medical Centre, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Christine Freitag
- Department of Child and Adolescent Psychiatry, Saarland University Hospital, Homburg, Germany
| | - Susann Friedel
- Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - Michael Gill
- Department of Psychiatry, Trinity Centre for Health Sciences, St. James's Hospital, Dublin, Ireland
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - Christian Jacob
- ADHD Clinical Research Program, Department of Psychiatry and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | - Klaus Peter Lesch
- ADHD Clinical Research Program, Department of Psychiatry and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | - Sandra K. Loo
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience & Human Behavior, UCLA, Los Angeles, California
| | - Francisco Lopera
- Neurosciences Group, University of Antioquia, Medellín, Colombia
| | - James T. McCracken
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience & Human Behavior, UCLA, Los Angeles, California
| | - James J. McGough
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience & Human Behavior, UCLA, Los Angeles, California
| | - Jobst Meyer
- Department of Neurobehavioral Genetics, University of Trier, Trier, Germany
| | - Eric Mick
- Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - Ana Miranda
- Department of Developmental and Educational Psychology, University of Valencia, Valencia, Spain
| | - Maximilian Muenke
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Fernando Mulas
- Department of Neuropaediatric, La Fe University Hospital, Faculty of Medicine, Valencia, Spain
| | | | - T.Trang Nguyen
- Institute of Medical Biometry and Epidemiology, Philipps-University Marburg, Marburg, Germany
| | - Robert D. Oades
- University Clinic for Child and Adolescent Psychiatry, Essen, Germany
| | | | | | - David Pineda
- Neurosciences Group, University of Antioquia, Medellín, Colombia
| | - Andreas Reif
- ADHD Clinical Research Program, Department of Psychiatry and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | - Tobias J. Renner
- ADHD Clinical Research Program, Department of Child and Adolescent Psychiatry and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | | | - Marcel Romanos
- ADHD Clinical Research Program, Department of Child and Adolescent Psychiatry and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | | | - Helmut Schäfer
- Institute of Medical Biometry and Epidemiology, Philipps-University Marburg, Marburg, Germany
| | - Joseph Sergeant
- Vrije Universiteit, De Boelelaan, Amsterdam, The Netherlands
| | - Richard J. Sinke
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Susan L. Smalley
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience & Human Behavior, UCLA, Los Angeles, California
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, UCLA, Los Angeles, California
| | - Edmund Sonuga-Barke
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
- Child Study Center, New York University, New York, New York
- School of Psychology, Institute for Disorder on Impulse and Attention, University of Southampton, Highfield, Southampton, UK
| | | | - Emma van der Meulen
- Department of Child and Adolescent Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Susanne Walitza
- ADHD Clinical Research Program, Department of Child and Adolescent Psychiatry and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | - Andreas Warnke
- ADHD Clinical Research Program, Department of Child and Adolescent Psychiatry and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | - Cathryn M Lewis
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Stephen V. Faraone
- Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, New York
| | - Philip Asherson
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
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Trikalinos TA, Salanti G, Zintzaras E, Ioannidis JP. Meta‐Analysis Methods. GENETIC DISSECTION OF COMPLEX TRAITS 2008; 60:311-34. [DOI: 10.1016/s0065-2660(07)00413-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Abstract
Although single chi-square analysis of the North American Rheumatoid Arthritis Consortium (NARAC) data identifies many single-nucleotide polymorphisms (SNPs) with p-values less than 0.05, none remain significant after Bonferroni correction. In contrast, CHROMSCAN evades heavy Bonferroni correction and auto-correlation between SNPs by using composite likelihood to model association across all markers in a region and permutation to assess significance. Analysis by CHROMSCAN identifies a 36-kb interval that includes the most significant SNP (msSNP) observed in a 10-Mb target suggested by linkage. Unexpectedly, stratification by gender and age of onset shows that association evidence comes almost entirely from females with age of onset less than 40. Combining evidence from a meta-analysis of linkage studies and three subsets of the NARAC data provides significant evidence for a determinant of rheumatoid arthritis in a 36-kb interval and illustrates the principle that estimates of location and its information are more powerful than estimates of p-values alone.
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Affiliation(s)
- William Tapper
- Human Genetics Division, University of Southampton, Southampton General Hospital, Tremona Road, Southampton, Hampshire SO16 6YD, UK.
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7
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Saunders CL, Chiodini BD, Sham P, Lewis CM, Abkevich V, Adeyemo AA, de Andrade M, Arya R, Berenson GS, Blangero J, Boehnke M, Borecki IB, Chagnon YC, Chen W, Comuzzie AG, Deng HW, Duggirala R, Feitosa MF, Froguel P, Hanson RL, Hebebrand J, Huezo-Dias P, Kissebah AH, Li W, Luke A, Martin LJ, Nash M, Ohman M, Palmer LJ, Peltonen L, Perola M, Price RA, Redline S, Srinivasan SR, Stern MP, Stone S, Stringham H, Turner S, Wijmenga C, Collier DA. Meta-analysis of genome-wide linkage studies in BMI and obesity. Obesity (Silver Spring) 2007; 15:2263-75. [PMID: 17890495 DOI: 10.1038/oby.2007.269] [Citation(s) in RCA: 116] [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: 01/31/2023]
Abstract
OBJECTIVE The objective was to provide an overall assessment of genetic linkage data of BMI and BMI-defined obesity using a nonparametric genome scan meta-analysis. RESEARCH METHODS AND PROCEDURES We identified 37 published studies containing data on over 31,000 individuals from more than >10,000 families and obtained genome-wide logarithm of the odds (LOD) scores, non-parametric linkage (NPL) scores, or maximum likelihood scores (MLS). BMI was analyzed in a pooled set of all studies, as a subgroup of 10 studies that used BMI-defined obesity, and for subgroups ascertained through type 2 diabetes, hypertension, or subjects of European ancestry. RESULTS Bins at chromosome 13q13.2- q33.1, 12q23-q24.3 achieved suggestive evidence of linkage to BMI in the pooled analysis and samples ascertained for hypertension. Nominal evidence of linkage to these regions and suggestive evidence for 11q13.3-22.3 were also observed for BMI-defined obesity. The FTO obesity gene locus at 16q12.2 also showed nominal evidence for linkage. However, overall distribution of summed rank p values <0.05 is not different from that expected by chance. The strongest evidence was obtained in the families ascertained for hypertension at 9q31.1-qter and 12p11.21-q23 (p < 0.01). CONCLUSION Despite having substantial statistical power, we did not unequivocally implicate specific loci for BMI or obesity. This may be because genes influencing adiposity are of very small effect, with substantial genetic heterogeneity and variable dependence on environmental factors. However, the observation that the FTO gene maps to one of the highest ranking bins for obesity is interesting and, while not a validation of this approach, indicates that other potential loci identified in this study should be investigated further.
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Affiliation(s)
- Catherine L Saunders
- King's College London, Guy's, King's & St. Thomas' School of Medicine, London, United Kingdom
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8
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Forabosco P, Ng MYM, Bouzigon E, Fisher SA, Levinson DF, Lewis CM. Data acquisition for meta-analysis of genome-wide linkage studies using the genome search meta-analysis method. Hum Hered 2007; 64:74-81. [PMID: 17483599 DOI: 10.1159/000101425] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The Genome Search Meta-Analysis (GSMA) method enables researchers to pool results across genome-wide linkage studies, to increase the power to detect linkage. RESULTS from individual studies must be extracted, with the maximum evidence for linkage placed into bins, usually of 30 cM width, and ranked within the study. Ranks are then summed across studies, with high summed ranks potentially showing evidence for linkage in the meta-analysis. OBJECTIVES In this paper we study the properties of the GSMA method considering two different issues: (1) data binning from genome-wide results when indexed markers or graphs are available, based on either predefined boundary markers, or equal-length bins; (2) the use of selected instead of genome-wide results, using simulation to estimate power and type I error rates of GSMA. This is relevant when published papers show only summary results (e.g. with NPL score >1). RESULTS Using digitizing software to extract linkage statistics from graphs and assigning equal bin length is accurate, with the resulting ranking of bins similar to those defined through boundary markers. Simulation results show that power can fall substantially when genome-wide results are not available, particularly when only results from a single marker are available in a linked region. However there is no increase in false positive findings. CONCLUSIONS The GSMA method is robust across different bin definitions and methods of data presentation and extraction. Using studies based on only the top ranked bins does not produce false positive results, but lacks power to detect genes conferring a modest increase in risk. Therefore, we advise that effort should be made to obtain genome-wide results from investigators or from published papers to avoid limiting the utility of the GSMA.
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Affiliation(s)
- Paola Forabosco
- Department of Medical and Molecular Genetics, King's College London School of Medicine at Guy's, King's College and St. Thomas' Hospitals, London, UK
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Hermanowski J, Bouzigon E, Forabosco P, Ng MY, Fisher SA, Lewis CM. Meta-analysis of genome-wide linkage studies for multiple sclerosis, using an extended GSMA method. Eur J Hum Genet 2007; 15:703-10. [PMID: 17377519 DOI: 10.1038/sj.ejhg.5201818] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Many genome-wide linkage studies in multiple sclerosis (MS) have been performed, but results are disappointing, with linkage confirmed only in the HLA region. We combined results from all available, non-overlapping genome-wide linkage studies in MS using the Genome Search Meta-Analysis method (GSMA). The GSMA is a rank-based analysis, which assesses the strongest evidence for linkage within bins of traditionally 30 cM width on the autosomes and X chromosome. Genome-wide evidence for linkage was confirmed on chromosome 6p (HLA region; P=0.00004). Suggestive evidence for linkage was found on chromosomes 10q (P=0.0077), 18p (P=0.0054) and 20p (P=0.0079). To explore how these results could be affected by bin definition, we analysed the data using different bin widths (20 and 40 cM) and using a shifted 30 cM bin by moving bin boundaries by 15 cM. Consistently significant results were obtained for the 6p region. The regions on 10q and 18p provided suggestive evidence for linkage in some analyses, and, interestingly, a region on 6q, that showed only nominal significance in the original analysis, yielded increased, suggestive significance in two of the additional analyses. These regions may provide targets to focus candidate gene studies or to prioritise results from genome-wide association studies.
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Affiliation(s)
- Jane Hermanowski
- Department of Medical and Molecular Genetics, King's College London School of Medicine at Guy's, King's College and St Thomas' Hospitals, London, UK
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Zintzaras E, Kitsios G. Identification of chromosomal regions linked to premature myocardial infarction: a meta-analysis of whole-genome searches. J Hum Genet 2006; 51:1015-1021. [PMID: 17024316 DOI: 10.1007/s10038-006-0053-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2006] [Accepted: 08/13/2006] [Indexed: 10/24/2022]
Abstract
Myocardial infarction (MI) is a complication of coronary artery disease and the leading cause of death in the Western world. MI is considered a distinct phenotype with an increased genetic component for its premature type. MI's exact inheritance pattern is still unknown. Genome searches for identifying susceptibility loci for premature MI produced inconclusive or inconsistent results. Thus, a genome search meta-analysis (GSMA) was applied to available genome search data on premature MI. GSMA is a non-parametric method to identify genetic regions that rank high, on average in terms of linkage statistics across genome searches unweighted or weighted by study size. The significance of each region's average and heterogeneity, unadjusted or adjusted by neighbouring average simulated ranks, was calculated using a Monte Carlo test. The meta-analysis involved five genome searches in Caucasians. Eight regions (6p22.3-6p21.1, 14p13-14q13.1, 13q33.1-13q34, 5p15.33-5p15.1, 8q13.2-8q22.2, 1p36.21-1p35.2, 12q24.31-12q24.33, 8q24.21-8q24.3) were found to have significant average rank by either unweighted or weighted analyses. In addition, region 8q24.21-8q24.3 produced significant low heterogeneity (P (unadjusted)=0.03 and P (adjusted)=0.05). Four regions (6p22.3-6p21.1, 14p13-14q13.1, 8q13.2-8q22.2, 8q24.21-8q24.3) were not identified by the individual studies. The meta-analysis suggests that these four regions should be further investigated for genes that confer susceptibility to MI.
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Affiliation(s)
- Elias Zintzaras
- Department of Biomathematics, University of Thessaly School of Medicine, Papakyriazi 22, 41222, Larissa, Greece.
| | - Georgios Kitsios
- Department of Biomathematics, University of Thessaly School of Medicine, Papakyriazi 22, 41222, Larissa, Greece
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Zintzaras E, Kitsios G, Harrison GA, Laivuori H, Kivinen K, Kere J, Messinis I, Stefanidis I, Ioannidis JPA. Heterogeneity-based genome search meta-analysis for preeclampsia. Hum Genet 2006; 120:360-70. [PMID: 16868762 DOI: 10.1007/s00439-006-0214-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Accepted: 05/18/2006] [Indexed: 02/04/2023]
Abstract
Preeclampsia is a pregnancy-related disorder that causes maternal and fetal morbidity and mortality. Its exact inheritance pattern is still unknown, and genome searches for identifying susceptibility loci for preeclampsia have thus far produced inconclusive or inconsistent results. We performed a heterogeneity-based genome search meta-analysis (HEGESMA) that synthesized the available genome scan data on preeclampsia. HEGESMA identifies genetic regions (bins) that rank highly on average in terms of linkage statistics across genome scans (searches). The significance of each bin's average rank and heterogeneity across scans was calculated using Monte Carlo tests. The meta-analysis involved four genome-scans on general preeclampsia and five scans on severe preeclampsia. In general preeclampsia, 13 bins had significantly high average rank (Prank< 0.05) by either unweighted or weighted analyses, while four of them (2p11.2-2q21.1, 9q21.32-9q31.2, 2p15-2p11.2, 2q32.1-2q35) were formally significant by both analyses. Heterogeneity of bin 2.8 (2q32.1-2q35) was significantly low in both unweighted and weighted analysis (PQ< 0.01). In severe preeclampsia, 10 bins had significantly high average rank by either unweighted or weighted analyses and five of them (3q11.1-3q21.2, 2q37.1-2q37.3, 18p11.32-18p11.22, 2p15-2p11.2, 7q34-7q36.3) were significant by both analyses. Bin 2q37.1-2q37.3 showed marginal low heterogeneity in unweighted and weighted analysis (PQ= 0.06). Results should be interpreted with caution as the p values were modest. Further investigation of these regions by genotyping with additional markers and families may help to direct the identification of candidate genes for preeclampsia.
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Affiliation(s)
- Elias Zintzaras
- Department of Biomathematics, University of Thessaly School of Medicine, Papakyriazi 22, Larissa, 41222, Greece.
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