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Ferar K, Hall TO, Crawford DC, Rowley R, Satterfield BA, Li R, Gragert L, Karlson EW, de Andrade M, Kullo IJ, McCarty CA, Kho A, Hayes MG, Ritchie MD, Crane PK, Mirel DB, Carlson C, Connolly JJ, Hakonarson H, Crenshaw AT, Carrell D, Luo Y, Dikilitas O, Denny JC, Jarvik GP, Crosslin DR. Author Correction: Genetic variation in the human leukocyte antigen region confers susceptibility to Clostridioides difficile infection. Sci Rep 2023; 13:19972. [PMID: 37968452 PMCID: PMC10652012 DOI: 10.1038/s41598-023-47359-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023] Open
Affiliation(s)
- Kathleen Ferar
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA.
| | - Taryn O Hall
- Optum Genomics, UnitedHealth Group, Minnetonka, MN, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Rongling Li
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Loren Gragert
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | | | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Catherine A McCarty
- University of Minnesota Medical School, Duluth, MN, USA
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | - Abel Kho
- Divisions of General Internal Medicine and Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marylyn D Ritchie
- Department of Biochemistry and Molecular Biology, Center for Systems Genomics, Pennsylvania State University, University Park, PA, USA
| | - Paul K Crane
- Division of General Internal Medicine, University of Washington, Seattle, WA, USA
| | | | - Christopher Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John J Connolly
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - David Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Yuan Luo
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ozan Dikilitas
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA.
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Ferar K, Hall TO, Crawford DC, Rowley R, Satterfield BA, Li R, Gragert L, Karlson EW, de Andrade M, Kullo IJ, McCarty CA, Kho A, Hayes MG, Ritchie MD, Crane PK, Mirel DB, Carlson C, Connolly JJ, Hakonarson H, Crenshaw AT, Carrell D, Luo Y, Dikilitas O, Denny JC, Jarvik GP, Crosslin DR. Genetic variation in the human leukocyte antigen region confers susceptibility to Clostridioides difficile infection. Sci Rep 2023; 13:18532. [PMID: 37898691 PMCID: PMC10613277 DOI: 10.1038/s41598-023-45649-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 10/22/2023] [Indexed: 10/30/2023] Open
Abstract
Clostridioides difficile (C. diff.) infection (CDI) is a leading cause of hospital acquired diarrhea in North America and Europe and a major cause of morbidity and mortality. Known risk factors do not fully explain CDI susceptibility, and genetic susceptibility is suggested by the fact that some patients with colons that are colonized with C. diff. do not develop any infection while others develop severe or recurrent infections. To identify common genetic variants associated with CDI, we performed a genome-wide association analysis in 19,861 participants (1349 cases; 18,512 controls) from the Electronic Medical Records and Genomics (eMERGE) Network. Using logistic regression, we found strong evidence for genetic variation in the DRB locus of the MHC (HLA) II region that predisposes individuals to CDI (P > 1.0 × 10-14; OR 1.56). Altered transcriptional regulation in the HLA region may play a role in conferring susceptibility to this opportunistic enteric pathogen.
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Affiliation(s)
- Kathleen Ferar
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA.
| | - Taryn O Hall
- Optum Genomics, UnitedHealth Group, Minnetonka, MN, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Rongling Li
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Loren Gragert
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | | | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Catherine A McCarty
- University of Minnesota Medical School, Duluth, MN, USA
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | - Abel Kho
- Divisions of General Internal Medicine and Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marylyn D Ritchie
- Department of Biochemistry and Molecular Biology, Center for Systems Genomics, Pennsylvania State University, University Park, PA, USA
| | - Paul K Crane
- Division of General Internal Medicine, University of Washington, Seattle, WA, USA
| | | | - Christopher Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John J Connolly
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - David Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Yuan Luo
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ozan Dikilitas
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA.
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3
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Mahajan A, Go MJ, Zhang W, Below JE, Gaulton KJ, Ferreira T, Horikoshi M, Johnson AD, Ng MCY, Prokopenko I, Saleheen D, Wang X, Zeggini E, Abecasis GR, Adair LS, Almgren P, Atalay M, Aung T, Baldassarre D, Balkau B, Bao Y, Barnett AH, Barroso I, Basit A, Been LF, Beilby J, Bell GI, Benediktsson R, Bergman RN, Boehm BO, Boerwinkle E, Bonnycastle LL, Burtt N, Cai Q, Campbell H, Carey J, Cauchi S, Caulfield M, Chan JCN, Chang LC, Chang TJ, Chang YC, Charpentier G, Chen CH, Chen H, Chen YT, Chia KS, Chidambaram M, Chines PS, Cho NH, Cho YM, Chuang LM, Collins FS, Cornelis MC, Couper DJ, Crenshaw AT, van Dam RM, Danesh J, Das D, de Faire U, Dedoussis G, Deloukas P, Dimas AS, Dina C, Doney AS, Donnelly PJ, Dorkhan M, van Duijn C, Dupuis J, Edkins S, Elliott P, Emilsson V, Erbel R, Eriksson JG, Escobedo J, Esko T, Eury E, Florez JC, Fontanillas P, Forouhi NG, Forsen T, Fox C, Fraser RM, Frayling TM, Froguel P, Frossard P, Gao Y, Gertow K, Gieger C, Gigante B, Grallert H, Grant GB, Grrop LC, Groves CJ, Grundberg E, Guiducci C, Hamsten A, Han BG, Hara K, Hassanali N, Hattersley AT, Hayward C, Hedman AK, Herder C, Hofman A, Holmen OL, Hovingh K, Hreidarsson AB, Hu C, Hu FB, Hui J, Humphries SE, Hunt SE, Hunter DJ, Hveem K, Hydrie ZI, Ikegami H, Illig T, Ingelsson E, Islam M, Isomaa B, Jackson AU, Jafar T, James A, Jia W, Jöckel KH, Jonsson A, Jowett JBM, Kadowaki T, Kang HM, Kanoni S, Kao WHL, Kathiresan S, Kato N, Katulanda P, Keinanen-Kiukaanniemi KM, Kelly AM, Khan H, Khaw KT, Khor CC, Kim HL, Kim S, Kim YJ, Kinnunen L, Klopp N, Kong A, Korpi-Hyövälti E, Kowlessur S, Kraft P, Kravic J, Kristensen MM, Krithika S, Kumar A, Kumate J, Kuusisto J, Kwak SH, Laakso M, Lagou V, Lakka TA, Langenberg C, Langford C, Lawrence R, Leander K, Lee JM, Lee NR, Li M, Li X, Li Y, Liang J, Liju S, Lim WY, Lind L, Lindgren CM, Lindholm E, Liu CT, Liu JJ, Lobbens S, Long J, Loos RJF, Lu W, Luan J, Lyssenko V, Ma RCW, Maeda S, Mägi R, Männisto S, Matthews DR, Meigs JB, Melander O, Metspalu A, Meyer J, Mirza G, Mihailov E, Moebus S, Mohan V, Mohlke KL, Morris AD, Mühleisen TW, Müller-Nurasyid M, Musk B, Nakamura J, Nakashima E, Navarro P, Ng PK, Nica AC, Nilsson PM, Njølstad I, Nöthen MM, Ohnaka K, Ong TH, Owen KR, Palmer CNA, Pankow JS, Park KS, Parkin M, Pechlivanis S, Pedersen NL, Peltonen L, Perry JRB, Peters A, Pinidiyapathirage JM, Platou CG, Potter S, Price JF, Qi L, Radha V, Rallidis L, Rasheed A, Rathman W, Rauramaa R, Raychaudhuri S, Rayner NW, Rees SD, Rehnberg E, Ripatti S, Robertson N, Roden M, Rossin EJ, Rudan I, Rybin D, Saaristo TE, Salomaa V, Saltevo J, Samuel M, Sanghera DK, Saramies J, Scott J, Scott LJ, Scott RA, Segrè AV, Sehmi J, Sennblad B, Shah N, Shah S, Shera AS, Shu XO, Shuldiner AR, Sigurđsson G, Sijbrands E, Silveira A, Sim X, Sivapalaratnam S, Small KS, So WY, Stančáková A, Stefansson K, Steinbach G, Steinthorsdottir V, Stirrups K, Strawbridge RJ, Stringham HM, Sun Q, Suo C, Syvänen AC, Takayanagi R, Takeuchi F, Tay WT, Teslovich TM, Thorand B, Thorleifsson G, Thorsteinsdottir U, Tikkanen E, Trakalo J, Tremoli E, Trip MD, Tsai FJ, Tuomi T, Tuomilehto J, Uitterlinden AG, Valladares-Salgado A, Vedantam S, Veglia F, Voight BF, Wang C, Wareham NJ, Wennauer R, Wickremasinghe AR, Wilsgaard T, Wilson JF, Wiltshire S, Winckler W, Wong TY, Wood AR, Wu JY, Wu Y, Yamamoto K, Yamauchi T, Yang M, Yengo L, Yokota M, Young R, Zabaneh D, Zhang F, Zhang R, Zheng W, Zimmet PZ, Altshuler D, Bowden DW, Cho YS, Cox NJ, Cruz M, Hanis CL, Kooner J, Lee JY, Seielstad M, Teo YY, Boehnke M, Parra EJ, Chambers JC, Tai ES, McCarthy MI, Morris AP. Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nat Genet 2014; 46:234-44. [PMID: 24509480 PMCID: PMC3969612 DOI: 10.1038/ng.2897] [Citation(s) in RCA: 777] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 01/17/2014] [Indexed: 11/18/2022]
Abstract
To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS) including 26,488 cases and 83,964 controls of European, East Asian, South Asian, and Mexican and Mexican American ancestry. We observed significant excess in directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven novel T2D susceptibility loci. Furthermore, we observed considerable improvements in fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterisation of complex trait loci, and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry.
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4
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Stewart SE, Yu D, Scharf JM, Neale BM, Fagerness JA, Mathews CA, Arnold PD, Evans PD, Gamazon ER, Osiecki L, McGrath L, Haddad S, Crane J, Hezel D, Illman C, Mayerfeld C, Konkashbaev A, Liu C, Pluzhnikov A, Tikhomirov A, Edlund CK, Rauch SL, Moessner R, Falkai P, Maier W, Ruhrmann S, Grabe HJ, Lennertz L, Wagner M, Bellodi L, Cavallini MC, Richter MA, Cook EH, Kennedy JL, Rosenberg D, Stein DJ, Hemmings SMJ, Lochner C, Azzam A, Chavira DA, Fournier E, Garrido H, Sheppard B, Umaña P, Murphy DL, Wendland JR, Veenstra-VanderWeele J, Denys D, Blom R, Deforce D, Van Nieuwerburgh F, Westenberg HGM, Walitza S, Egberts K, Renner T, Miguel EC, Cappi C, Hounie AG, Conceição do Rosário M, Sampaio AS, Vallada H, Nicolini H, Lanzagorta N, Camarena B, Delorme R, Leboyer M, Pato CN, Pato MT, Voyiaziakis E, Heutink P, Cath DC, Posthuma D, Smit JH, Samuels J, Bienvenu OJ, Cullen B, Fyer AJ, Grados MA, Greenberg BD, McCracken JT, Riddle MA, Wang Y, Coric V, Leckman JF, Bloch M, Pittenger C, Eapen V, Black DW, Ophoff RA, Strengman E, Cusi D, Turiel M, Frau F, Macciardi F, Gibbs JR, Cookson MR, Singleton A, Hardy J, Crenshaw AT, Parkin MA, Mirel DB, Conti DV, Purcell S, Nestadt G, Hanna GL, Jenike MA, Knowles JA, Cox N, Pauls DL, Pauls DL. Genome-wide association study of obsessive-compulsive disorder. Mol Psychiatry 2013; 18:788-98. [PMID: 22889921 PMCID: PMC4218751 DOI: 10.1038/mp.2012.85] [Citation(s) in RCA: 214] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 05/03/2012] [Accepted: 05/07/2012] [Indexed: 02/07/2023]
Abstract
Obsessive-compulsive disorder (OCD) is a common, debilitating neuropsychiatric illness with complex genetic etiology. The International OCD Foundation Genetics Collaborative (IOCDF-GC) is a multi-national collaboration established to discover the genetic variation predisposing to OCD. A set of individuals affected with DSM-IV OCD, a subset of their parents, and unselected controls, were genotyped with several different Illumina SNP microarrays. After extensive data cleaning, 1465 cases, 5557 ancestry-matched controls and 400 complete trios remained, with a common set of 469,410 autosomal and 9657 X-chromosome single nucleotide polymorphisms (SNPs). Ancestry-stratified case-control association analyses were conducted for three genetically-defined subpopulations and combined in two meta-analyses, with and without the trio-based analysis. In the case-control analysis, the lowest two P-values were located within DLGAP1 (P=2.49 × 10(-6) and P=3.44 × 10(-6)), a member of the neuronal postsynaptic density complex. In the trio analysis, rs6131295, near BTBD3, exceeded the genome-wide significance threshold with a P-value=3.84 × 10(-8). However, when trios were meta-analyzed with the case-control samples, the P-value for this variant was 3.62 × 10(-5), losing genome-wide significance. Although no SNPs were identified to be associated with OCD at a genome-wide significant level in the combined trio-case-control sample, a significant enrichment of methylation QTLs (P<0.001) and frontal lobe expression quantitative trait loci (eQTLs) (P=0.001) was observed within the top-ranked SNPs (P<0.01) from the trio-case-control analysis, suggesting these top signals may have a broad role in gene expression in the brain, and possibly in the etiology of OCD.
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Affiliation(s)
- S Evelyn Stewart
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry, Massachusetts General Hospital, Boston,
Massachusetts, USA,British Columbia Mental Health and Addictions Research Institute, University
of British Columbia, Vancouver, BC, Canada
| | - Dongmei Yu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - Jeremiah M Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry, Massachusetts General Hospital, Boston,
Massachusetts, USA,Department of Neurology, Massachusetts General Hospital, Boston,
Massachusetts, USA,Department of Neurology, Brigham and Women's Hospital, Boston,
Massachusetts,, USA,Program in Medical and Population Genetics, Broad Institute of Harvard and
MIT, Cambridge MA
| | - Benjamin M Neale
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Analytic and Translational Genetics Unit, Massachusetts General Hospital,
Boston Massachusetts, USA,Program in Medical and Population Genetics, Broad Institute of Harvard and
MIT, Cambridge MA
| | - Jesen A Fagerness
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - Carol A Mathews
- Department of Psychiatry, University of California, San Francisco, USA
| | - Paul D Arnold
- Program in Genetics and Genome Biology, The Hospital for Sick Children,
Toronto, Ontario, Canada,Department of Psychiatry, University of Toronto, Toronto, Ontario,
Canada
| | - Patrick D Evans
- Section of Genetic Medicine, Department of Medicine, University of Chicago,
Chicago, Illinois, USA
| | - Eric R Gamazon
- Section of Genetic Medicine, Department of Medicine, University of Chicago,
Chicago, Illinois, USA
| | - Lisa Osiecki
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - Lauren McGrath
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - Stephen Haddad
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - Jacquelyn Crane
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - Dianne Hezel
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - Cornelia Illman
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - Catherine Mayerfeld
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - Anuar Konkashbaev
- Section of Genetic Medicine, Department of Medicine, University of Chicago,
Chicago, Illinois, USA
| | - Chunyu Liu
- Department of Psychiatry, University of Chicago, Chicago, IL, USA
| | - Anna Pluzhnikov
- Section of Genetic Medicine, Department of Medicine, University of Chicago,
Chicago, Illinois, USA
| | - Anna Tikhomirov
- Section of Genetic Medicine, Department of Medicine, University of Chicago,
Chicago, Illinois, USA
| | - Christopher K Edlund
- Department of Preventative Medicine, Division of Biostatistics, Keck School
of Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles,
California, USA,Epigenome Center, Keck School of Medicine, University of Southern
California, Los Angeles, California, USA
| | - Scott L Rauch
- Partners Psychiatry and McLean Hospital, Boston, Massachusetts, USA
| | - Rainald Moessner
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn,
Germany
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, University of
Göttingen, Göttingen, Germany
| | - Wolfgang Maier
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn,
Germany
| | - Stephan Ruhrmann
- Department of Psychiatry and Psychotherapy, University of Cologne, Cologne,
Germany
| | - Hans-Jörgen Grabe
- Department of Psychiatry and Psychotherapy, Helios-Hospital Stralsund,
University Medicine Greifswald, Greifswald, Germany
| | - Leonard Lennertz
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn,
Germany
| | - Michael Wagner
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn,
Germany
| | - Laura Bellodi
- Psychiatry Universita Vita-Salute San Raffaele, Milano Italy
| | | | - Margaret A Richter
- Department of Psychiatry, University of Toronto, Toronto, Ontario,
Canada,Department of Psychiatry, Sunnybrook Health Sciences Centre, Toronto,
Ontario
| | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of
Illinois at Chicago, USA
| | - James L Kennedy
- Department of Psychiatry, University of Toronto, Toronto, Ontario,
Canada,Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - David Rosenberg
- Child Psychiatry and Psychology, Wayne State University, Detroit, Michigan,
USA,Children's Hospital of Michigan, Detroit, Michigan, USA
| | - Dan J Stein
- University of Cape Town, Cape Town, South Africa
| | | | | | - Amin Azzam
- Department of Psychiatry, University of California, San Francisco, USA
| | - Denise A Chavira
- Department of Psychiatry, University of California, San Diego, La Jolla,
California, USA
| | | | | | - Brooke Sheppard
- Department of Psychiatry, University of California, San Francisco, USA
| | - Paul Umaña
- Hospital Nacional de Niños, San José, Costa Rica
| | - Dennis L Murphy
- Laboratory of Clinical Science, NIMH Intramural Research Program, Bethesda,
MD, USA
| | - Jens R Wendland
- Laboratory of Clinical Science, NIMH Intramural Research Program, Bethesda,
MD, USA,CNS Clinical Biomarker Group, Pharma Research and Early Development, F.
Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Jeremy Veenstra-VanderWeele
- Departments of Psychiatry, Pediatrics, and Pharmacology, Kennedy Center for
Research on Human Development, and Brain Institute, Vanderbilt University, Nashville,
Tennessee, USA
| | - Damiaan Denys
- Department of Psychiatry, Academic Medical Center and Netherlands Institute
for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences
(NIN-KNAW), Amsterdam, The Netherlands
| | - Rianne Blom
- Department of Psychiatry, Academic Medical Center and Netherlands Institute
for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences
(NIN-KNAW), Amsterdam, The Netherlands
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent,
Belgium
| | | | - Herman GM Westenberg
- Department of Psychiatry, Academic Medical Center and Netherlands Institute
for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences
(NIN-KNAW), Amsterdam, The Netherlands
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry, University of Zurich,
Switzerland
| | - Karin Egberts
- Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy, University of Würzburg, Germany
| | - Tobias Renner
- Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy, University of Würzburg, Germany
| | | | - Carolina Cappi
- Department of Psychiatry, Faculdade de Medicina da Universidade de Sao
Paulo, Brazil
| | - Ana G Hounie
- Department of Psychiatry, Faculdade de Medicina da Universidade de Sao
Paulo, Brazil
| | | | - Aline S Sampaio
- Department of Psychiatry, Faculdade de Medicina da Universidade de Sao
Paulo, Brazil,University Health Care Services - SMURB, Federal University of Bahia,
Salvador, State of Bahia, Brazil
| | - Homero Vallada
- Department of Psychiatry, Faculdade de Medicina da Universidade de Sao
Paulo, Brazil
| | - Humberto Nicolini
- Centre for Genomic Sciences, University of Mexico City, Mexico,Carracci Medical Group, Mexico City, Mexico
| | | | - Beatriz Camarena
- Instituto Nacional de Psiquiatría Ramón de la Fuente
Muñiz, Depto. de Genética Psiquiátrica, México, D. F.,
México
| | - Richard Delorme
- AP-HP, Robert Debré Hospital, Department of Child and Adolescent
Psychiatry, Paris, France, INSERM U955,Institut Mondor de Recherche Biomédicale, Psychiatric Genetics,
Créteil, F 94000, France, Foundation Fondamental, French National Science
Foundation, France
| | - Marion Leboyer
- AP-HP, Robert Debré Hospital, Department of Child and Adolescent
Psychiatry, Paris, France, INSERM U955,Institut Mondor de Recherche Biomédicale, Psychiatric Genetics,
Créteil, F 94000, France, Foundation Fondamental, French National Science
Foundation, France
| | - Carlos N Pato
- Department of Psychiatry and The Behavioral Sciences, Zilkha Neurogenetic
Institute, Keck School of Medicine, University of Southern California, Los Angeles,
USA
| | - Michele T Pato
- Department of Psychiatry and The Behavioral Sciences, Zilkha Neurogenetic
Institute, Keck School of Medicine, University of Southern California, Los Angeles,
USA
| | - Emanuel Voyiaziakis
- Department of Psychiatry and The Behavioral Sciences, Zilkha Neurogenetic
Institute, Keck School of Medicine, University of Southern California, Los Angeles,
USA
| | - Peter Heutink
- Section of Medical Genomics, Department of Clinical Genetics, VU University
Medical Center Amsterdam, The Netherlands
| | - Danielle C Cath
- Department of Psychiatry, VU University Medical Center and Department of
Clinical and Health Psychology, Utrecht University, Utrecht, The Netherlands,Department of Psychiatry, EMGO Institute, VU University Medical Center,
Utrecht, The Netherlands
| | - Danielle Posthuma
- Section of Medical Genomics, Department of Clinical Genetics, VU University
Medical Center Amsterdam, The Netherlands
| | - Jan H Smit
- Department of Psychiatry, EMGO Institute, VU University Medical Center,
Utrecht, The Netherlands
| | - Jack Samuels
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University
School of Medicine, Baltimore, Maryland, USA
| | - O Joseph Bienvenu
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University
School of Medicine, Baltimore, Maryland, USA
| | - Bernadette Cullen
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University
School of Medicine, Baltimore, Maryland, USA
| | - Abby J Fyer
- Department of Psychiatry, College of Physicians and Surgeons at Columbia
University, New York City, New York, USA,New York State Psychiatric Institute, New York City, New York, USA
| | - Marco A Grados
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University
School of Medicine, Baltimore, Maryland, USA
| | - Benjamin D Greenberg
- Department of Psychiatry and Human Behavior, Brown Medical School, Butler
Hospital, Providence, Rhode Island, USA
| | - James T McCracken
- Department of Psychiatry and Biobehavioral Sciences, University of
California, Los Angeles, School of Medicine, California, USA
| | - Mark A Riddle
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University
School of Medicine, Baltimore, Maryland, USA
| | - Ying Wang
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University
School of Medicine, Baltimore, Maryland, USA
| | - Vladimir Coric
- Child Study Centre and Department of Psychiatry, Yale University, New
Haven, Connecticut, USA
| | - James F Leckman
- Child Study Centre, Pediatrics and Psychology, Yale University, New Haven,
Connecticut, USA
| | - Michael Bloch
- Child Study Centre and Department of Psychiatry, Yale University, New
Haven, Connecticut, USA
| | - Christopher Pittenger
- Child Study Centre and Department of Psychiatry, Yale University, New
Haven, Connecticut, USA
| | - Valsamma Eapen
- Infant, Child and Adolescent Psychiatry, University of New South Wales,
Academic Unit of Child Psychiatry, Sydney, Australia
| | - Donald W Black
- University of Iowa, Roy J. and Lucille A. Carver College of Medicine, Iowa
City, Iowa, USA
| | - Roel A Ophoff
- UCLA Center for Neurobehavioral Genetics, Los Angeles, California, USA and
University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eric Strengman
- UCLA Center for Neurobehavioral Genetics, Los Angeles, California, USA and
University Medical Center Utrecht, Utrecht, The Netherlands
| | - Daniele Cusi
- Department of Medicine, Surgery and Dentistry, Graduate School of
Nephrology, University of Milano, Italy,Division of Nephrology, San Paolo Hospital, Milano, Italy
| | - Maurizio Turiel
- Department of Health Technologies, University of Milano, Italy
| | - Francesca Frau
- Department of Medicine, Surgery and Dentistry, Graduate School of
Nephrology, University of Milano, Italy,Filarete Foundation, Milano, Italy
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, School of Medicine, University
of California Irvine (UCI), California, USA
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National
Institutes of Health, Bethesda, Maryland, USA
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National
Institutes of Health, Bethesda, Maryland, USA
| | - Andrew Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National
Institutes of Health, Bethesda, Maryland, USA
| | | | - John Hardy
- Department of Molecular Neuroscience, University College of London,
Institute of Neurology, Queen Square, London, UK
| | | | | | | | | | - David V Conti
- Department of Preventative Medicine, Division of Biostatistics, Keck School
of Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles,
California, USA,Epigenome Center, Keck School of Medicine, University of Southern
California, Los Angeles, California, USA
| | - Shaun Purcell
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry, Massachusetts General Hospital, Boston,
Massachusetts, USA,Department of Neurology, Brigham and Women's Hospital, Boston,
Massachusetts,, USA,The Broad Institute of Harvard-MIT, Cambridge, MA, USA
| | - Gerald Nestadt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University
School of Medicine, Baltimore, Maryland, USA
| | - Gregory L Hanna
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Michael A Jenike
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - James A Knowles
- Department of Psychiatry and The Behavioral Sciences, Zilkha Neurogenetic
Institute, Keck School of Medicine, University of Southern California, Los Angeles,
USA
| | - Nancy Cox
- Section of Genetic Medicine, Department of Medicine, University of Chicago,
Chicago, Illinois, USA
| | - David L Pauls
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry, Massachusetts General Hospital, Boston,
Massachusetts, USA,Corresponding Authors: Dr. S. Evelyn Stewart, Department of
Psychiatry, University of British Columbia, Vancouver, BC, Canada, V5Z 4H4, Tel: (604)
875-2000 ext. 4725; Fax: (604) 875-3871; ; Dr. David
L. Pauls, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics
Research, Massachusetts General Hospital, Boston, MA 02114. Tel: (617) 726-0793; Fax:
(617) 726-0830;
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5
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Morris AP, Voight BF, Teslovich TM, Ferreira T, Segrè AV, Steinthorsdottir V, Strawbridge RJ, Khan H, Grallert H, Mahajan A, Prokopenko I, Kang HM, Dina C, Esko T, Fraser RM, Kanoni S, Kumar A, Lagou V, Langenberg C, Luan J, Lindgren CM, Müller-Nurasyid M, Pechlivanis S, Rayner NW, Scott LJ, Wiltshire S, Yengo L, Kinnunen L, Rossin EJ, Raychaudhuri S, Johnson AD, Dimas AS, Loos RJF, Vedantam S, Chen H, Florez JC, Fox C, Liu CT, Rybin D, Couper DJ, Kao WHL, Li M, Cornelis MC, Kraft P, Sun Q, van Dam RM, Stringham HM, Chines PS, Fischer K, Fontanillas P, Holmen OL, Hunt SE, Jackson AU, Kong A, Lawrence R, Meyer J, Perry JRB, Platou CGP, Potter S, Rehnberg E, Robertson N, Sivapalaratnam S, Stančáková A, Stirrups K, Thorleifsson G, Tikkanen E, Wood AR, Almgren P, Atalay M, Benediktsson R, Bonnycastle LL, Burtt N, Carey J, Charpentier G, Crenshaw AT, Doney ASF, Dorkhan M, Edkins S, Emilsson V, Eury E, Forsen T, Gertow K, Gigante B, Grant GB, Groves CJ, Guiducci C, Herder C, Hreidarsson AB, Hui J, James A, Jonsson A, Rathmann W, Klopp N, Kravic J, Krjutškov K, Langford C, Leander K, Lindholm E, Lobbens S, Männistö S, Mirza G, Mühleisen TW, Musk B, Parkin M, Rallidis L, Saramies J, Sennblad B, Shah S, Sigurðsson G, Silveira A, Steinbach G, Thorand B, Trakalo J, Veglia F, Wennauer R, Winckler W, Zabaneh D, Campbell H, van Duijn C, Uitterlinden AG, Hofman A, Sijbrands E, Abecasis GR, Owen KR, Zeggini E, Trip MD, Forouhi NG, Syvänen AC, Eriksson JG, Peltonen L, Nöthen MM, Balkau B, Palmer CNA, Lyssenko V, Tuomi T, Isomaa B, Hunter DJ, Qi L, Shuldiner AR, Roden M, Barroso I, Wilsgaard T, Beilby J, Hovingh K, Price JF, Wilson JF, Rauramaa R, Lakka TA, Lind L, Dedoussis G, Njølstad I, Pedersen NL, Khaw KT, Wareham NJ, Keinanen-Kiukaanniemi SM, Saaristo TE, Korpi-Hyövälti E, Saltevo J, Laakso M, Kuusisto J, Metspalu A, Collins FS, Mohlke KL, Bergman RN, Tuomilehto J, Boehm BO, Gieger C, Hveem K, Cauchi S, Froguel P, Baldassarre D, Tremoli E, Humphries SE, Saleheen D, Danesh J, Ingelsson E, Ripatti S, Salomaa V, Erbel R, Jöckel KH, Moebus S, Peters A, Illig T, de Faire U, Hamsten A, Morris AD, Donnelly PJ, Frayling TM, Hattersley AT, Boerwinkle E, Melander O, Kathiresan S, Nilsson PM, Deloukas P, Thorsteinsdottir U, Groop LC, Stefansson K, Hu F, Pankow JS, Dupuis J, Meigs JB, Altshuler D, Boehnke M, McCarthy MI. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet 2012; 44:981-90. [PMID: 22885922 PMCID: PMC3442244 DOI: 10.1038/ng.2383] [Citation(s) in RCA: 1413] [Impact Index Per Article: 117.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 07/11/2012] [Indexed: 11/09/2022]
Abstract
To extend understanding of the genetic architecture and molecular basis of type 2 diabetes (T2D), we conducted a meta-analysis of genetic variants on the Metabochip, including 34,840 cases and 114,981 controls, overwhelmingly of European descent. We identified ten previously unreported T2D susceptibility loci, including two showing sex-differentiated association. Genome-wide analyses of these data are consistent with a long tail of additional common variant loci explaining much of the variation in susceptibility to T2D. Exploration of the enlarged set of susceptibility loci implicates several processes, including CREBBP-related transcription, adipocytokine signaling and cell cycle regulation, in diabetes pathogenesis.
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Affiliation(s)
- Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, UK.
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6
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Cheng I, Chen GK, Nakagawa H, He J, Wan P, Laurie CC, Shen J, Sheng X, Pooler LC, Crenshaw AT, Mirel DB, Takahashi A, Kubo M, Nakamura Y, Al Olama AA, Benlloch S, Donovan JL, Guy M, Hamdy FC, Kote-Jarai Z, Neal DE, Wilkens LR, Monroe KR, Stram DO, Muir K, Eeles RA, Easton DF, Kolonel LN, Henderson BE, Le Marchand L, Haiman CA. Evaluating genetic risk for prostate cancer among Japanese and Latinos. Cancer Epidemiol Biomarkers Prev 2012; 21:2048-58. [PMID: 22923026 DOI: 10.1158/1055-9965.epi-12-0598] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND There have been few genome-wide association studies (GWAS) of prostate cancer among diverse populations. To search for novel prostate cancer risk variants, we conducted GWAS of prostate cancer in Japanese and Latinos. In addition, we tested prostate cancer risk variants and developed genetic risk models of prostate cancer for Japanese and Latinos. METHODS Our first-stage GWAS of prostate cancer included Japanese (cases/controls = 1,033/1,042) and Latino (cases/controls = 1,043/1,057) from the Multiethnic Cohort (MEC). Significant associations from stage I (P < 1.0 × 10(-4)) were examined in silico in GWAS of prostate cancer (stage II) in Japanese (cases/controls = 1,583/3,386) and Europeans (cases/controls = 1,854/1,894). RESULTS No novel stage I single-nucleotide polymorphism (SNP) outside of known risk regions reached genome-wide significance. For Japanese, in stage I, the most notable putative novel association was seen with 10 SNPs (P ≤ 8.0 × 10(-6)) at chromosome 2q33; however, this was not replicated in stage II. For Latinos, the most significant association was observed with rs17023900 at the known 3p12 risk locus (stage I: OR = 1.45; P = 7.01 × 10(-5) and stage II: OR = 1.58; P = 3.05 × 10(-7)). The majority of the established risk variants for prostate cancer, 79% and 88%, were positively associated with prostate cancer in Japanese and Latinos (stage I), respectively. The cumulative effects of these variants significantly influence prostate cancer risk (OR per allele = 1.10; P = 2.71 × 10(-25) and OR = 1.07; P = 1.02 × 10(-16) for Japanese and Latinos, respectively). CONCLUSION AND IMPACT Our GWAS of prostate cancer did not identify novel genome-wide significant variants. However, our findings show that established risk variants for prostate cancer significantly contribute to risk among Japanese and Latinos.
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Affiliation(s)
- Iona Cheng
- Epidemiology Program, University of Hawaii Cancer Center, 1236 Lauhala Street, Suite 407, Honolulu, HI 96813, USA.
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7
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Zuvich RL, Armstrong LL, Bielinski SJ, Bradford Y, Carlson CS, Crawford DC, Crenshaw AT, de Andrade M, Doheny KF, Haines JL, Hayes MG, Jarvik GP, Jiang L, Kullo IJ, Li R, Ling H, Manolio TA, Matsumoto ME, McCarty CA, McDavid AN, Mirel DB, Olson LM, Paschall JE, Pugh EW, Rasmussen LV, Rasmussen-Torvik LJ, Turner SD, Wilke RA, Ritchie MD. Pitfalls of merging GWAS data: lessons learned in the eMERGE network and quality control procedures to maintain high data quality. Genet Epidemiol 2012; 35:887-98. [PMID: 22125226 DOI: 10.1002/gepi.20639] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genome-wide association studies (GWAS) are a useful approach in the study of the genetic components of complex phenotypes. Aside from large cohorts, GWAS have generally been limited to the study of one or a few diseases or traits. The emergence of biobanks linked to electronic medical records (EMRs) allows the efficient reuse of genetic data to yield meaningful genotype-phenotype associations for multiple phenotypes or traits. Phase I of the electronic MEdical Records and GEnomics (eMERGE-I) Network is a National Human Genome Research Institute-supported consortium composed of five sites to perform various genetic association studies using DNA repositories and EMR systems. Each eMERGE site has developed EMR-based algorithms to comprise a core set of 14 phenotypes for extraction of study samples from each site's DNA repository. Each eMERGE site selected samples for a specific phenotype, and these samples were genotyped at either the Broad Institute or at the Center for Inherited Disease Research using the Illumina Infinium BeadChip technology. In all, approximately 17,000 samples from across the five sites were genotyped. A unified quality control (QC) pipeline was developed by the eMERGE Genomics Working Group and used to ensure thorough cleaning of the data. This process includes examination of sample and marker quality and various batch effects. Upon completion of the genotyping and QC analyses for each site's primary study, eMERGE Coordinating Center merged the datasets from all five sites. This larger merged dataset reentered the established eMERGE QC pipeline. Based on lessons learned during the process, additional analyses and QC checkpoints were added to the pipeline to ensure proper merging. Here, we explore the challenges associated with combining datasets from different genotyping centers and describe the expansion to eMERGE QC pipeline for merged datasets. These additional steps will be useful as the eMERGE project expands to include additional sites in eMERGE-II, and also serve as a starting point for investigators merging multiple genotype datasets accessible through the National Center for Biotechnology Information in the database of Genotypes and Phenotypes. Our experience demonstrates that merging multiple datasets after additional QC can be an efficient use of genotype data despite new challenges that appear in the process.
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Affiliation(s)
- Rebecca L Zuvich
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
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8
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Turner S, Armstrong LL, Bradford Y, Carlson CS, Crawford DC, Crenshaw AT, de Andrade M, Doheny KF, Haines JL, Hayes G, Jarvik G, Jiang L, Kullo IJ, Li R, Ling H, Manolio TA, Matsumoto M, McCarty CA, McDavid AN, Mirel DB, Paschall JE, Pugh EW, Rasmussen LV, Wilke RA, Zuvich RL, Ritchie MD. Quality control procedures for genome-wide association studies. ACTA ACUST UNITED AC 2011; Chapter 1:Unit1.19. [PMID: 21234875 DOI: 10.1002/0471142905.hg0119s68] [Citation(s) in RCA: 198] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genome-wide association studies (GWAS) are being conducted at an unprecedented rate in population-based cohorts and have increased our understanding of the pathophysiology of complex disease. Regardless of context, the practical utility of this information will ultimately depend upon the quality of the original data. Quality control (QC) procedures for GWAS are computationally intensive, operationally challenging, and constantly evolving. Here we enumerate some of the challenges in QC of GWAS data and describe the approaches that the electronic MEdical Records and Genomics (eMERGE) network is using for quality assurance in GWAS data, thereby minimizing potential bias and error in GWAS results. We discuss common issues associated with QC of GWAS data, including data file formats, software packages for data manipulation and analysis, sex chromosome anomalies, sample identity, sample relatedness, population substructure, batch effects, and marker quality. We propose best practices and discuss areas of ongoing and future research.
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Affiliation(s)
- Stephen Turner
- Center for Human Genetics Research, Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee, USA
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9
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Welzel TM, Morgan TR, Bonkovsky HL, Naishadham D, Pfeiffer RM, Wright EC, Hutchinson AA, Crenshaw AT, Bashirova A, Carrington M, Dotrang M, Sterling RK, Lindsay KL, Fontana RJ, Lee WM, Di Bisceglie AM, Ghany MG, Gretch DR, Chanock SJ, Chung RT, O’Brien TR. Variants in interferon-alpha pathway genes and response to pegylated interferon-Alpha2a plus ribavirin for treatment of chronic hepatitis C virus infection in the hepatitis C antiviral long-term treatment against cirrhosis trial. Hepatology 2009; 49:1847-58. [PMID: 19434718 PMCID: PMC2692559 DOI: 10.1002/hep.22877] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
UNLABELLED Combination treatment with pegylated-interferon-alpha (PEG IFN-alpha) and ribavirin, the current recommended therapy for chronic hepatitis C virus (HCV) infection, results in a sustained virological response (SVR) in only about half of patients. Because genes involved in the interferon-alpha pathway may affect antiviral responses, we analyzed the relationship between variants in these genes and SVR among participants in the Hepatitis C Antiviral Long-Term treatment Against Cirrhosis (HALT-C) trial. Patients had advanced chronic hepatitis C that had previously failed to respond to interferon-based treatment. Participants were treated with peginterferon-alpha2a and ribavirin during the trial. Subjects with undetectable HCV RNA at week 72 were considered to have had an SVR. Subjects with detectable HCV RNA at week 20 were considered nonresponders. We used TaqMan assays to genotype 56 polymorphisms found in 13 genes in the interferon-alpha pathway. This analysis compares genotypes for participants with an SVR to nonresponders. The primary analysis was restricted to European American participants because a priori statistical power was low among the small number (n = 131) of African American patients. We used logistic regression to control the effect of other variables that are associated with treatment response. Among 581 European American patients, SVR was associated with IFNAR1 IVS1-22G (adjusted odds ratio, 0.57; P = 0.02); IFNAR2 Ex2-33C (adjusted odds ratio, 2.09; P = 0.02); JAK1 IVS22+112T (adjusted odds ratio, 1.66; P = 0.04); and ADAR Ex9+14A (adjusted odds ratio, 1.67; P = 0.03). For the TYK2-2256A promoter region variant, a borderline association was present among European American participants (OR, 1.51; P = 0.05) and a strong relationship among African American patients; all 10 with SVR who were genotyped for TYK2 -2256 carried the A variant compared with 68 of 120 (57%) nonresponders (P = 0.006). CONCLUSION Genetic polymorphisms in the interferon-alpha pathway may affect responses to antiviral therapy of chronic hepatitis C.
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Affiliation(s)
- Tania Mara Welzel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - Timothy R. Morgan
- Division of Gastroenterology, University of California - Irvine, Irvine, CA and Gastroenterology Service, VA Long Beach Healthcare System, Long Beach, CA
| | - Herbert L. Bonkovsky
- Departments of Medicine and The Liver-Biliary-Pancreatic Center, University of Connecticut Health Center, Farmington, CT and Carolinas Medical Center, Charlotte, NC
| | | | - Ruth M. Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - Elizabeth C. Wright
- Office of the Director, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - Amy A. Hutchinson
- Core Genotyping Facility, NCI/Division of Cancer Epidemiology and Genetics, Advanced Technology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD
| | - Andrew T. Crenshaw
- Core Genotyping Facility, NCI/Division of Cancer Epidemiology and Genetics, Advanced Technology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD
| | - Arman Bashirova
- Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Inc., Frederick, MD
| | | | - Richard K. Sterling
- Hepatology Section, Virginia Commonwealth University Medical Center, Richmond, VA
| | - Karen L. Lindsay
- Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Robert J. Fontana
- Division of Gastroenterology, University of Michigan Medical Center, Ann Arbor, MI
| | - William M. Lee
- Division of Digestive and Liver Diseases, University of Texas Southwestern Medical Center, Dallas, TX
| | - Adrian M. Di Bisceglie
- Division of Gastroenterology and Hepatology, Saint Louis University School of Medicine, St. Louis, MO
| | - Marc G. Ghany
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - David R. Gretch
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD,Core Genotyping Facility, NCI/Division of Cancer Epidemiology and Genetics, Advanced Technology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD
| | - Raymond T. Chung
- Gastrointestinal Unit, Medical Services, Massachusetts General Hospital, and the Department of Medicine, Harvard Medical School, Boston, MA
| | - Thomas R. O’Brien
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD,Corresponding author, Mailing Address: 6120 Executive Blvd., Room 6111, Rockville, MD 20852
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