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Cordell HJ, Fryett JJ, Ueno K, Darlay R, Aiba Y, Hitomi Y, Kawashima M, Nishida N, Khor SS, Gervais O, Kawai Y, Nagasaki M, Tokunaga K, Tang R, Shi Y, Li Z, Juran BD, Atkinson EJ, Gerussi A, Carbone M, Asselta R, Cheung A, de Andrade M, Baras A, Horowitz J, Ferreira MAR, Sun D, Jones DE, Flack S, Spicer A, Mulcahy VL, Byan J, Han Y, Sandford RN, Lazaridis KN, Amos CI, Hirschfield GM, Seldin MF, Invernizzi P, Siminovitch KA, Ma X, Nakamura M, Mells GF. Corrigendum to: "An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs" [J Hepatol 75 (2021) 572-581]. J Hepatol 2023; 78:883. [PMID: 36639314 DOI: 10.1016/j.jhep.2022.12.001] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - James J Fryett
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Rebecca Darlay
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Olivier Gervais
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Brian D Juran
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Elizabeth J Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Alessio Gerussi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Marco Carbone
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy; Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Angela Cheung
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York, USA
| | | | | | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, New York, USA
| | - David E Jones
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Steven Flack
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ann Spicer
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Victoria L Mulcahy
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jinyoung Byan
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA
| | - Richard N Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA
| | - Gideon M Hirschfield
- Toronto Centre for Liver Disease, Division of Gastroenterology and Hepatology, University of Toronto, Toronto, Ontario, Canada
| | | | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Katherine A Siminovitch
- Departments of Medicine, Immunology and Medical Sciences, University of Toronto, Toronto, Ontario, Canada; Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Ontario, Canada
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - George F Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom.
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Fryett JJ, Morris AP, Cordell HJ. Investigating the prediction of CpG methylation levels from SNP genotype data to help elucidate relationships between methylation, gene expression and complex traits. Genet Epidemiol 2022; 46:629-643. [PMID: 35930604 PMCID: PMC9804820 DOI: 10.1002/gepi.22496] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/27/2022] [Accepted: 07/19/2022] [Indexed: 01/09/2023]
Abstract
As popularised by PrediXcan (and related methods), transcriptome-wide association studies (TWAS), in which gene expression is imputed from single-nucleotide polymorphism (SNP) genotypes and tested for association with a phenotype, are a popular approach for investigating the role of gene expression in complex traits. Like gene expression, DNA methylation is an important biological process and, being under genetic regulation, may be imputable from SNP genotypes. Here, we investigate prediction of CpG methylation levels from SNP genotype data to help elucidate relationships between methylation, gene expression and complex traits. We start by examining how well CpG methylation can be predicted from SNP genotypes, comparing three penalised regression approaches and examining whether changing the window size improves prediction accuracy. Although methylation at most CpG sites cannot be accurately predicted from SNP genotypes, for a subset it can be predicted well. We next apply our methylation prediction models (trained using the optimal method and window size) to carry out a methylome-wide association study (MWAS) of primary biliary cholangitis. We intersect the regions identified via MWAS with those identified via TWAS, providing insight into the interplay between CpG methylation, gene expression and disease status. We conclude that MWAS has the potential to improve understanding of biological mechanisms in complex traits.
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Affiliation(s)
- James J. Fryett
- Population Health Sciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Andrew P. Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal ResearchUniversity of ManchesterManchesterUK
| | - Heather J. Cordell
- Population Health Sciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
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3
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Cordell HJ, Fryett JJ, Ueno K, Darlay R, Aiba Y, Hitomi Y, Kawashima M, Nishida N, Khor SS, Gervais O, Kawai Y, Nagasaki M, Tokunaga K, Tang R, Shi Y, Li Z, Juran BD, Atkinson EJ, Gerussi A, Carbone M, Asselta R, Cheung A, de Andrade M, Baras A, Horowitz J, Ferreira MA, Sun D, Jones DE, Flack S, Spicer A, Mulcahy VL, Byun J, Han Y, Sandford RN, Lazaridis KN, Amos CI, Hirschfield GM, Seldin MF, Invernizzi P, Siminovitch KA, Ma X, Nakamura M, Mells GF. Corrigendum to 'An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs' [J Hepatol 2021;75(3):572-581]. J Hepatol 2022; 76:489. [PMID: 34895949 PMCID: PMC8935376 DOI: 10.1016/j.jhep.2021.11.015] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Heather J. Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - James J. Fryett
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Rebecca Darlay
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Olivier Gervais
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan,Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan,Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China,Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China,Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Brian D. Juran
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Elizabeth J. Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States
| | - Alessio Gerussi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy,European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Marco Carbone
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy,European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy,Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Angela Cheung
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Julie Horowitz
- Regeneron Genetics Center, Tarrytown, New York, United States
| | | | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - David E. Jones
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Steven Flack
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ann Spicer
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Victoria L. Mulcahy
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Richard N. Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Christopher I. Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Gideon M. Hirschfield
- Toronto Centre for Liver Disease, Division of Gastroenterology and Hepatology, University of Toronto, Toronto, Ontario, Canada
| | | | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy,European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Katherine A. Siminovitch
- Departments of Medicine, Immunology and Medical Sciences, University of Toronto, Toronto, Ontario, Canada,Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Ontario, Canada
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
| | - George F. Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom,Corresponding author. Address: Academic Department of Medical Genetics, University of Cambridge, Box 238, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, United Kingdom.
| | - Canadian PBC ConsortiumSiminovitchKatherine A.252627HirschfieldGideon M.28MasonAndrew29VincentCatherine30XieGang31ZhangJinyi32Departments of Medicine, Immunology and Medical Sciences, University of Toronto, CanadaMount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute, CanadaToronto General Research Institute, Toronto, Ontario, CanadaToronto Centre for Liver Disease, Division of Gastroenterology and Hepatology, University of Toronto, Toronto, Ontario, CanadaDept of Medicine, University of Alberta, Edmonton, Alberta, CanadaUniversite de Montreal Hospital Centre, Saint-Luc Hospital, Montreal, Quebec, CanadaLunenfeld Tanenbaum Research Institute, Toronto, CanadaLunenfeld Tanenbaum Research Institute, Toronto, Canada
| | - Chinese PBC ConsortiumTangRuqi33MaXiong33LiZhiqiang3435ShiYongyong3435Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, ChinaBio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, ChinaAffiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, China
| | - Italian PBC Study GroupAffrontiAndrea36AlmasioPiero L.37AlvaroDomenico38AndreonePietro39AndriulliAngelo40AzzaroliFrancesco41BattezzatiPier Maria42BenedettiAntonio43BragazziMaria Consiglia44BrunettoMaurizia45BrunoSavino46CalvarusoVincenza47CardinaleVincenzo48CasellaGiovanni49CazzagonNora50CiaccioAntonio51CocoBarbara52ColliAgostino53ColloredoGuido54ColomboMassimo55ColomboSilvia56CristoferiLaura57CursaroCarmela58CrocèLory Saveria59CrosignaniAndrea60D’AmatoDaphne61DonatoFrancesca62EliaGianfranco63FabrisLuca64FagiuoliStefano65FerrariCarlo66FloreaniAnnarosa67GalliAndrea68GianniniEdoardo69GrattaglianoIgnazio70LamperticoPietro71LleoAna72MalinvernoFederica73MancusoClara74MarraFabio75MarzioniMarco76MassironiSara77MattaliaAlberto78MieleLuca79MilaniChiara80MoriniLorenzo81MoriscoFilomena82MuratoriLuigi83MuratoriPaolo84NiroGrazia A.85O’DonnellSarah86PicciottoAntonio87PortincasaPiero88RigamontiCristina89RoncaVincenzo90RosinaFloriano91SpinziGiancarlo92StrazzaboscoMario93TarocchiMirko94TiribelliClaudio95ToniuttoPierluigi96ValentiLuca97VinciMaria98ZuinMassimo99Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, ItalyGastroenterology & Hepatology Unit, Di.Bi.M.I.S., University of Palermo, Palermo, ItalyDepartment of Medico-Surgical Sciences and Biotechnologies, Polo Pontino, University Sapienza of Rome; Eleonora Lorillard Spencer-Cenci Foundation, Rome, ItalyDepartment of Medical and Surgical Sciences, Bologna University, Bologna, ItalyIRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, ItalyDepartment of Medical and Surgical Sciences (DIMEC) University of Bologna, Bologna, ItalySan Paolo Hospital Medical School, Università di Milano, Milan, ItalyUniversitàPolitecnica delle Marche, Ancona, ItalyDepartment of Medico-Surgical Sciences and Biotechnologies, Polo Pontino, University Sapienza of Rome, Rome, ItalyAzienda Ospedaliera Universitaria Pisana, Pisa, ItalyDepartment of Internal Medicine, Ospedale Fatebene Fratelli e Oftalmico, Milan, ItalySezione di Gastroenterologia e Epatologia, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S.) University of Palermo, Palermo, ItalyDepartment of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Viale dell'Università37, 00185, Rome, ItalyMedical Department, Desio Hospital, Desio, ItalyDepartment of Surgery, Oncology and Gastroenterology, University of Padua, Padova, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyAzienda Ospedaliera Universitaria Pisana, Pisa, ItalyDepartment of Internal Medicine, AO Provincia di Lecco, Lecco, ItalyDepartment of Internal Medicine, San Pietro Hospital, Bergamo, Ponte San Pietro, ItalyHumanitas Clinical and Research Center, IRCCS, Rozzano, ItalyTreviglio Hospital, Treviglio, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyHepatology Unit, Department of Medical and Surgical Sciences, University Hospital of Bologna, ItalyUniversity of Trieste, & Fondazione Italiana Fegato (FIF) Trieste, ItalySan Paolo Hospital Medical School, Universitàdi Milano, Milan, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyFondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan, ItalyAzienda Ospedaliero-Universitaria di Parma, Parma, ItalyUniversity of Padova, Padova, ItalyGastroenterologia Epatologia e Trapiantologia, Papa Giovanni XXIII Hospital, Bergamo, ItalyAzienda Ospedaliero-Universitaria di Parma, Parma, ItalyDepartment. of Surgical, Oncological and Gastroenterological Sciences, University of Padova, Padova, ItalyUniversity of Florence, Florence, ItalyGastroenterology Unit, Department Internal Medicine, Policlinico San Martino, University of Genoa, Genoa, ItalyItalian College of General Practicioners, ASL Bari, ItalyDivision of Gastroenterology and Hepatology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, ItalyDepartment of Biomedical Sciences, Humanitas University, Division of Internal Medicine and Hepatology, Department of Gastroenterology, Humanitas Clinical and Research Center IRCCS, Via A. Manzoni 56, 20089 Rozzano (MI), ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyUniversity of Florence, Florence, ItalyUniversità Politecnica delle Marche, Ancona, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalySanta Croce Carle Hospital, Cuneo, ItalyInternal Medicine, Gastroenterology and Liver Unit, A. Gemelli Polyclinic, Sacro Cuore Catholic University, 20123 Rome, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyMagenta Hospital, Magenta, ItalyUniversity of Naples, Federico II, Naples, ItalyDepartment of Clinical Medicine, University of Bologna, Bologna, ItalyDepartment of Clinical Medicine, University of Bologna, Bologna, ItalyIRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyUniversity of Genoa, Genoa, ItalyDepartment of Interdisciplinary Medicine, University Medical School, Bari, ItalyDepartment of Translational Medicine, Universitàdel Piemonte Orientale UPO, 28100 Novara, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyDivision of Gastroenterology & Hepatology, Center for Predictive Medicine, Gradenigo Hospital, Turin, ItalyAzienda Ospedaliera Valduce, Como, ItalyYale University, New Haven, Connecticut, USAUniversity of Florence, Florence, ItalyUniversity of Trieste, & Fondazione Italiana Fegato (FIF) Trieste, ItalyUniversity of Udine, Udine, ItalyInternal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Policlinico Milano, Department of Pathophysiology and Transplantation, Universitàdegli Studi di Milano, Milan, ItalyOspedale Niguarda, Milan, ItalySan Paolo Hospital Medical School, Università di Milano, Milan, Italy
| | - Japan-PBC-GWAS ConsortiumNakamuraHitomi100AbiruSeigo100NagaokaShinya100KomoriAtsumasa100YatsuhashiHiroshi100IshibashiHiromi100ItoMasahiro100MigitaKiyoshi101OhiraHiromasa101KatsushimaShinji102NaganumaAtsushi102SugiKazuhiro102KomatsuTatsuji102MannamiTomohiko102MatsushitaKouki102YoshizawaKaname102MakitaFujio102NikamiToshiki102NishimuraHideo102KounoHiroshi102KounoHirotaka102OtaHajime102KomuraTakuya102NakamuraYoko102ShimadaMasaaki102HirashimaNoboru102KomedaToshiki102ArioKeisuke102NakamutaMakoto102YamashitaTsutomu102FurutaKiyoshi102KikuchiMasahiro102NaeshiroNoriaki102TakahashiHironao102ManoYutaka102TsunematsuSeiji102YabuuchiIwao102ShimadaYusuke102YamauchiKazuhiko102SugimotoRie102SakaiHironori102MitaEiji102KodaMasaharu102TsurutaSatoru102KamitsukasaHiroshi102SatoTakeaki102MasakiNaohiko102KobataTatsuro102FukushimaNobuyoshi102OharaYukio102MuroToyokichi102TakesakiEiichi102TakakiHitoshi102YamamotoTetsuo102KatoMichio102NagaokiYuko102HayashiShigeki102IshidaJinya102WatanabeYukio102KobayashiMasakazu102KogaMichiaki102SaoshiroTakeo102YaguraMichiyasu102HirataKeisuke102TanakaAtsushu103TakikawaHajime103ZeniyaMikio104AbeMasanori105OnjiMorikazu105KanekoShuichi106HondaMasao106AraiKuniaki106Arinaga-HinoTeruko107HashimotoEtsuko108TaniaiMakiko108UmemuraTakeji109JoshitaSatoru109NakaoKazuhiko110IchikawaTatsuki110ShibataHidetaka110YamagiwaSatoshi111SeikeMasataka112HondaKoichi112SakisakaShotaro113TakeyamaYasuaki113HaradaMasaru114SenjuMichio114YokosukaOsamu115KandaTatsuo115UenoYoshiyuki116KikuchiKentaro117EbinumaHirotoshi118HimotoTakashi119YasunamiMichio120MurataKazumoto121MizokamiMasashi121KawataKazuhito122ShimodaShinji123MiyakeYasuhiro124TakakiAkinobu124YamamotoKazuhide124HiranoKatsuji125IchidaTakafumi125IdoAkio126TsubouchiHirohito126ChayamaKazuaki127HaradaKenichi128NakanumaYasuni128MaeharaYoshihiko129TaketomiAkinobu129ShirabeKen129SoejimaYuji129MoriAkira130YagiShintaro130UemotoShinji130HEgawa131TanakaTomohiro132YamashikiNoriyo132TamuraSumito133SugawaraYasuhiro133KokudoNorihiro133Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, JapanDepartment of Gastroenterology and Rheumatic Diseases, Fukushima Medical University of Medicine, Fukushima, JapanHeadquaters of PBC Research in the NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Nagasaki, JapanDepartment of Medicine, Teikyo University School of Medicine, Tokyo, JapanDepartment of Gastroenterology and Hepatology, Tokyo Jikei University School of Medicine, Tokyo, JapanDepartment of Gastroenterology and Metabology, Ehime University Graduate School of Medicine, Matsuyama, JapanDepartment of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, JapanDivision of Gastroenterology, Department of Medicine, Kurume University School of Medicine, Kurume, JapanDepartment of Medicine and Gastroenterology, Tokyo Women’s Medical University, Tokyo, JapanDepartment of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, Matsumoto, JapanDepartment of Gastroenterology and Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, JapanDivision of Gastroenterology and Hepatology,Niigata University Graduate School of Medical and Dental Sciences, Niigata, JapanFaculty of Medicine, Oita University, Oita, JapanDepartment of Gastroenterology and Medicine, Fukuoka University School of Medicine, Fukuoka, JapanThe Third Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, JapanDepartment of Medicine and Clinical Oncology, Graduate School of Medicine, Chiba University, Chiba, JapanDepartment of Gastroenterology, Yamagata University Faculty of Medicine, Yamagata, JapanDepartment of Internal Medicine, Teikyo University Mizonokuchi Hospital, Kawasaki, JapanDivision of Gastroenterology and Hepatology, Department of Internal Medicine, Keio Graduate School of Medicine, Tokyo, JapanDepartment of Medical Technology, Kagawa Prefectural University of Health Sciences, Kagawa, JapanDepartment of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasakin, JapanThe Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, JapanHepatology Division, Department of Internal Medicine II, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka JapanDepartment of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, JapanDepartment of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, JapanDepartment of Gastroenterology and Hepatology, Juntendo University Shizuoka Hospital, Shizuoka, JapanDepartment of Digestive and Lifestyle–Related Disease, Kagoshima University Graduate School of Medical and Dental Science, Kagoshima, JapanDepartment of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, JapanDepartment of Human Pathology, Kanazawa University Graduate School of Medicine, Kanazawa, JapanDepartment of Surgery and Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, JapanDivision of Hepato-Biliary-Pancreatic and Transplant Surgery, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, JapanDepartment of Surgery, Tokyo Women’s Medical University, Tokyo, JapanOrgan Transplantation Service, The University of Tokyo, Tokyo, JapanHepatobiliary and Pancreatic Surgery Division and Artificial Organ and Transplantation Division, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Japan
| | - US PBC ConsortiumJuranBrian D.134AtkinsonElizabeth J.135CheungAngela136de AndradeMariza137LazaridisKonstantinos N.138ChalasaniNaga139LuketicVel140OdinJoseph141ChopraKapil142BarasAris143HorowitzJulie143AbecasisGoncalo143CantorMichael143CoppolaGiovanni143EconomidesAris143LottaLuca A.143OvertonJohn D.143ReidJeffrey G.143ShuldinerAlan143BeechertChristina143ForsytheCaitlin143FullerErin D.143GuZhenhua143LattariMichael143LopezAlexander143OvertonJohn D.143SchleicherThomas D.143PadillaMaria Sotiropoulos143ToledoKarina143WidomLouis143WolfSarah E.143PradhanManasi143ManoochehriKia143UlloaRicardo H.143BaiXiaodong143BalasubramanianSuganthi143BarnardLeland143BlumenfeldAndrew143EomGisu143HabeggerLukas143HawesAlicia143KhalidShareef143ReidJeffrey G.143MaxwellEvan K.143SalernoWilliam143StaplesJeffrey C.143JonesMarcus B.143MitnaulLyndon J.143Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United StatesDivision of Biomedical Statistics and Informatics Mayo Clinic, Rochester, Minnesota, United StatesDivision of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United StatesDivision of Biomedical Statistics and Informatics Mayo Clinic, Rochester, Minnesota, United StatesDivision of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United StatesIndiana University, Indiana, United StatesVirginia Commonwealth University, Virginia, United StatesIcahn School of Medicine, Mount Sinai, New York, United StatesUniversity of Pittsburgh, United StatesRegeneron, United States
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4
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Cordell HJ, Fryett JJ, Ueno K, Darlay R, Aiba Y, Hitomi Y, Kawashima M, Nishida N, Khor SS, Gervais O, Kawai Y, Nagasaki M, Tokunaga K, Tang R, Shi Y, Li Z, Juran BD, Atkinson EJ, Gerussi A, Carbone M, Asselta R, Cheung A, de Andrade M, Baras A, Horowitz J, Ferreira MAR, Sun D, Jones DE, Flack S, Spicer A, Mulcahy VL, Byan J, Han Y, Sandford RN, Lazaridis KN, Amos CI, Hirschfield GM, Seldin MF, Invernizzi P, Siminovitch KA, Ma X, Nakamura M, Mells GF. An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs. J Hepatol 2021; 75:572-581. [PMID: 34033851 PMCID: PMC8811537 DOI: 10.1016/j.jhep.2021.04.055] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 03/11/2021] [Accepted: 04/07/2021] [Indexed: 01/15/2023]
Abstract
BACKGROUNDS & AIMS Primary biliary cholangitis (PBC) is a chronic liver disease in which autoimmune destruction of the small intrahepatic bile ducts eventually leads to cirrhosis. Many patients have inadequate response to licensed medications, motivating the search for novel therapies. Previous genome-wide association studies (GWAS) and meta-analyses (GWMA) of PBC have identified numerous risk loci for this condition, providing insight into its aetiology. We undertook the largest GWMA of PBC to date, aiming to identify additional risk loci and prioritise candidate genes for in silico drug efficacy screening. METHODS We combined new and existing genotype data for 10,516 cases and 20,772 controls from 5 European and 2 East Asian cohorts. RESULTS We identified 56 genome-wide significant loci (20 novel) including 46 in European, 13 in Asian, and 41 in combined cohorts; and a 57th genome-wide significant locus (also novel) in conditional analysis of the European cohorts. Candidate genes at newly identified loci include FCRL3, INAVA, PRDM1, IRF7, CCR6, CD226, and IL12RB1, which each play key roles in immunity. Pathway analysis reiterated the likely importance of pattern recognition receptor and TNF signalling, JAK-STAT signalling, and differentiation of T helper (TH)1 and TH17 cells in the pathogenesis of this disease. Drug efficacy screening identified several medications predicted to be therapeutic in PBC, some of which are well-established in the treatment of other autoimmune disorders. CONCLUSIONS This study has identified additional risk loci for PBC, provided a hierarchy of agents that could be trialled in this condition, and emphasised the value of genetic and genomic approaches to drug discovery in complex disorders. LAY SUMMARY Primary biliary cholangitis (PBC) is a chronic liver disease that eventually leads to cirrhosis. In this study, we analysed genetic information from 10,516 people with PBC and 20,772 healthy individuals recruited in Canada, China, Italy, Japan, the UK, or the USA. We identified several genetic regions associated with PBC. Each of these regions contains several genes. For each region, we used diverse sources of evidence to help us choose the gene most likely to be involved in causing PBC. We used these 'candidate genes' to help us identify medications that are currently used for treatment of other conditions, which might also be useful for treatment of PBC.
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Affiliation(s)
- Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - James J Fryett
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Rebecca Darlay
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Olivier Gervais
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Brian D Juran
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Elizabeth J Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States
| | - Alessio Gerussi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Marco Carbone
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy; Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Angela Cheung
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Julie Horowitz
- Regeneron Genetics Center, Tarrytown, New York, United States
| | | | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - David E Jones
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Steven Flack
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ann Spicer
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Victoria L Mulcahy
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jinyoung Byan
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Richard N Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Gideon M Hirschfield
- Toronto Centre for Liver Disease, Division of Gastroenterology and Hepatology, University of Toronto, Toronto, Ontario, Canada
| | | | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Katherine A Siminovitch
- Departments of Medicine, Immunology and Medical Sciences, University of Toronto, Toronto, Ontario, Canada; Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Ontario, Canada
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan; Department of Hepatology, Nagasaki Graduate School of Biomedical Sciences, Japan
| | - George F Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom.
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Fryett JJ, Morris AP, Cordell HJ. Investigation of prediction accuracy and the impact of sample size, ancestry, and tissue in transcriptome-wide association studies. Genet Epidemiol 2020; 44:425-441. [PMID: 32190932 PMCID: PMC8641384 DOI: 10.1002/gepi.22290] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/05/2020] [Accepted: 03/06/2020] [Indexed: 01/14/2023]
Abstract
In transcriptome-wide association studies (TWAS), gene expression values are predicted using genotype data and tested for association with a phenotype. The power of this approach to detect associations relies, at least in part, on the accuracy of the prediction. Here we compare the prediction accuracy of six different methods-LASSO, Ridge regression, Elastic net, Best Linear Unbiased Predictor, Bayesian Sparse Linear Mixed Model, and Random Forests-by performing cross-validation using data from the Geuvadis Project. We also examine prediction accuracy (a) at different sample sizes, (b) when ancestry of the prediction model training and testing populations is different, and (c) when the tissue used to train the model is different from the tissue to be predicted. We find that, for most genes, the expression cannot be accurately predicted, but in general sparse statistical models tend to outperform polygenic models at prediction. Average prediction accuracy is reduced when the model training set size is reduced or when predicting across ancestries and is marginally reduced when predicting across tissues. We conclude that using sparse statistical models and the development of large reference panels across multiple ethnicities and tissues will lead to better prediction of gene expression, and thus may improve TWAS power.
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Affiliation(s)
- James J. Fryett
- Population Health Sciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Andrew P. Morris
- Division of Musculoskeletal and Dermatological SciencesUniversity of ManchesterManchesterUK
| | - Heather J. Cordell
- Population Health Sciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
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