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Pathway-based analysis of primary biliary cirrhosis genome-wide association studies

Abstract

Genome-wide association studies (GWAS) have successfully identified several loci associated with primary biliary cirrhosis (PBC) risk. Pathway analysis complements conventional GWAS analysis. We applied the recently developed linear combination test for pathways to datasets drawn from independent PBC GWAS in Italian and Canadian subjects. Of the Kyoto Encyclopedia of Genes and Genomes and BioCarta pathways tested, 25 pathways in the Italian dataset (449 cases, 940 controls) and 26 pathways in the Canadian dataset (530 cases, 398 controls) were associated with PBC susceptibility (P<0.05). After correcting for multiple comparisons, only the eight most significant pathways in the Italian dataset had FDR <0.25 with tumor necrosis factor/stress-related signaling emerging as the top pathway (P=7.38 × 10−4, FDR=0.18). Two pathways, phosphatidylinositol signaling and hedgehog signaling, were replicated in both datasets (P<0.05), and subjected to two additional complementary pathway tests. Both pathway signals remained significant in the Italian dataset on modified gene set enrichment analysis (P<0.05). In both GWAS, variants nominally associated with PBC were significantly overrepresented in the phosphatidylinositol pathway (Fisher exact P<0.05). These results point to established and novel pathway-level associations with inherited predisposition to PBC that, on further independent replication and functional validation, may provide fresh insights into PBC etiology.

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Acknowledgements

This study was supported by NIH R01DK056839, NIH R01DK091823, NIH K08AR055688, Hypergenes (European Network for Genetic-Epidemiological Studies HEALTH-F4-2007-201550), Canadian Institutes for Health Research (MOP74621), the Ontario Research Fund (RE01-061), the Canadian PBC Society, a Canada Research Chair award and the Sherman Family Chair in Genomic Medicine to KAS. The authors thank C Coltescu, AL Mason, P Milkiewicz, RP Meyers, JA Odin, V Liakina, C Vincent and C Levy who assisted in recruiting cases for the Canadian-based PBC study.

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Correspondence to C I Amos.

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Contributors Piero L Almasio (Gastroenterology and Hepatology Unit, DiBiMIS, University of Palermo, Palermo), Domenico Alvaro (Department of Medico-Surgical Sciences and Biotechnologies, Fondazione Eleonora Lorillard Spencer Cenci, University Sapienza of Rome, Rome), Pietro Andreone (Dipartimento di Medicina Clinica, Università di Bologna, Bologna), Angelo Andriulli (IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo), Cristina Barlassina (Department of Medicine, Surgery, and Dentistry, Università degli Studi di Milano, Milan), Antonio Benedetti (Università Politecnica delle Marche, Ancona), Francesca Bernuzzi (Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano), Ilaria Bianchi (Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano), MariaConsiglia Bragazzi (Department of Medico-Surgical Sciences and Biotechnologies, Fondazione Eleonora Lorillard Spencer Cenci, University Sapienza of Rome, Rome), Maurizia Brunetto (Azienda Ospedaliera Universitaria Pisana, Pisa), Savino Bruno (Department of Internal Medicine, Ospedale Fatebene Fratelli e Oftalmico, Milan), Lisa Caliari (Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano), Giovanni Casella (Medical Department, Desio Hospital, Desio), Barbara Coco (Azienda Ospedaliera Universitaria Pisana, Pisa), Agostino Colli (Department of Internal Medicine, AO Provincia di Lecco, Lecco), Massimo Colombo (Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan), Silvia Colombo (Treviglio Hospital, Treviglio), Carmela Cursaro (Dipartimento di Medicina Clinica, Università di Bologna, Bologna), Lory Saveria Croce (University of Trieste, and Fondazione Italiana Fegato (FIF), Trieste), Andrea Crosignani (San Paolo Hospital Medical School, Università di Milano, Milan), Francesca Donato (Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan), Gianfranco Elia (Azienda Ospedaliero-Universitaria di Parma, Parma) Luca Fabris (University of Padova, Padova), Annarosa Floreani (Department of Surgical, Oncological and Gastroenterological Sciences, University of Padova, Padova), Andrea Galli (University of Florence, Florence), Ignazio Grattagliano (Italian College of General Practicioners, ASL Bari), Roberta Lazzari (Department of Surgical, Oncological and Gastroenterological SciencesUniversity of Padova, Padova), Ana Lleo (Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano), Fabio Macaluso (Gastroenterology and Hepatology Unit, DiBiMIS, University of Palermo, Palermo), Fabio Marra (University of Florence, Florence), Marco Marzioni (Università Politecnica delle Marche, Ancona), Elisabetta Mascia (Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano), Alberto Mattalia (Santa Croce Carle Hospital, Cuneo), Renzo Montanari (Ospedale di Negrar, Verona), Lorenzo Morini (Magenta Hospital, Magenta), Filomena Morisco (University of Naples, Federico II, Naples), Luigi Muratori (Department of Clinical Medicine, University of Bologna, Bologna), Paolo Muratori (Department of Clinical Medicine, University of Bologna, Bologna), Grazia Niro (IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo), Antonio Picciotto (University of Genoa, Genoa), Mauro Podda (Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano) Piero Portincasa (Department of Interdisciplinary Medicine, University Medical School, Bari), Daniele Prati (Ospedale Alessandro Manzoni, Lecco, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan), Chiara Raggi (Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano), Floriano Rosina (Division of Gastroenterology and Hepatology, Center for Predictive Medicine, Gradenigo Hospital, Turin), Sonia Rossi (Department of Internal Medicine, Ospedale Fatebene Fratelli e Oftalmico, Milan), Ilaria Sogno (Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano),Giancarlo Spinzi (Azienda Ospedaliera Valduce, Como), Mario Strazzabosco (Yale University, New Haven, Connecticut 06511, USA and University of Milan-Bicocca, Monza), Sonia Tarallo (Division of Gastroenterology and Hepatology, Center for Predictive Medicine, Gradenigo Hospital, Turin), Mirko Tarocchi (University of Florence, Florence), Claudio Tiribelli (University of Trieste, and Fondazione Italiana Fegato (FIF), Trieste), Pierluigi Toniutto (University of Udine, Udine), Maria Vinci (Ospedale Niguarda, Milan), Massimo Zuin (San Paolo Hospital Medical School, Università di Milano, Milan).

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Kar, S., Seldin, M., Chen, W. et al. Pathway-based analysis of primary biliary cirrhosis genome-wide association studies. Genes Immun 14, 179–186 (2013). https://doi.org/10.1038/gene.2013.1

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