GWAS summary-based pathway analysis correcting for the genetic confounding impact of environmental exposures

被引:3
作者
Fan, Qianrui [1 ]
Zhang, Feng [1 ]
Wang, Wenyu [1 ]
Xu, Jiawen [2 ]
Hao, Jingcan [1 ]
He, Awen [1 ]
Wen, Yan [1 ]
Li, Ping [1 ]
Liang, Xiao [1 ]
Du, Yanan [1 ]
Liu, Li [1 ]
Wu, Cuiyan [1 ]
Wang, Sen [1 ]
Wang, Xi [1 ]
Ning, Yujie [1 ]
Guo, Xiong [1 ]
机构
[1] Xi An Jiao Tong Univ, Key Lab Trace Elements & Endem Dis, Natl Hlth & Family Planning Commiss, Sch Publ Hlth,Hlth Sci Ctr, Yanta West Rd 76, Xian 710061, Shaanxi, Peoples R China
[2] Xi An Jiao Tong Univ, Hlth Sci Ctr, Xian, Shaanxi, Peoples R China
关键词
genome-wide association studies; pathway analysis; environmental exposures; complex diseases; GENOME-WIDE ASSOCIATION; MENDELIAN RANDOMIZATION; RISK LOCI; IDENTIFY; SMOKING; DISEASE; TRAITS;
D O I
10.1093/bib/bbx025
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Genome-wide association study (GWAS)-based pathway association analysis is a powerful approach for the genetic studies of human complex diseases. However, the genetic confounding effects of environment exposure-related genes can decrease the accuracy of GWAS-based pathway association analysis of target diseases. In this study, we developed a pathway association analysis approach, named Mendelian randomization-based pathway enrichment analysis (MRPEA), which was capable of correcting the genetic confounding effects of environmental exposures, using the GWAS summary data of environmental exposures. After analyzing the real GWAS summary data of cardiovascular disease and cigarette smoking, we observed significantly improved performance of MRPEA compared with traditional pathway association analysis (TPAA) without adjusting for environmental exposures. Further, simulation studies found that MRPEA generally outperformed TPAA under various scenarios. We hope that MRPEA could help to fill the gap of TPAA and identify novel causal pathways for complex diseases.
引用
收藏
页码:725 / 730
页数:6
相关论文
共 27 条
[1]   A global reference for human genetic variation [J].
Altshuler, David M. ;
Durbin, Richard M. ;
Abecasis, Goncalo R. ;
Bentley, David R. ;
Chakravarti, Aravinda ;
Clark, Andrew G. ;
Donnelly, Peter ;
Eichler, Evan E. ;
Flicek, Paul ;
Gabriel, Stacey B. ;
Gibbs, Richard A. ;
Green, Eric D. ;
Hurles, Matthew E. ;
Knoppers, Bartha M. ;
Korbel, Jan O. ;
Lander, Eric S. ;
Lee, Charles ;
Lehrach, Hans ;
Mardis, Elaine R. ;
Marth, Gabor T. ;
McVean, Gil A. ;
Nickerson, Deborah A. ;
Wang, Jun ;
Wilson, Richard K. ;
Boerwinkle, Eric ;
Doddapaneni, Harsha ;
Han, Yi ;
Korchina, Viktoriya ;
Kovar, Christie ;
Lee, Sandra ;
Muzny, Donna ;
Reid, Jeffrey G. ;
Zhu, Yiming ;
Chang, Yuqi ;
Feng, Qiang ;
Fang, Xiaodong ;
Guo, Xiaosen ;
Jian, Min ;
Jiang, Hui ;
Jin, Xin ;
Lan, Tianming ;
Li, Guoqing ;
Li, Jingxiang ;
Li, Yingrui ;
Liu, Shengmao ;
Liu, Xiao ;
Lu, Yao ;
Ma, Xuedi ;
Tang, Meifang ;
Wang, Bo .
NATURE, 2015, 526 (7571) :68-+
[2]   The pathophysiology of cigarette C-V smoking and cardiovascular disease - An update [J].
Ambrose, JA ;
Barua, RS .
JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY, 2004, 43 (10) :1731-1737
[3]   A genome-wide association study of alcohol dependence [J].
Bierut, Laura J. ;
Agrawal, Arpana ;
Bucholz, Kathleen K. ;
Doheny, Kimberly F. ;
Laurie, Cathy ;
Pugh, Elizabeth ;
Fisher, Sherri ;
Fox, Louis ;
Howells, William ;
Bertelsen, Sarah ;
Hinrichs, Anthony L. ;
Almasy, Laura ;
Breslau, Naomi ;
Culverhouse, Robert C. ;
Dick, Danielle M. ;
Edenberg, Howard J. ;
Foroud, Tatiana ;
Grucza, Richard A. ;
Hatsukami, Dorothy ;
Hesselbrock, Victor ;
Johnson, Eric O. ;
Kramer, John ;
Krueger, Robert F. ;
Kuperman, Samuel ;
Lynskey, Michael ;
Mann, Karl ;
Neuman, Rosalind J. ;
Noethen, Markus M. ;
Nurnberger, John I., Jr. ;
Porjesz, Bernice ;
Ridinger, Monika ;
Saccone, Nancy L. ;
Saccone, Scott F. ;
Schuckit, Marc A. ;
Tischfield, Jay A. ;
Wang, Jen C. ;
Rietschel, Marcella ;
Goate, Alison M. ;
Rice, John P. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (11) :5082-5087
[4]   A second generation human haplotype map of over 3.1 million SNPs [J].
Frazer, Kelly A. ;
Ballinger, Dennis G. ;
Cox, David R. ;
Hinds, David A. ;
Stuve, Laura L. ;
Gibbs, Richard A. ;
Belmont, John W. ;
Boudreau, Andrew ;
Hardenbol, Paul ;
Leal, Suzanne M. ;
Pasternak, Shiran ;
Wheeler, David A. ;
Willis, Thomas D. ;
Yu, Fuli ;
Yang, Huanming ;
Zeng, Changqing ;
Gao, Yang ;
Hu, Haoran ;
Hu, Weitao ;
Li, Chaohua ;
Lin, Wei ;
Liu, Siqi ;
Pan, Hao ;
Tang, Xiaoli ;
Wang, Jian ;
Wang, Wei ;
Yu, Jun ;
Zhang, Bo ;
Zhang, Qingrun ;
Zhao, Hongbin ;
Zhao, Hui ;
Zhou, Jun ;
Gabriel, Stacey B. ;
Barry, Rachel ;
Blumenstiel, Brendan ;
Camargo, Amy ;
Defelice, Matthew ;
Faggart, Maura ;
Goyette, Mary ;
Gupta, Supriya ;
Moore, Jamie ;
Nguyen, Huy ;
Onofrio, Robert C. ;
Parkin, Melissa ;
Roy, Jessica ;
Stahl, Erich ;
Winchester, Ellen ;
Ziaugra, Liuda ;
Altshuler, David ;
Shen, Yan .
NATURE, 2007, 449 (7164) :851-U3
[5]   Genome-wide meta-analyses identify multiple loci associated with smoking behavior [J].
Furberg, Helena ;
Kim, YunJung ;
Dackor, Jennifer ;
Boerwinkle, Eric ;
Franceschini, Nora ;
Ardissino, Diego ;
Bernardinelli, Luisa ;
Mannucci, Pier M. ;
Mauri, Francesco ;
Merlini, Piera A. ;
Absher, Devin ;
Assimes, Themistocles L. ;
Fortmann, Stephen P. ;
Iribarren, Carlos ;
Knowles, Joshua W. ;
Quertermous, Thomas ;
Ferrucci, Luigi ;
Tanaka, Toshiko ;
Bis, Joshua C. ;
Furberg, Curt D. ;
Haritunians, Talin ;
McKnight, Barbara ;
Psaty, Bruce M. ;
Taylor, Kent D. ;
Thacker, Evan L. ;
Almgren, Peter ;
Groop, Leif ;
Ladenvall, Claes ;
Boehnke, Michael ;
Jackson, Anne U. ;
Mohlke, Karen L. ;
Stringham, Heather M. ;
Tuomilehto, Jaakko ;
Benjamin, Emelia J. ;
Hwang, Shih-Jen ;
Levy, Daniel ;
Preis, Sarah Rosner ;
Vasan, Ramachandran S. ;
Duan, Jubao ;
Gejman, Pablo V. ;
Levinson, Douglas F. ;
Sanders, Alan R. ;
Shi, Jianxin ;
Lips, Esther H. ;
Mckay, James D. ;
Agudo, Antonio ;
Barzan, Luigi ;
Bencko, Vladimir ;
Benhamou, Simone ;
Castellsague, Xavier .
NATURE GENETICS, 2010, 42 (05) :441-U134
[6]   The uneasy ethical and legal underpinnings of large-scale genomic biobanks [J].
Greely, Henry T. .
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, 2007, 8 :343-364
[7]  
Han Z, 2016, PLOS GENET, V12
[8]   Genome-wide associations for birth weight and correlations with adult disease [J].
Horikoshi, Momoko ;
Beaumont, Robin N. ;
Day, Felix R. ;
Warrington, Nicole M. ;
Kooijman, Marjolein N. ;
Fernandez-Tajes, Juan ;
Feenstra, Bjarke ;
van Zuydam, Natalie R. ;
Gaulton, Kyle J. ;
Grarup, Niels ;
Bradfield, Jonathan P. ;
Strachan, David P. ;
Li-Gao, Ruifang ;
Ahluwalia, Tarunveer S. ;
Kreiner, Eskil ;
Rueedi, Rico ;
Lyytikainen, Leo-Pekka ;
Cousminer, Diana L. ;
Wu, Ying ;
Thiering, Elisabeth ;
Wang, Carol A. ;
Have, Christian T. ;
Hottenga, Jouke-Jan ;
Vilor-Tejedor, Natalia ;
Joshi, Peter K. ;
Boh, Eileen Tai Hui ;
Ntalla, Ioanna ;
Pitkanen, Niina ;
Mahajan, Anubha ;
van Leeuwen, Elisabeth M. ;
Joro, Raimo ;
Lagou, Vasiliki ;
Nodzenski, Michael ;
Diver, Louise A. ;
Zondervan, Krina T. ;
Bustamante, Mariona ;
Marques-Vidal, Pedro ;
Mercader, Josep M. ;
Bennett, Amanda J. ;
Rahmioglu, Nilufer ;
Nyholt, Dale R. ;
Ma, Ronald C. W. ;
Tam, Claudia H. T. ;
Tam, Wing Hung ;
Ganesh, Santhi K. ;
van Rooij, Frank J. A. ;
Jones, Samuel E. ;
Loh, Po-Ru ;
Ruth, Katherine S. ;
Tuke, Marcus A. .
NATURE, 2016, 538 (7624) :248-+
[9]   Genome-wide association study of primary sclerosing cholangitis identifies new risk loci and quantifies the genetic relationship with inflammatory bowel disease [J].
Ji, Sun-Gou ;
Juran, Brian D. ;
Mucha, Soeren ;
Folseraas, Trine ;
Jostins, Luke ;
Melum, Espen ;
Kumasaka, Natsuhiko ;
Atkinson, Elizabeth J. ;
Schlicht, Erik M. ;
Liu, Jimmy Z. ;
Shah, Tejas ;
Gutierrez-Achury, Javier ;
Boberg, Kirsten M. ;
Bergquist, Annika ;
Vermeire, Severine ;
Eksteen, Bertus ;
Durie, Peter R. ;
Farkkila, Martti ;
Mueller, Tobias ;
Schramm, Christoph ;
Sterneck, Martina ;
Weismueller, Tobias J. ;
Gotthardt, Daniel N. ;
Ellinghaus, David ;
Braun, Felix ;
Teufel, Andreas ;
Laudes, Mattias ;
Lieb, Wolfgang ;
Jacobs, Gunnar ;
Beuers, Ulrich ;
Weersma, Rinse K. ;
Wijmenga, Cisca ;
Marschall, Hanns-Ulrich ;
Milkiewicz, Piotr ;
Pares, Albert ;
Kontula, Kimmo ;
Chazouilleres, Olivier ;
Invernizzi, Pietro ;
Goode, Elizabeth ;
Spiess, Kelly ;
Moore, Carmel ;
Sambrook, Jennifer ;
Ouwehand, Willem H. ;
Roberts, David J. ;
Danesh, John ;
Floreani, Annarosa ;
Gulamhusein, Aliya F. ;
Eaton, John E. ;
Schreiber, Stefan ;
Coltescu, Catalina .
NATURE GENETICS, 2017, 49 (02) :269-273
[10]   Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants [J].
Jin, Ying ;
Andersen, Genevieve ;
Yorgov, Daniel ;
Ferrara, Tracey M. ;
Ben, Songtao ;
Brownson, Kelly M. ;
Holland, Paulene J. ;
Birlea, Stanca A. ;
Siebert, Janet ;
Hartmann, Anke ;
Lienert, Anne ;
van Geel, Nanja ;
Lambert, Jo ;
Luiten, Rosalie M. ;
Wolkerstorfer, Albert ;
van der Veen, J. P. Wietze ;
Bennett, Dorothy C. ;
Taieb, Alain ;
Ezzedine, Khaled ;
Kemp, E. Helen ;
Gawkrodger, David J. ;
Weetman, Anthony P. ;
Koks, Sulev ;
Prans, Ele ;
Kingo, Kulli ;
Karelson, Maire ;
Wallace, Margaret R. ;
McCormack, Wayne T. ;
Overbeck, Andreas ;
Moretti, Silvia ;
Colucci, Roberta ;
Picardo, Mauro ;
Silverberg, Nanette B. ;
Olsson, Mats ;
Valle, Yan ;
Korobko, Igor ;
Boehm, Markus ;
Lim, Henry W. ;
Hamzavi, Iltefat ;
Zhou, Li ;
Mi, Qing-Sheng ;
Fain, Pamela R. ;
Santorico, Stephanie A. ;
Spritz, Richard A. .
NATURE GENETICS, 2016, 48 (11) :1418-1424