LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

被引:3286
作者
Bulik-Sullivan, Brendan K. [1 ,2 ,3 ,4 ]
Loh, Po-Ru [1 ,5 ]
Finucane, Hilary K. [5 ,6 ]
Ripke, Stephan [2 ,3 ,4 ]
Yang, Jian [7 ]
Patterson, Nick [1 ]
Daly, Mark J. [1 ,2 ,3 ,4 ]
Price, Alkes L. [1 ,5 ,8 ]
Neale, Benjamin M. [1 ,2 ,3 ,4 ]
机构
[1] Broad Inst MIT & Harvard, Program Med & Populat Genet, Cambridge, MA 02142 USA
[2] Massachusetts Gen Hosp, Dept Med, Analyt & Translat Genet Unit, Boston, MA 02114 USA
[3] Harvard Univ, Sch Med, Boston, MA USA
[4] Broad Inst MIT & Harvard, Stanley Ctr Psychiat Res, Cambridge, MA USA
[5] Harvard TH Chan Sch Publ Hlth, Dept Epidemiol, Boston, MA USA
[6] MIT, Dept Math, Cambridge, MA 02139 USA
[7] Univ Queensland, Queensland Brain Inst, Brisbane, Qld, Australia
[8] Harvard TH Chan Sch Publ Hlth, Dept Biostat, Boston, MA USA
基金
美国国家卫生研究院; 美国国家科学基金会;
关键词
GENETIC ARCHITECTURE; IDENTIFIES; 13; METAANALYSIS; LOCI; LINKAGE; TRAITS; MODELS; REGIONS; RISK;
D O I
10.1038/ng.3211
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Both polygenicity (many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield an inflated distribution of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from a true polygenic signal and bias. We have developed an approach, LD Score regression, that quantifies the contribution of each by examining the relationship between test statistics and linkage disequilibrium (LD). The LD Score regression intercept can be used to estimate a more powerful and accurate correction factor than genomic control. We find strong evidence that polygenicity accounts for the majority of the inflation in test statistics in many GWAS of large sample size.
引用
收藏
页码:291 / +
页数:7
相关论文
共 43 条
[1]   Hundreds of variants clustered in genomic loci and biological pathways affect human height [J].
Allen, Hana Lango ;
Estrada, Karol ;
Lettre, Guillaume ;
Berndt, Sonja I. ;
Weedon, Michael N. ;
Rivadeneira, Fernando ;
Willer, Cristen J. ;
Jackson, Anne U. ;
Vedantam, Sailaja ;
Raychaudhuri, Soumya ;
Ferreira, Teresa ;
Wood, Andrew R. ;
Weyant, Robert J. ;
Segre, Ayellet V. ;
Speliotes, Elizabeth K. ;
Wheeler, Eleanor ;
Soranzo, Nicole ;
Park, Ju-Hyun ;
Yang, Jian ;
Gudbjartsson, Daniel ;
Heard-Costa, Nancy L. ;
Randall, Joshua C. ;
Qi, Lu ;
Smith, Albert Vernon ;
Maegi, Reedik ;
Pastinen, Tomi ;
Liang, Liming ;
Heid, Iris M. ;
Luan, Jian'an ;
Thorleifsson, Gudmar ;
Winkler, Thomas W. ;
Goddard, Michael E. ;
Lo, Ken Sin ;
Palmer, Cameron ;
Workalemahu, Tsegaselassie ;
Aulchenko, Yurii S. ;
Johansson, Asa ;
Zillikens, M. Carola ;
Feitosa, Mary F. ;
Esko, Tonu ;
Johnson, Toby ;
Ketkar, Shamika ;
Kraft, Peter ;
Mangino, Massimo ;
Prokopenko, Inga ;
Absher, Devin ;
Albrecht, Eva ;
Ernst, Florian ;
Glazer, Nicole L. ;
Hayward, Caroline .
NATURE, 2010, 467 (7317) :832-838
[2]   An integrated map of genetic variation from 1,092 human genomes [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. ;
Schmidt, Jeanette P. ;
Sherry, Stephen T. ;
Wang, Jun ;
Wilson, Richard K. ;
Gibbs, Richard A. ;
Dinh, Huyen ;
Kovar, Christie ;
Lee, Sandra ;
Lewis, Lora ;
Muzny, Donna ;
Reid, Jeff ;
Wang, Min ;
Wang, Jun ;
Fang, Xiaodong ;
Guo, Xiaosen ;
Jian, Min ;
Jiang, Hui ;
Jin, Xin ;
Li, Guoqing ;
Li, Jingxiang ;
Li, Yingrui ;
Li, Zhuo ;
Liu, Xiao ;
Lu, Yao ;
Ma, Xuedi ;
Su, Zhe ;
Tai, Shuaishuai ;
Tang, Meifang .
NATURE, 2012, 491 (7422) :56-65
[3]   Integrating common and rare genetic variation in diverse human populations [J].
Altshuler, David M. ;
Gibbs, Richard A. ;
Peltonen, Leena ;
Dermitzakis, Emmanouil ;
Schaffner, Stephen F. ;
Yu, Fuli ;
Bonnen, Penelope E. ;
de Bakker, Paul I. W. ;
Deloukas, Panos ;
Gabriel, Stacey B. ;
Gwilliam, Rhian ;
Hunt, Sarah ;
Inouye, Michael ;
Jia, Xiaoming ;
Palotie, Aarno ;
Parkin, Melissa ;
Whittaker, Pamela ;
Chang, Kyle ;
Hawes, Alicia ;
Lewis, Lora R. ;
Ren, Yanru ;
Wheeler, David ;
Muzny, Donna Marie ;
Barnes, Chris ;
Darvishi, Katayoon ;
Hurles, Matthew ;
Korn, Joshua M. ;
Kristiansson, Kati ;
Lee, Charles ;
McCarroll, Steven A. ;
Nemesh, James ;
Keinan, Alon ;
Montgomery, Stephen B. ;
Pollack, Samuela ;
Price, Alkes L. ;
Soranzo, Nicole ;
Gonzaga-Jauregui, Claudia ;
Anttila, Verneri ;
Brodeur, Wendy ;
Daly, Mark J. ;
Leslie, Stephen ;
McVean, Gil ;
Moutsianas, Loukas ;
Nguyen, Huy ;
Zhang, Qingrun ;
Ghori, Mohammed J. R. ;
McGinnis, Ralph ;
McLaren, William ;
Takeuchi, Fumihiko ;
Grossman, Sharon R. .
NATURE, 2010, 467 (7311) :52-58
[4]   Genetic signatures of strong recent positive selection at the lactase gene [J].
Bersaglieri, T ;
Sabeti, PC ;
Patterson, N ;
Vanderploeg, T ;
Schaffner, SF ;
Drake, JA ;
Rhodes, M ;
Reich, DE ;
Hirschhorn, JN .
AMERICAN JOURNAL OF HUMAN GENETICS, 2004, 74 (06) :1111-1120
[5]   Genomic control for association studies [J].
Devlin, B ;
Roeder, K .
BIOMETRICS, 1999, 55 (04) :997-1004
[6]   Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk [J].
Ehret, Georg B. ;
Munroe, Patricia B. ;
Rice, Kenneth M. ;
Bochud, Murielle ;
Johnson, Andrew D. ;
Chasman, Daniel I. ;
Smith, Albert V. ;
Tobin, Martin D. ;
Verwoert, Germaine C. ;
Hwang, Shih-Jen ;
Pihur, Vasyl ;
Vollenweider, Peter ;
O'Reilly, Paul F. ;
Amin, Najaf ;
Bragg-Gresham, Jennifer L. ;
Teumer, Alexander ;
Glazer, Nicole L. ;
Launer, Lenore ;
Zhao, Jing Hua ;
Aulchenko, Yurii ;
Heath, Simon ;
Sober, Siim ;
Parsa, Afshin ;
Luan, Jian'an ;
Arora, Pankaj ;
Dehghan, Abbas ;
Zhang, Feng ;
Lucas, Gavin ;
Hicks, Andrew A. ;
Jackson, Anne U. ;
Peden, John F. ;
Tanaka, Toshiko ;
Wild, Sarah H. ;
Rudan, Igor ;
Igl, Wilmar ;
Milaneschi, Yuri ;
Parker, Alex N. ;
Fava, Cristiano ;
Chambers, John C. ;
Fox, Ervin R. ;
Kumari, Meena ;
Go, Min Jin ;
van der Harst, Pim ;
Kao, Wen Hong Linda ;
Sjogren, Marketa ;
Vinay, D. G. ;
Alexander, Myriam ;
Tabara, Yasuharu ;
Shaw-Hawkins, Sue ;
Whincup, Peter H. .
NATURE, 2011, 478 (7367) :103-109
[7]   Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture [J].
Estrada, Karol ;
Styrkarsdottir, Unnur ;
Evangelou, Evangelos ;
Hsu, Yi-Hsiang ;
Duncan, Emma L. ;
Ntzani, Evangelia E. ;
Oei, Ling ;
Albagha, Omar M. E. ;
Amin, Najaf ;
Kemp, John P. ;
Koller, Daniel L. ;
Li, Guo ;
Liu, Ching-Ti ;
Minster, Ryan L. ;
Moayyeri, Alireza ;
Vandenput, Liesbeth ;
Willner, Dana ;
Xiao, Su-Mei ;
Yerges-Armstrong, Laura M. ;
Zheng, Hou-Feng ;
Alonso, Nerea ;
Eriksson, Joel ;
Kammerer, Candace M. ;
Kaptoge, Stephen K. ;
Leo, Paul J. ;
Thorleifsson, Gudmar ;
Wilson, Scott G. ;
Wilson, James F. ;
Aalto, Ville ;
Alen, Markku ;
Aragaki, Aaron K. ;
Aspelund, Thor ;
Center, Jacqueline R. ;
Dailiana, Zoe ;
Duggan, David J. ;
Garcia, Melissa ;
Garcia-Giralt, Natalia ;
Giroux, Sylvie ;
Hallmans, Goran ;
Hocking, Lynne J. ;
Husted, Lise Bjerre ;
Jameson, Karen A. ;
Khusainova, Rita ;
Kim, Ghi Su ;
Kooperberg, Charles ;
Koromila, Theodora ;
Kruk, Marcin ;
Laaksonen, Marika ;
Lacroix, Andrea Z. ;
Lee, Seung Hun .
NATURE GENETICS, 2012, 44 (05) :491-+
[8]   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
[9]   Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution [J].
Heid, Iris M. ;
Jackson, Anne U. ;
Randall, Joshua C. ;
Winkler, Thomas W. ;
Qi, Lu ;
Steinthorsdottir, Valgerdur ;
Thorleifsson, Gudmar ;
Zillikens, M. Carola ;
Speliotes, Elizabeth K. ;
Maegi, Reedik ;
Workalemahu, Tsegaselassie ;
White, Charles C. ;
Bouatia-Naji, Nabila ;
Harris, Tamara B. ;
Berndt, Sonja I. ;
Ingelsson, Erik ;
Willer, Cristen J. ;
Weedon, Michael N. ;
Luan, Jianan ;
Vedantam, Sailaja ;
Esko, Tonu ;
Kilpelaeinen, Tuomas O. ;
Kutalik, Zoltan ;
Li, Shengxu ;
Monda, Keri L. ;
Dixon, Anna L. ;
Holmes, Christopher C. ;
Kaplan, Lee M. ;
Liang, Liming ;
Min, Josine L. ;
Moffatt, Miriam F. ;
Molony, Cliona ;
Nicholson, George ;
Schadt, Eric E. ;
Zondervan, Krina T. ;
Feitosa, Mary F. ;
Ferreira, Teresa ;
Allen, Hana Lango ;
Weyant, Robert J. ;
Wheeler, Eleanor ;
Wood, Andrew R. ;
Estrada, Karol ;
Goddard, Michael E. ;
Lettre, Guillaume ;
Mangino, Massimo ;
Nyholt, Dale R. ;
Purcell, Shaun ;
Smith, Albert Vernon ;
Visscher, Peter M. ;
Yang, Jian .
NATURE GENETICS, 2010, 42 (11) :949-U160
[10]   The Genome-wide Patterns of Variation Expose Significant Substructure in a Founder Population [J].
Jakkula, Eveliina ;
Rehnstroem, Karola ;
Varilo, Teppo ;
Pietilaeinen, Olli P. H. ;
Paunio, Tiina ;
Pedersen, Nancy L. ;
deFaire, Ulf ;
Jaervelin, Marjo-Riitta ;
Saharinen, Juha ;
Freimer, Nelson ;
Ripatti, Samuli ;
Purcell, Shaun ;
Collins, Andrew ;
Daly, Mark J. ;
Palotie, Aarno ;
Peltonen, Leena .
AMERICAN JOURNAL OF HUMAN GENETICS, 2008, 83 (06) :787-794