Partitioning heritability by functional annotation using genome-wide association summary statistics

被引:1523
作者
Finucane, Hilary K. [1 ,2 ]
Bulik-Sullivan, Brendan [3 ,4 ,5 ]
Gusev, Alexander [2 ]
Trynka, Gosia [6 ,7 ,8 ,9 ,10 ]
Reshef, Yakir [11 ]
Loh, Po-Ru [2 ]
Anttila, Verneri [3 ,4 ,5 ,9 ]
Xu, Han [12 ,13 ]
Zang, Chongzhi [12 ,13 ]
Farh, Kyle [3 ,4 ,14 ]
Ripke, Stephan [3 ,4 ,5 ]
Day, Felix R. [15 ]
Purcell, Shaun [6 ,7 ,16 ]
Stahl, Eli [16 ]
Lindstrom, Sara [2 ]
Perry, John R. B. [15 ]
Okada, Yukinori [17 ,18 ]
Raychaudhuri, Soumya [6 ,7 ,8 ,9 ,19 ]
Daly, Mark J. [3 ,4 ,5 ,9 ]
Patterson, Nick [9 ]
Neale, Benjamin M. [3 ,4 ,5 ,9 ]
Price, Alkes L. [2 ,9 ]
机构
[1] MIT, Dept Math, Cambridge, MA 02139 USA
[2] Harvard Univ, TH Chan Sch Publ Hlth, Dept Epidemiol, Boston, MA 02115 USA
[3] Massachusetts Gen Hosp, Analyt & Translat Genet Unit, Boston, MA 02114 USA
[4] Harvard Univ, Sch Med, Boston, MA USA
[5] Broad Inst MIT & Harvard, Stanley Ctr Psychiat Res, Cambridge, MA USA
[6] Harvard Univ, Sch Med, Div Genet, Brigham & Womens Hosp, Boston, MA USA
[7] Harvard Univ, Sch Med, Div Rheumatol, Brigham & Womens Hosp, Boston, MA USA
[8] Partners Ctr Personalized Genet Med, Boston, MA USA
[9] Broad Inst MIT & Harvard, Program Med & Populat Genet, Cambridge, MA USA
[10] Wellcome Trust Sanger Inst, Cambridge, England
[11] Harvard Univ, Dept Comp Sci, Cambridge, MA 02138 USA
[12] Dana Farber Canc Inst, Dept Biostat & Computat Biol, Boston, MA 02115 USA
[13] Harvard Univ, TH Chan Sch Publ Hlth, Boston, MA 02115 USA
[14] Broad Inst MIT & Harvard, Epigen Program, Cambridge, MA USA
[15] Univ Cambridge, MRC, Epidemiol Unit, Sch Clin Med,Inst Metab Sci, Cambridge, England
[16] Mt Sinai Sch Med, Dept Psychiat, New York, NY USA
[17] Tokyo Med & Dent Univ, Grad Sch Med & Dent Sci, Dept Human Genet & Dis Divers, Tokyo, Japan
[18] RIKEN, Ctr Integrat Med Sci, Lab Stat Anal, Yokohama, Kanagawa, Japan
[19] Univ Manchester, Fac Med & Human Sci, Manchester, Lancs, England
基金
英国惠康基金; 美国国家卫生研究院;
关键词
GENETIC ARCHITECTURE; CELL-TYPES; VARIANTS; LOCI; SUSCEPTIBILITY; PROPORTION; ENHANCERS;
D O I
10.1038/ng.3404
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Recent work has demonstrated that some functional categories of the genome contribute disproportionately to the heritability of complex diseases. Here we analyze a broad set of functional elements, including cell type-specific elements, to estimate their polygenic contributions to heritability in genome-wide association studies (GWAS) of 17 complex diseases and traits with an average sample size of 73,599. To enable this analysis, we introduce a new method, stratified LD score regression, for partitioning heritability from GWAS summary statistics while accounting for linked markers. This new method is computationally tractable at very large sample sizes and leverages genome-wide information. Our findings include a large enrichment of heritability in conserved regions across many traits, a very large immunological disease-specific enrichment of heritability in FANTOM5 enhancers and many cell type-specific enrichments, including significant enrichment of central nervous system cell types in the heritability of body mass index, age at menarche, educational attainment and smoking behavior.
引用
收藏
页码:1228 / +
页数:11
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