Graham SE, Clarke SL, Wu K-HH, Kanoni S, Zajac GJM, Ramdas S, Surakka I, Ntalla I, Vedantam S, Winkler TW, et al. The power of genetic diversity in genome-wide association studies of lipids. Nature. 2021;600:675–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Conti DV, Darst BF, Moss LC, Saunders EJ, Sheng X, Chou A, Schumacher FR, Olama AAA, Benlloch S, Dadaev T, et al. Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction. Nat Genet. 2021;53:65–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Giri A, Hellwege JN, Keaton JM, Park J, Qiu C, Warren HR, Torstenson ES, Kovesdy CP, Sun YV, Wilson OD, et al. Trans-ethnic association study of blood pressure determinants in over 750,000 individuals. Nat Genet. 2019;51:51–62.
Article
CAS
PubMed
Google Scholar
Kato N, Loh M, Takeuchi F, Verweij N, Wang X, Zhang WH, Kelly TN, Saleheen D, Lehne B, Leach IM, et al. Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation. Nat Genet. 2015;47:1282–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Spracklen CN, Horikoshi M, Kim YJ, Lin K, Bragg F, Moon S, Suzuki K, Tam CHT, Tabara Y, Kwak S-H, et al. Identification of type 2 diabetes loci in 433,540 East Asian individuals. Nature. 2020;582:240–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vujkovic M, Keaton JM, Lynch JA, Miller DR, Zhou J, Tcheandjieu C, Huffman JE, Assimes TL, Lorenz K, Zhu X, et al. Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis. Nat Genet. 2020;52:680–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sun S, Zhu J, Zhou X. Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies. Nat Methods. 2020;17:193–200.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lam M, Chen C-Y, Li Z, Martin AR, Bryois J, Ma X, Gaspar H, Ikeda M, Benyamin B, Brown BC, et al. Comparative genetic architectures of schizophrenia in East Asian and European populations. Nat Genet. 2019;51:1670–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Visscher PM, Wray NR, Zhang Q, Sklar P, McCarthy MI, Brown MA, Yang J. 10 Years of GWAS discovery: biology, function, and translation. Am J Hum Genet. 2017;101:5–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tam V, Patel N, Turcotte M, Bossé Y, Paré G, Meyre D. Benefits and limitations of genome-wide association studies. Nat Rev Genet. 2019;20:467–84.
Article
CAS
PubMed
Google Scholar
Wojcik GL, Graff M, Nishimura KK, Tao R, Haessler J, Gignoux CR, Highland HM, Patel YM, Sorokin EP, Avery CL, et al. Genetic analyses of diverse populations improves discovery for complex traits. Nature. 2019;570:514–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci. 2009;106:9362–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boyle EA, Li YI, Pritchard JK. An expanded view of complex traits: from polygenic to omnigenic. Cell. 2017;169:1177–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gurdasani D, Barroso I, Zeggini E, Sandhu MS. Genomics of disease risk in globally diverse populations. Nat Rev Genet. 2019;20:520–35.
Article
CAS
PubMed
Google Scholar
Chen J, Spracklen CN, Marenne G, Varshney A, Corbin LJ, Ja Luan, Willems SM, Wu Y, Zhang X, Horikoshi M, et al. The trans-ancestral genomic architecture of glycemic traits. Nat Genet. 2021;53:840–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Breen G, Li QQ, Roth BL, O’Donnell P, Didriksen M, Dolmetsch R, O’Reilly PF, Gaspar HA, Manji H, Huebel C, et al. Translating genome-wide association findings into new therapeutics for psychiatry. Nat Neurosci. 2016;19:1392–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carlson CS, Matise TC, North KE, Haiman CA, Fesinmeyer MD, Buyske S, Schumacher FR, Peters U, Franceschini N, Ritchie MD, et al. Generalization and dilution of association results from European GWAS in populations of non-European ancestry: the PAGE study. PLoS Biol. 2013;11:e1001661.
Article
CAS
PubMed
PubMed Central
Google Scholar
Waters KM, Stram DO, Hassanein MT, Le Marchand L, Wilkens LR, Maskarinec G, Monroe KR, Kolonel LN, Altshuler D, Henderson BE, Haiman CA. Consistent association of type 2 diabetes risk variants found in europeans in diverse racial and ethnic groups. PLoS Genet. 2010;6:e1001078.
Article
PubMed
PubMed Central
Google Scholar
Marigorta UM, Navarro A. High trans-ethnic replicability of GWAS results implies common causal variants. PLoS Genet. 2013;9:e1003566.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kraft P, Zeggini E, Ioannidis JP. Replication in genome-wide association studies. Stat sci. 2009;24:561.
Article
PubMed
PubMed Central
Google Scholar
Li Y, Lan L, Wang Y, Yang C, Tang W, Cui G, Luo S, Cheng Y, Liu Y, Liu J, Jin Y. Extremely cold and hot temperatures increase the risk of diabetes mortality in metropolitan areas of two Chinese cities. Environ Res. 2014;134:91–7.
Article
CAS
PubMed
Google Scholar
Liu JZ, van Sommeren S, Huang H, Ng SC, Alberts R, Takahashi A, Ripke S, Lee JC, Jostins L, Shah T. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat Genet. 2015;47:979–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ikeda M, Takahashi A, Kamatani Y, Okahisa Y, Kunugi H, Mori N, Sasaki T, Ohmori T, Okamoto Y, Kawasaki H. A genome-wide association study identifies two novel susceptibility loci and trans population polygenicity associated with bipolar disorder. Mol Psychiatry. 2018;23:639–47.
Article
CAS
PubMed
Google Scholar
Bigdeli TB, Ripke S, Peterson RE, Trzaskowski M, Bacanu S-A, Abdellaoui A, Andlauer T, Beekman A, Berger K, Blackwood DH. Genetic effects influencing risk for major depressive disorder in China and Europe. Transl Psychiatry. 2017;7:e1074–e1074.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guo J, Bakshi A, Wang Y, Jiang L, Yengo L, Goddard ME, Visscher PM, Yang J. Quantifying genetic heterogeneity between continental populations for human height and body mass index. Sci Rep. 2021;11:1–9.
Google Scholar
Brown BC, Ye CJ, Price AL, Zaitlen N. Consortium AGENTD: transethnic genetic-correlation estimates from summary statistics. Am J Hum Genet. 2016;99:76–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Veturi Y, de Campos G, Yi N, Huang W, Vazquez AI, Kühnel B. Modeling heterogeneity in the genetic architecture of ethnically diverse groups using random effect interaction models. Genetics. 2019;211:1395–407.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lu H, Wang T, Zhang J, Zhang S, Huang S, Zeng P. Evaluating marginal genetic correlation of associated loci for complex diseases and traits between European and East Asian populations. Hum Genet. 2021;140:1285–97.
Article
CAS
PubMed
Google Scholar
Kim MS, Patel KP, Teng AK, Berens AJ, Lachance J. Genetic disease risks can be misestimated across global populations. Genome Biol. 2018;19:179.
Article
PubMed
PubMed Central
Google Scholar
Guo J, Wu Y, Zhu Z, Zheng Z, Trzaskowski M, Zeng J, Robinson MR, Visscher PM, Yang J. Global genetic differentiation of complex traits shaped by natural selection in humans. Nat Commun. 1865;2018:9.
Google Scholar
Robinson MR, Hemani G, Medina-Gomez C, Mezzavilla M, Esko- T, Shakhbazov K, Powell JE, Vinkhuyzen A, Berndt SI, Gustafsson S, et al. Population genetic differentiation of height and body mass index across Europe. Nat Genet. 2015;47:1357–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li YR, Keating BJ. Trans-ethnic genome-wide association studies: advantages and challenges of mapping in diverse populations. Genome Med. 2014;6:91.
Article
PubMed
PubMed Central
Google Scholar
Zaitlen N, Paşaniuc B, Gur T, Ziv E, Halperin E. Leveraging genetic variability across populations for the identification of causal variants. Am J Hum Genet. 2010;86:23–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Morris AP. Transethnic meta-analysis of genomewide association studies. Genet Epidemiol. 2011;35:809–22.
Article
PubMed
PubMed Central
Google Scholar
Fu J, Festen EAM, Wijmenga C. Multi-ethnic studies in complex traits. Hum Mol Genet. 2011;20:R206-13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Coram MA, Fang H, Candille SI, Assimes TL, Tang H. Leveraging multi-ethnic evidence for risk assessment of quantitative traits in minority populations. Am J Hum Genet. 2017;101:218–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Coram MA, Candille SI, Duan Q, Chan KHK, Li Y, Kooperberg C, Reiner AP, Tang H. Leveraging multi-ethnic evidence for mapping complex traits in minority populations: an empirical Bayes approach. Am J Hum Genet. 2015;96:740–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Spracklen CN, Chen P, Kim YJ, Wang X, Cai H, Li S, Long J, Wu Y, Wang YX, Takeuchi F. Association analyses of East Asian individuals and trans-ancestry analyses with European individuals reveal new loci associated with cholesterol and triglyceride levels. Hum Mol Genet. 2017;26:1770–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rosenberg NA, Huang L, Jewett EM, Szpiech ZA, Jankovic I, Boehnke M. Genome-wide association studies in diverse populations. Nat Rev Genet. 2010;11:356–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bustamante CD, Burchard EG, De la Vega FM. Genomics for the world. Nature. 2011;475:163–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Teo Y-Y, Small KS, Kwiatkowski DP. Methodological challenges of genome-wide association analysis in Africa. Nat Rev Genet. 2010;11:149–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Galinsky KJ, Reshef YA, Finucane HK, Loh P-R, Zaitlen N, Patterson NJ, Brown BC, Price AL. Estimating cross-population genetic correlations of causal effect sizes. Genet Epidemiol. 2019;43:180–8.
Article
PubMed
Google Scholar
Ongen H, Brown AA, Delaneau O, Panousis NI, Nica AC, Dermitzakis ET, Consortium GT. Estimating the causal tissues for complex traits and diseases. Nat Genet. 2017;49:1676–83.
Article
CAS
PubMed
Google Scholar
Barfield R, Shen J, Just AC, Vokonas PS, Schwartz J, Baccarelli AA, VanderWeele TJ, Lin X. Testing for the indirect effect under the null for genome-wide mediation analyses. Genet Epidemiol. 2017;41:824–33.
Article
PubMed
PubMed Central
Google Scholar
Zeng P, Shao Z, Zhou X. Statistical methods for mediation analysis in the era of high-throughput genomics: current successes and future challenges. Comput Struct Biotechnol J. 2021;19:3209–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shao Z, Wang T, Zhang M, Jiang Z, Huang S, Zeng P. IUSMMT: survival mediation analysis of gene expression with multiple DNA methylation exposures and its application to cancers of TCGA. PLoS Comput Biol. 2021;17:e1009250.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dai JY, Stanford JL, LeBlanc M. A multiple-testing procedure for high-dimensional mediation hypotheses. J Am Stat Assoc. 2022;117:198–213. https://doi.org/10.1080/01621459.2020.1765785.
Article
CAS
PubMed
Google Scholar
Eicher JD, Landowski C, Stackhouse B, Sloan A, Chen W, Jensen N, Lien J-P, Leslie R, Johnson AD. GRASP v2. 0: an update on the genome-wide repository of associations between SNPs and phenotypes. Nucleic Acids Res. 2015;43:D799–804.
Article
CAS
PubMed
Google Scholar
Li MJ, Liu Z, Wang P, Wong MP, Nelson MR, Kocher J-PA, Yeager M, Sham PC, Chanock SJ, Xia Z, Wang J. GWASdb: v2 an update database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res. 2016;44:D869–76.
Article
CAS
PubMed
Google Scholar
McMahon A, Malangone C, Suveges D, Sollis E, Cunningham F, Riat HS, MacArthur JAL, Hayhurst J, Morales J, Guillen JA, et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 2019;47:D1005–12.
Article
PubMed
Google Scholar
Wang J, Huang D, Zhou Y, Yao H, Liu H, Zhai S, Wu C, Zheng Z, Zhao K, Wang Z, et al. CAUSALdb: a database for disease/trait causal variants identified using summary statistics of genome-wide association studies. Nucleic Acids Res. 2019;48:D807–16.
PubMed Central
Google Scholar
Shao Z, Wang T, Qiao J, Zhang Y, Huang S, Zeng P. A comprehensive comparison of multilocus association methods with summary statistics in genome-wide association studies. BMC Bioinformatics. 2022;23:359.
Article
PubMed
PubMed Central
Google Scholar
de Leeuw CA, Mooij JM, Heskes T, Posthuma D. MAGMA: generalized gene-set analysis of GWAS data. PLoS Comput Biol. 2015;11:e1004219.
Article
PubMed
PubMed Central
Google Scholar
Lu H, Qiao J, Shao Z, Wang T, Huang S, Zeng P. A comprehensive gene-centric pleiotropic association analysis for 14 psychiatric disorders with GWAS summary statistics. BMC Med. 2021;19:314.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang T, Lu H, Zeng P. Identifying pleiotropic genes for complex phenotypes with summary statistics from a perspective of composite null hypothesis testing. Brief Bioinform. 2022;23:bbab389.
Article
PubMed
Google Scholar
Langaas M, Lindqvist BH, Ferkingstad E. Estimating the proportion of true null hypotheses, with application to DNA microarray data. J R Stat Soc Ser B. 2005;67:555–72.
Article
Google Scholar
Jin J, Cai TT. Estimating the null and the proportion of nonnull effects in large-scale multiple comparisons. J Am Stat Assoc. 2007;102:495–506.
Article
CAS
Google Scholar
Efron B. Large-scale simultaneous hypothesis testing. J Am Stat Assoc. 2004;99:96–104.
Article
Google Scholar
Imai K, Keele L, Yamamoto T. Identification, inference and sensitivity analysis for causal mediation effects. Stat Sci. 2010;25:51–71.
Article
Google Scholar
VanderWeele T. Explanation in causal inference methods for mediation and interaction. Oxford: Oxford University Press; 2015.
Google Scholar
Lin D-Y, Sullivan PF. Meta-analysis of genome-wide association studies with overlapping subjects. Am J Hum Genet. 2009;85:862–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zeng P, Hao X, Zhou X. Pleiotropic mapping and annotation selection in genome-wide association studies with penalized Gaussian mixture models. Bioinformatics. 2018;34:2797–807.
Article
CAS
PubMed
PubMed Central
Google Scholar
LeBlanc M, Zuber V, Thompson WK, Andreassen OA, Frigessi A, Andreassen BK, Psychiat GC. A correction for sample overlap in genome-wide association studies in a polygenic pleiotropy-informed framework. BMC Genomics. 2018;19:494.
Article
PubMed
PubMed Central
Google Scholar
Huang Y-T. Genome-wide analyses of sparse mediation effects under composite null hypotheses. Ann Appl Stat. 2019;13:60–84.
Article
Google Scholar
Liu Z, Shen J, Barfield R, Schwartz J, Baccarelli AA, Lin X. Large-scale hypothesis testing for causal mediation effects with applications in genome-wide epigenetic studies. J Am Stat Assoc. 2022;117:67–81. https://doi.org/10.1080/01621459.2021.1914634.
Article
CAS
PubMed
Google Scholar
Altshuler DM, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Donnelly P, Eichler EE, Flicek P, Gabriel SB, et al. A global reference for human genetic variation. Nature. 2015;526:68–74.
Article
CAS
Google Scholar
Liu JZ, McRae AF, Nyholt DR, Medland SE, Wray NR, Brown KM, Hayward NK, Montgomery GW, Visscher PM, Martin NG, Macgregor S. A versatile gene-based test for genome-wide association studies. Am J Hum Genet. 2010;87:139–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cardon LR, Palmer LJ. Population stratification and spurious allelic association. Lancet. 2003;361:598–604.
Article
PubMed
Google Scholar
Jiang Y, Epstein MP, Conneely KN. Assessing the impact of population stratification on association studies of rare variation. Hum Hered. 2013;76:28–35.
Article
PubMed
Google Scholar
van den Berg S, Vandenplas J, van Eeuwijk FA, Lopes MS, Veerkamp RF. Significance testing and genomic inflation factor using high-density genotypes or whole-genome sequence data. J Anim Breed Genet. 2019;136:418–29.
Article
PubMed
PubMed Central
Google Scholar
Zeng P, Zhao Y, Qian C, Zhang L, Zhang R, Gou J, Liu J, Liu L, Chen F. Statistical analysis for genome-wide association study. J Biomed Res. 2015;29:285–97.
PubMed
Google Scholar
Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010;20:110–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15:1034–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kryazhimskiy S, Plotkin JB. The population genetics of dN/dS. PLoS Genet. 2008;4:e1000304.
Article
PubMed
PubMed Central
Google Scholar
Shang L, Smith JA, Zhao W, Kho M, Turner ST, Mosley TH, Kardia SLR, Zhou X. Genetic architecture of gene expression in European and African Americans: an eQTL mapping study in GENOA. Am J Hum Genet. 2020;106:496–512.
Article
CAS
PubMed
PubMed Central
Google Scholar
Coram Marc A, Duan Q, Hoffmann Thomas J, Thornton T, Knowles Joshua W, Johnson Nicholas A, Ochs-Balcom Heather M, Donlon Timothy A, Martin Lisa W, Eaton Charles B, et al. Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations. Am J Hum Genet. 2013;92:904–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, et al. Patterns of cis regulatory variation in diverse human populations. PLoS Genet. 2012;8:e1002639.
Article
CAS
PubMed
PubMed Central
Google Scholar
Popejoy AB, Fullerton SM. Genomics is failing on diversity. Nature. 2016;538:161–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baye TM, Abebe T, Wilke RA. Genotype-environment interactions and their translational implications. Per Med. 2011;8:59–70.
Article
PubMed
PubMed Central
Google Scholar
Shi H, Gazal S, Kanai M, Koch EM, Schoech AP, Siewert KM, Kim SS, Luo Y, Amariuta T, Huang H, et al. Population-specific causal disease effect sizes in functionally important regions impacted by selection. Nat Commun. 2021;12:1098–1098.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wheeler E, Leong A, Liu CT, Hivert MF, Strawbridge RJ, Podmore C, Li M, Yao J, Sim X, Hong J, et al. Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: a transethnic genome-wide meta-analysis. PLoS Med. 2017;14:e1002383.
Article
PubMed
PubMed Central
Google Scholar
Dastani Z, Johnson T, Kronenberg F, Nelson CP, Assimes TL, März W, Richards JB, Consortium C, Consortium A. The shared allelic architecture of adiponectin levels and coronary artery disease. Atherosclerosis. 2013;229:145–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zeng P, Zhao Y, Liu J, Liu L, Zhang L, Wang T, Huang S, Chen F. Likelihood ratio tests in rare variant detection for continuous phenotypes. Ann Hum Genet. 2014;78:320–32.
Article
PubMed
Google Scholar
Zeng P, Zhou X. Non-parametric genetic prediction of complex traits with latent Dirichlet process regression models. Nat Commun. 2017;8:456.
Article
PubMed
PubMed Central
Google Scholar
Sun R, Hui S, Bader GD, Lin X, Kraft P. Powerful gene set analysis in GWAS with the generalized Berk-Jones statistic. PLoS Genet. 2019;15:e1007530.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sun R, Lin X. Genetic variant set-based tests using the generalized berk-jones statistic with application to a genome-wide association study of breast cancer. J Am Stat Assoc. 2020;115:1079–91.
Article
CAS
PubMed
Google Scholar
Wu MC, Lee S, Cai T, Li Y, Boehnke M, Lin X. Rare-variant association testing for sequencing data with the sequence Kernel association test. Am J Hum Genet. 2011;89:82–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zeng P, Dai J, Jin S, Zhou X. Aggregating multiple expression prediction models improves the power of transcriptome-wide association studies. Hum Mol Genet. 2021;30:939–51.
Article
CAS
PubMed
Google Scholar
Liu Y, Xie J. Cauchy combination test: a powerful test with analytic p-value calculation under arbitrary dependency structures. J Am Stat Assoc. 2020;115:393–402.
Article
CAS
PubMed
Google Scholar
Liu Y, Chen S, Li Z, Morrison AC, Boerwinkle E, Lin X. ACAT: a fast and powerful p value combination method for rare-variant analysis in sequencing studies. Am J Hum Genet. 2019;104:410–21.
Article
CAS
PubMed
PubMed Central
Google Scholar