Comment: A Human Genetics Perspective

References

• Bulik-Sullivan, B., Finucane, H.K., Anttila, V., Gusev, A., Day, F.R., Loh, P.R.; ReproGen Consortium; Psychiatric Genomics Consortium; Genetic Consortium for Anorexia Nervosa of the Wellcome Trust Case Control Consortium 3, Duncan, L., Perry, J.R., Patterson, N., Robinson, E.B., Daly, M.J., Price, A.L., and Neale, B.M. (2015), “An Atlas of Genetic Correlations Across Human Diseases and Traits,” Nature Genetics, 47, 1236–1241.
   PubMed Web of Science ®Google Scholar
• Chen, C.Y., Pollack, S., Hunter, D.J., Hirschhorn, J.N., Kraft, P., and Price, A.L. (2013a), “Improved Ancestry Inference Using Weights From External Reference Panels,” Bioinformatics, 29, 1399–1406.
   PubMed Web of Science ®Google Scholar
• Chen, Y.-H., Chatterjee, N., and Carroll, R.J. (2013b), “Using Shared Genetic Controls in Studies of Gene-environment Interactions,” Biometrika, 100, 319–338.
   PubMed Web of Science ®Google Scholar
• Farh, K.K., Marson, A., Zhu, J., Kleinewietfeld, M., Housley, W.J., Beik, S., Shoresh, N., Whitton, H., Ryan, R.J., Shishkin, A.A., Hatan, M., Carrasco-Alfonso, M.J., Mayer, D., Luckey, C.J., Patsopoulos, N.A., De Jager, P.L., Kuchroo, V.K., Epstein, C.B., Daly, M.J., Hafler, D.A., and Bernstein, B.E. (2015), “Genetic and Epigenetic Fine Mapping of Causal Autoimmune Disease Variants,” Nature, 518, 337–343.
   PubMed Web of Science ®Google Scholar
• Finucane, H.K., Bulik-Sullivan, B., Gusev, A., Trynka, G., Reshef, Y., Loh, P.R., Anttila, V., Xu, H., Zang, C., Farh, K., Ripke, S., Day, F.R.; ReproGen Consortium; Schizophrenia Working Group of the Psychiatric Genomics Consortium; RACI Consortium, Purcell, S., Stahl, E., Lindstrom, S., Perry, J.R., Okada, Y., Raychaudhuri, S., Daly, M.J., Patterson, N., Neale, B.M., and Price, A.L. (2015), “Partitioning Heritability by Functional Annotation Using Genome-wide Association Summary Statistics,” Nature Genetics, 47, 1228–1235.
   PubMed Web of Science ®Google Scholar
• Han, B., and Eskin, E. (2011), “Random-Effects Model Aimed at Discovering Associations in Meta-Analysis of Genome-wide Association Studies,” The American Journal of Human Genetics, 88, 586–598.
   PubMed Web of Science ®Google Scholar
• He, D., Han, B., and Eskin, E. (2013), “Hap-seq: An Optimal Algorithm for Haplotype Phasing With Imputation Using Sequencing Data,” Journal of Computational Biology, 20, 80–92.
   PubMed Web of Science ®Google Scholar
• Howie, B., Fuchsberger, C., Stephens, M., Marchini, J., and Abecasis, G.R. (2012), “Fast and Accurate Genotype Imputation in Genome-wide Association Studies Through Pre-phasing,” Nature Genetics, 44, 955–959.
   PubMed Web of Science ®Google Scholar
• Hubisz, M.J., and Pollard, K.S. (2014), “Exploring the Genesis and Functions of Human Accelerated Regions Sheds Light on Their Role in Human Evolution,” Current Opinion in Genetics & Development, 29, 15–21.
   PubMed Web of Science ®Google Scholar
• Kanehisa, M., and Goto, S. (2000), “KEGG: Kyoto Encyclopedia of Genes and Genomes,” Nucleic Acids Research, 28, 27–30.
   PubMed Web of Science ®Google Scholar
• Kellis, M., Wold, B., Snyder, M.P., Bernstein, B.E., Kundaje, A., Marinov, G.K., Ward, L.D., Birney, E., Crawford, G.E., Dekker, J., Dunham, I., Elnits, L.L., Farnham, P.J., Feingold, E.A., Gerstein, M., Giddings, M.C., Gilbert, D.M., Gingeras, T.R., Green, E.D., Guigo, R., Hubbard, T., Kent, J., Lieb, J.D., Myers, R.M., Pazin, M.J., Ren, B., Stamatoyannopoulos, J.A., Weng, Z., White, K.P., and Hardison, R.C. (2014), “Defining Functional DNA Elements in the Human Genome,” Proceedings of the National Academy of Science of United States of America, 111, 6131–6138.
   PubMed Web of Science ®Google Scholar
• Kichaev, G., Yang, W.Y., Lindstrom, S., Hormozdiari, F., Eskin, E., Price, A.L., Kraft, P., and Pasaniuc, B. (2014), “Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-mapping Studies,” PLoS Genetics, 10, e1004722.
   PubMed Web of Science ®Google Scholar
• Kircher, M., Witten, D.M., Jain, P., O’Roak, B.J., Cooper, G.M., and Shendure, J. (2014), “A General Framework for Estimating the Relative Pathogenicity of Human Genetic Variants,” Nature Genetics, 46, 310–315.
   PubMed Web of Science ®Google Scholar
• Lee, D., Bigdeli, T.B., Williamson, V.S., Vladimirov, V.I., Riley, B.P., Fanous, A.H., and Bacanu, S.A. (2015), “DISTMIX: Direct Imputation of Summary Statistics for Unmeasured SNPs From Mixed Ethnicity Cohorts,” Bioinformatics, 31, 3099–3104.
   PubMed Web of Science ®Google Scholar
• McVean, G. A., et al. (2012), “An Integrated Map of Genetic Variation From 1,092 Human Genomes,” Nature, 491, 56–65.
   PubMed Web of Science ®Google Scholar
• Mefford, J.A., and Witte, J.S. (2012), “The Covariate's Dilemma,” PLoS Genetics, 8, e1003096.
   Web of Science ®Google Scholar
• Park, D.S., Brown, B., Eng, C., Huntsman, S., Hu, D., Torgerson, D.G., Burchard, E.G., and Zaitlen, N. (2015), “Adapt-Mix: Learning Local Genetic Correlation Structure Improves Summary Statistics-Based Analyses,” Bioinformatics, 31, i181–i189.
   Google Scholar
• Pasaniuc, B., Zaitlen, N., Shi, H., Bhatia, G., Gusev, A., Pickrell, J., Hirschhorn, J., Strachan, D.P., Patterson, N., and Price, A.L. (2014), “Fast and Accurate Imputation of Summary Statistics Enhances Evidence of Functional Enrichment,” Bioinformatics, 30, 2906–2914.
   PubMed Web of Science ®Google Scholar
• Pickrell, J.K. (2014), “Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits,” American Journal of Human Genetics, 94, 559–573.
   PubMed Web of Science ®Google Scholar
• Pirinen, M., Donnelly, P., and Spencer, C.C. (2012), “Including Known Covariates Can Reduce Power to Detect Genetic Effects in Case-control Studies,” Nature Genetics, 44, 848–851.
   PubMed Web of Science ®Google Scholar
• Rose, S., and Laan, M.J. (2009), “Why Match? Investigating Matched Case-Control Study Designs With Causal Effect Estimation,” The International Journal of Biostatistics, 5, DOI: 10.2202/1557-4679.1127.
   PubMedGoogle Scholar
• Rothman, K.J., Greenland, S., and Lash, T.L. (2008), Modern Epidemiology (3rd ed.), Philadelphia, PA: Lippincott, Williams & Wilkins.
   Google Scholar
• Vilhjálmsson, B.J., Yang, J., Finucane, H.K., Gusev, A., Lindström, S., Ripke, S., Genovese, G., Loh, P.R., Bhatia, G., Do, R., Hayeck, T., Won, H.H.; Schizophrenia Working Group of the Psychiatric Genomics Consortium; Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) study, Kathiresan, S., Pato, M., Pato, C., Tamimi, R., Stahl, E., Zaitlen, N., Pasaniuc, B., Belbin, G., Kenny, E.E., Schierup, M.H., De Jager, P., Patsopoulos, N.A., McCarroll, S., Daly, M., Purcell, S., Chasman, D., Neale, B., Goddard, M., Visscher, P.M., Kraft, P., Patterson, N., Price, A.L., and Discovery Biology and Risk of Inherited Variants in Breast Cancer DRIVE Study (2015), “Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores,” The American Journal of Human Genetics, 97, 576–592.
   PubMed Web of Science ®Google Scholar
• Vitalis, R., Gautier, M., Dawson, K.J., and Beaumont, M.A. (2014), “Detecting and Measuring Selection From Gene Frequency Data,” Genetics, 196, 799–817.
   PubMed Web of Science ®Google Scholar
• Zaitlen, N., Lindstrom, S., Pasaniuc, B., Cornelis, M., Genovese, G., Pollack, S., Barton, A., Bickeböller, H., Bowden, D.W., Eyre, S., Freedman, B.I., Friedman, D.J., Field, J.K., Groop, L., Haugen, A., Heinrich, J., Henderson, B.E., Hicks, P.J., Hocking, L.J., Kolonel, L.N., Landi, M.T., Langefeld, C.D., Le Marchand, L., Meister, M., Morgan, A.W., Raji, O.Y., Risch, A., Rosenberger, A., Scherf, D., Steer, S., Walshaw, M.M., Waters, K.M., Wilson, A.G., Wordsworth, P., Zienolddiny, S., Tchetgen, E.T., Haiman, C., Hunter, D.J., Plenge, R.M., Worthington, J., Christiani, D.C., Schaumberg, D.A., Chasman, D.I., Altshuler, D., Voight, B., Kraft, P., Patterson, N., and Price, A.L. (2012a), “Informed Conditioning on Clinical Covariates Increases Power in Case-Control Association Studies,” PLoS Genetics, 8, e1003032.
   Google Scholar
• Zaitlen, N., Paşaniuc, B., Patterson, N., Pollack, S., Voight, B., Groop, L., Altshuler, D., Henderson, B.E., Kolonel, L.N., Le Marchand, L., Waters, K., Haiman, C.A., Stranger, B.E., Dermitzakis, E.T., Kraft, P., and Price, A.L. (2012b), “Analysis of Case-Control Association Studies With Known Risk Variants,” Bioinformatics, 28, 1729–1737.
   PubMed Web of Science ®Google Scholar