Park JH, Wacholder S, Gail MH, Peters U, Jacobs KB, Chanock SJ, et al. Estimation of effect size distribution from genome-wide association studies and implications for future discoveries. Nat Genet. 2010;42:570–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sullivan PF. The genetics of schizophrenia. PLoS Med. 2005;2:e212.
Article
PubMed
PubMed Central
CAS
Google Scholar
Woo HJ, Yu C, Kumar K, Reifman J. Large-scale interaction effects reveal missing heritability in schizophrenia, bipolar disorder and posttraumatic stress disorder. Transl Psychiatry. 2017;7:e1089.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen GB, Lee SH, Brion MJA, Montgomery GW, Wray NR, Radford-Smith GL, et al. Estimation and partitioning of (co)heritability of inflammatory bowel disease from GWAS and immunochip data. Hum Mol Genet. 2014;23:4710–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maher B. The case of the missing heritability. Nature. 2008;456:18–21.
Article
CAS
PubMed
Google Scholar
Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, et al. Finding the missing heritability of complex diseases. Nature. 2013;461:747–53.
Article
CAS
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
Purcell SM, Wray NR, Stone JL, Visscher PM, O’Donovan MC, Sullivan PF, et al. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature. 2009;460:748–52.
Article
CAS
PubMed
Google Scholar
Makowsky R, Pajewski NM, Klimentidis YC, Vazquez AI, Duarte CW, Allison DB, et al. Beyond missing heritability: prediction of complex traits. PLoS Genet. 2011;7:e1002051.
Article
CAS
PubMed
PubMed Central
Google Scholar
Abraham G, Havulinna AS, Bhalala OG, Byars SG, De Livera AM, Yetukuri L, et al. Genomic prediction of coronary heart disease. Eur Heart J. 2016;37:3267–78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wainschtein P, Jain DP, Yengo L, Zheng Z, Group TopmAW, Visscher PM. Recovery of trait heritability from whole genome sequence data. bioRxiv. 2019.
Itsara A, Cooper GM, Baker C, Girirajan S, Li J, Absher D, et al. Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet. 2008;84:148–61.
Article
CAS
Google Scholar
Sherman RM, Forman J, Antonescu V, Puiu D, Daya M, Rafaels N, et al. Assembly of a pan-genome from deep sequencing of 910 humans of African descent. Nat Genet. 2019;51:30-35.
Hunter DJ. Gene-environment interactions in human diseases. Nat Rev Genet. 2005;6:287–98.
Article
CAS
PubMed
Google Scholar
Zambelli-Weiner A, Ehrlich E, Stockton ML, Grant AV, Zhang S, Levett PN, et al. Evaluation of the CD14/-260 polymorphism and house dust endotoxin exposure in the Barbados Asthma Genetics Study. J Allergy Clin Immunol. 2005;115:1203–9.
Article
CAS
PubMed
Google Scholar
Simpson A, John SL, Jury F, Niven R, Woodcock A, Ollier WER, et al. Endotoxin exposure, CD14, and allergic disease. Am J Respir Crit Care Med. 2006;174:386–92.
Article
CAS
PubMed
Google Scholar
Ober C, Vercelli D. Gene-environment interactions in human disease: nuisance or opportunity? Trends Genet. 2011;27:107–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Aschard H. A perspective on interaction effects in genetic association studies. Genet Epidemiol. 2016;40:678–88.
Article
PubMed
PubMed Central
Google Scholar
Patel CJ, Kerr J, Thomas DC, Mukherjee B, Ritz B, Chatterjee N, et al. Opportunities and challenges for environmental exposure assessment in population-based studies. Cancer Epidemiol Biomarkers Prev. 2017;26:1370–80.
Article
PubMed
PubMed Central
Google Scholar
McAllister K, Mechanic LE, Amos C, Aschard H, Blair IA, Chatterjee N, et al. Current challenges and new opportunities for gene-environment interaction studies of complex diseases. Am J Epidemiol. 2017;186:753–61.
Article
PubMed
PubMed Central
Google Scholar
Hasin Y, Seldin M, Lusis A. Multi-omics approaches to disease. Genome Biol. 2017;18:83.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zitnik M, Nguyen F, Wang B, Leskovec J, Goldenberg A, Hoffman MM. Machine learning for integrating data in biology and medicine: principles, practice, and opportunities. Inf Fusion. 2019;50:71–91.
Falconer DS, Mackay TFC. Introduction to quantitative genetics. 4th ed. Pearson Education Limited: Harlow, Essex; 1996.
Google Scholar
Richardson K, Norgate S. The equal environments assumption of classical twin studies may not hold. Br J Educ Psychol. 2005;75:339–50.
Article
PubMed
Google Scholar
Polderman TJC, Benyamin B, De Leeuw CA, Sullivan PF, Van Bochoven A, Visscher PM, et al. Meta-analysis of the heritability of human traits based on fifty years of twin studies. Nat Genet. 2015;47:702–9.
Article
CAS
PubMed
Google Scholar
Feldman MW, Ramachandran S. Missing compared to what? Revisiting heritability, genes and culture. Philos Trans R Soc B. 2018;373:20170064.
Article
Google Scholar
Trerotola M, Relli V, Simeone P, Alberti S. Epigenetic inheritance and the missing heritability. Human Genomics. 2015;9:17.
Bourrat P, Lu Q. Dissolving the missing heritability problem. Philos Sci. 2017;84:1055–67.
Article
Google Scholar
Slatkin M. Epigenetic inheritance and the missing heritability problem. Genetics. 2009;182:845–50.
Article
PubMed
PubMed Central
Google Scholar
Lu Q, Bourrat P. The evolutionary gene and the extended evolutionary synthesis. Br J Philos Sci. 2018;69:775–800.
Article
Google Scholar
Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. Current understanding of the human microbiome. Nat Med. 2018;24:392–400.
Article
CAS
PubMed
PubMed Central
Google Scholar
Moran NA, Sloan DB. The hologenome concept: helpful or hollow? PLoS Biol. 2015;13:e1002311.
Article
PubMed
PubMed Central
CAS
Google Scholar
Douglas AE, Werren JH. Holes in the hologenome: why host-microbe symbioses are not holobionts. MBio. 2016;7:e02099–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rosenberg E, Zilber-Rosenberg I. The hologenome concept of evolution after 10 years. Microbiome. 2018;6:78.
Article
PubMed
PubMed Central
Google Scholar
Zilber-Rosenberg I, Rosenberg E. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev. 2008;32:723–35.
Article
CAS
PubMed
Google Scholar
Org E, Parks BW, Joo JWJ, Emert B, Schwartzman W, Kang EY, et al. Genetic and environmental control of host-gut microbiota interactions. Genome Res. 2015;25:1558–69.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marques FZ. Missing heritability of hypertension and our microbiome. Circulation. 2018;138:1381–3.
Article
PubMed
Google Scholar
Zheng P, Zeng B, Liu M, Chen J, Pan J, Han Y, et al. The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice. Sci Adv. 2019;5:eaau8317.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sandoval-Motta S, Aldana M, Martínez-Romero E, Frank A. The human microbiome and the missing heritability problem. Front Genet. 2017;8:80.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shreiner J, Kao JY, Young VB. The gut microbiome in health and disease. Curr Opin Gastroenterol. 2015;31:69–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goodrich JK, Davenport ER, Clark AG, Ley RE. The relationship between the human genome and microbiome comes into view. Annu Rev Genet. 2017;51:413–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, et al. Human genetics shape the gut microbiome. Cell. 2014;159:789–99.
Article
CAS
PubMed
PubMed Central
Google Scholar
Turpin W, Espin-Garcia O, Xu W, Silverberg MS, Kevans D, Smith MI, et al. Association of host genome with intestinal microbial composition in a large healthy cohort. Nat Genet. 2016;48:1413–7.
Article
CAS
PubMed
Google Scholar
Lim MY, You HJ, Yoon HS, Kwon B, Lee JY, Lee S, et al. The effect of heritability and host genetics on the gut microbiota and metabolic syndrome. Gut. 2017;66:1031–8.
Article
CAS
PubMed
Google Scholar
Hansen EE, Lozupone CA, Rey FE, Wu M, Guruge JL, Narra A, et al. Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins. PNAS USA. 2011;108:4599–606.
Rothschild D, Weissbrod O, Barkan E, Korem T, Zeevi D, Costea PI, et al. Environmental factors dominate over host genetics in shaping human gut microbiota composition. Nature. 2018;555:210–5.
Article
CAS
PubMed
Google Scholar
Dong TS, Gupta A. Influence of early life, diet, and the environment on the microbiome. Clin Gastroenterol Hepatol. 2019;17:231–42.
Doolittle WF, Booth A. It’s the song, not the singer: an exploration of holobiosis and evolutionary theory. Biol Philos. 2017;32:5–24.
Article
Google Scholar
Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, et al. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–14.
Article
CAS
Google Scholar
Suez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M, Bashiardes S, et al. Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT. Cell. 2018;174:1406–1423.e16.
Article
CAS
PubMed
Google Scholar
Segata N, Korpela K, Bork P, Coelho LP, Kandels-Lewis S, Costea P, et al. Selective maternal seeding and environment shape the human gut microbiome. Genome Res. 2018;28:561–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, et al. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host Microbe. 2018;24:133–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanders JG, Powell S, Kronauer DJC, Vasconcelos HL, Frederickson ME, Pierce NE. Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes. Mol Ecol. 2014;23:1268–83.
Article
PubMed
Google Scholar
Mayhew AJ, Meyre D. Assessing the heritability of complex traits in humans: methodological challenges and opportunities. Curr Genomics. 2017;18:332–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Q, Chen R, Cheng F, Wei Q, Ji Y, Yang H, et al. A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data. Nat Neurosci. 2019;22:691–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao Y, Jhamb D, Shu L, Arneson D, Rajpal DK, Yang X. Multi-omics integration reveals molecular networks and regulators of psoriasis. BMC Syst Biol. 2019;13:8.
Article
PubMed
PubMed Central
Google Scholar
Vangay P, Johnson AJ, Ward TL, Al-Ghalith GA, Shields-Cutler RR, Hillmann BM, et al. US immigration westernizes the human gut microbiome. Cell. 2018;175:962–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, et al. American Gut: an open platform for citizen science. mSystems. 2018;3:e00031–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Magi R, Lindgren CM, Morris AP. Meta-analysis of sex-specific genome-wide association studies. Genet Epidemiol. 2010;34:846–53.
Article
PubMed
PubMed Central
Google Scholar
Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006;38:904–9.
Article
CAS
PubMed
Google Scholar
Pirinen M, Donnelly P, Spencer CCA. Including known covariates can reduce power to detect genetic effects in case-control studies. Nat Genet. 2012;44:848–51.
Article
CAS
PubMed
Google Scholar
Aschard H, Vilhjálmsson BJ, Joshi AD, Price AL, Kraft P. Adjusting for heritable covariates can bias effect estimates in genome-wide association studies. Am J Hum Genet. 2015;96:329–39.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zaitlen N, Lindström S, Pasaniuc B, Cornelis M, Genovese G, Pollack S, et al. Informed conditioning on clinical covariates increases power in case-control association studies. PLoS Genet. 2012;8:e1003032.
Article
CAS
PubMed
PubMed Central
Google Scholar