Tam V, Patel N, Turcotte M, Bosse Y, Pare G, Meyre D. Benefits and limitations of genome-wide association studies. Nat Rev Genet. 2019;20:467–84.
Article CAS PubMed 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
Bayat A, Hosking B, Jain Y, Hosking C, Kodikara M, Reti D, et al. Fast and accurate exhaustive higher-order epistasis search with BitEpi. Sci Rep. 2021;11:15923.
Article CAS PubMed PubMed Central Google Scholar
Wan X, Yang C, Yang Q, Xue H, Fan X, Tang NLS, et al. BOOST: A fast approach to detecting gene-gene interactions in genome-wide case-control studies. Am J Hum Genet. 2010;87:325–40.
Article CAS PubMed PubMed Central Google Scholar
Ma L, Brautbar A, Boerwinkle E, Sing CF, Clark AG, Keinan A. Knowledge-driven analysis identifies a gene–gene interaction affecting high-density lipoprotein cholesterol levels in multi-ethnic populations. PLOS Genet. 2012;8:e1002714.
Article CAS PubMed PubMed Central Google Scholar
Terada A, Okada-Hatakeyama M, Tsuda K, Sese J. Statistical significance of combinatorial regulations. Proc Natl Acad Sci USA. 2013;110:12996–3001.
Article CAS PubMed PubMed Central Google Scholar
Terada A, Yamada R, Tsuda K, Sese J. LAMPLINK: detection of statistically significant SNP combinations from GWAS data. Bioinformatics. 2016;32:3513.
Article CAS PubMed PubMed Central Google Scholar
Minato S, Uno T, Tsuda K, Terada A, Sese J. A fast method of statistical assessment for combinatorial hypotheses based on frequent itemset enumeration. Machine Learning and Knowledge Discovery in Databases. 2014;8725:422–36.
Okada Y, Wu D, Trynka G, Raj T, Terao C, Ikari K, et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature. 2014;506:376–81.
Article CAS PubMed Google Scholar
Raychaudhuri S, Sandor C, Stahl EA, Freudenberg J, Lee HS, Jia X, et al. Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Nat Genet. 2012;44:291–6.
Article CAS PubMed PubMed Central Google Scholar
Qiao B, Huang CH, Cong L, Xie J, Lo SH, Zheng T. Genome-wide gene-based analysis of rheumatoid arthritis-associated interaction with PTPN22 and HLA-DRB1. BMC Proc. 2009;3:S132.
Article PubMed PubMed Central Google Scholar
Genin E, Coustet B, Allanore Y, Ito I, Teruel M, Constantin A, et al. Epistatic interaction between BANK1 and BLK in rheumatoid arthritis: results from a large trans-ethnic meta-analysis. PLoS One. 2013;8:e61044.
Article CAS PubMed PubMed Central Google Scholar
Diaz-Gallo LM, Ramskold D, Shchetynsky K, Folkersen L, Chemin K, Brynedal B, et al. Systematic approach demonstrates enrichment of multiple interactions between non-HLA risk variants and HLA-DRB1 risk alleles in rheumatoid arthritis. Ann Rheum Dis. 2018;77:1454–62.
Article CAS PubMed Google Scholar
Stahl EA, Wegmann D, Trynka G, Gutierrez-Achury J, Do R, Voight BF, et al. Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis. Nat Genet. 2012;44:483–9.
Article CAS PubMed PubMed Central Google Scholar
Nagai A, Hirata M, Kamatani Y, Muto K, Matsuda K, Kiyohara Y, et al. Overview of the BioBank Japan Project: Study design and profile. J Epidemiol. 2017;27:S2–8.
Article PubMed PubMed Central Google Scholar
Setoh K, Matsuda F, Cohort Profile: The Nagahama Prospective Genome Cohort for Comprehensive Human Bioscience (The Nagahama Study). In: Yano M, Matsuda F, Sakuntabhai A, Hirota S, editors. Socio-Life Science and the COVID-19 Outbreak: Public Health and Public Policy [Internet]. Singapore: Springer Singapore; 2022. p. 127–43. Available from: https://doi.org/10.1007/978-981-16-5727-6_7.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559–75.
Article CAS PubMed PubMed Central Google Scholar
Delaneau O, Marchini J, Zagury JF. A linear complexity phasing method for thousands of genomes. Nat Methods. 2011;9:179–81.
Das S, Forer L, Schonherr S, Sidore C, Locke AE, Kwong A, et al. Next-generation genotype imputation service and methods. Nat Genet. 2016;48:1284–7.
Article CAS PubMed PubMed Central Google Scholar
Gao X, Starmer J, Martin ER. A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms. Genet Epidemiol. 2008;32:361–9.
Kendall MG. A new measure of rank correlation. Biometrika. 1938;30:81–93.
Viechtbauer W. Conducting meta-analyses in R with the metafor package. J Stat Softw. 2010;36:1–48.
Lex A, Gehlenborg N, Strobelt H, Vuillemot R, Pfister H. UpSet: visualization of intersecting sets. IEEE Trans Vis Comput Graph. 2014;20:1983–92.
Article PubMed PubMed Central Google Scholar
Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, 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 CAS PubMed Google Scholar
Naito T, Suzuki K, Hirata J, Kamatani Y, Matsuda K, Toda T, et al. A deep learning method for HLA imputation and trans-ethnic MHC fine-mapping of type 1 diabetes. Nat Commun. 2021;12:1639.
Article CAS PubMed PubMed Central Google Scholar
Okada Y, Kim K, Han B, Pillai NE, Ong RT, Saw WY, et al. Risk for ACPA-positive rheumatoid arthritis is driven by shared HLA amino acid polymorphisms in Asian and European populations. Hum Mol Genet. 2014;23:6916–26.
Article CAS PubMed PubMed Central Google Scholar
Pillai NE, Okada Y, Saw WY, Ong RTH, Wang X, Tantoso E, et al. Predicting HLA alleles from high-resolution SNP data in three Southeast Asian populations. Hum Mol Genet. 2014;23:4443–51.
Article CAS PubMed Google Scholar
Mitsuhashi N, Toyo-oka L, Katayama T, Kawashima M, Kawashima S, Miyazaki K, et al. TogoVar: A comprehensive Japanese genetic variation database. Hum Genome Var. 2022;9:1–9.
Robinson J, Soormally AR, Hayhurst JD, Marsh SGE. The IPD-IMGT/HLA Database – New developments in reporting HLA variation. Hum Immunol. 2016;77:233–7.
Article CAS PubMed Google Scholar
Kawaguchi S, Matsuda F. High-definition genomic analysis of HLA genes via comprehensive HLA allele genotyping. Methods Mol Biol. 2020;2131:31–8.
Freudenberg J, Lee HS, Han BG, Shin HD, Kang YM, Sung YK, et al. Genome-wide association study of rheumatoid arthritis in Koreans: population-specific loci as well as overlap with European susceptibility loci. Arthritis Rheum. 2011;63:884–93.
Article CAS PubMed Google Scholar
Lefranc MP, Duprat E, Kaas Q, Tranne M, Thiriot A, Lefranc G. IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily (MhcSF) G-LIKE-DOMAIN. Dev Comp Immunol. 2005;29:917–38.
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