584063-Bourgonje

97 Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. 57, 289-300. Zhernakova, D.V., Le, T.H., Kurilshikov, A., Atanasovska, B., Bonder, M.J., Sanna, S., Claringbould, A., Võsa, U., Deelen, P., Franke, L., et al. (2018). Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome. Nat. Genet. 50, 1524–1532. Das, S., Forer, L., Schönherr, S., Sidore, C., Locke, A.E., Kwong, A., Vrieze, S.I., Chew, E.Y., Levy, S., McGue, M., et al. (2016). Next-generation genotype imputation service and methods. Nat. Genet. 48, 1284–1287. Deelen, P., Bonder, M.J., van der Velde, K.J., Westra, H.-J., Winder, E., Hendriksen, D., Franke, L., and Swertz, M.A. (2014). Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration. BMC Res. Notes 7, 901. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A.R., Bender, D., Maller, J., Sklar, P., de Bakker, P.I.W., Daly, M.J., et al. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575. Yang, J., Lee, S.H., Goddard, M.E., and Visscher, P.M. (2011). GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88, 76–82. Yang, J., Benyamin, B., McEvoy, B.P., Gordon, S., Henders, A.K., Nyholt, D.R., Madden, P.A., Heath, A.C., Martin, N.G., Montgomery, G.W., et al. (2010). Common SNPs explain a large proportion of the heritability for human height. Nat. Genet. 42, 565–569. Lee, S.H., Yang, J., Goddard, M.E., Visscher, P.M., and Wray, N.R. (2012). Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism-derived genomic relationships and restricted maximum likelihood. Bioinformatics 28, 2540–2542. Hu, S., Uniken Venema, W.T., Westra, H.-J., Vich Vila, A., Barbieri, R., Voskuil, M.D., Blokzijl, T., Jansen, B.H., Li, Y., Daly, M.J., et al. (2021). Inflammation status modulates the effect of host genetic variation on intestinal gene expression in inflammatory bowel disease. Nat. Commun. 12, 1122. Willer, C.J., Li, Y., and Abecasis, G.R. (2010). METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics 26, 2190–2191. McLaren, W., Gil, L., Hunt, S.E., Riat, H.S., Ritchie, G.R.S., Thormann, A., Flicek, P., and Cunningham, F. (2016). The Ensembl Variant Effect Predictor. Genome Biol. 17, 122. Alexander, T.A., and Machiela, M.J. (2020). LDpop: an interactive online tool to calculate and visualize geographic LD patterns. BMC Bioinformatics 21, 14. Machiela, M.J., and Chanock, S.J. (2015). LDlink: a web-based application for exploring populationspecific haplotype structure and linking correlated alleles of possible functional variants. Bioinformatics 31, 3555–3557. Jia, X., Han, B., Onengut-Gumuscu, S., Chen, W.-M., Concannon, P.J., Rich, S.S., Raychaudhuri, S., and de Bakker, P.I.W. (2013). Imputing amino acid polymorphisms in human leukocyte antigens. PLoS One 8, e64683. McCarthy, S., Das, S., Kretzschmar, W., Delaneau, O., Wood, A.R., Teumer, A., Kang, H.M., Fuchsberger, C., Danecek, P., Sharp, K., et al., the Haplotype Reference Consortium (2016). A reference panel of 64,976 haplotypes for genotype imputation. Nature Genetics 48, 1279–1283. Robinson, J., Barker, D.J., Georgiou, X., Cooper, M.A., Flicek, P., and Marsh, S.G.E. (2020). IPD-IMGT/HLA Database. Nucleic Acids Res. 48, D948–D955. Reynisson, B., Alvarez, B., Paul, S., Peters, B., and Nielsen, M. (2020a). NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Research 48, W449–W454. Zhou, P., Jin, B., Li, H., and Huang, S.-Y. (2018). HPEPDOCK: a web server for blind peptide– protein docking based on a hierarchical algorithm. Nucleic Acids Res. 46, W443–W450. 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 Determinants of the human antibody epitope repertoire

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