DOI QR코드

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MergeReference: A Tool for Merging Reference Panels for HLA Imputation

  • Cook, Seungho (Department of Convergence Medicine, University of Ulsan College of Medicine and Asan Institute for Life Sciences, Asan Medical Center) ;
  • Han, Buhm (Department of Convergence Medicine, University of Ulsan College of Medicine and Asan Institute for Life Sciences, Asan Medical Center)
  • 투고 : 2017.08.07
  • 심사 : 2017.08.30
  • 발행 : 2017.09.30

초록

Recently developed computational methods allow the imputation of human leukocyte antigen (HLA) genes using intergenic single nucleotide polymorphism markers. To improve the imputation accuracy in HLA imputation, it is essential to increase the sample size and the diversity of alleles in the reference panel. Our software, MergeReference, helps achieve this goal by providing a streamlined pipeline for combining multiple reference panels into one.

키워드

참고문헌

  1. Hu X, Deutsch AJ, Lenz TL, Onengut-Gumuscu S, Han B, Chen WM, et al. Additive and interaction effects at three amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes risk. Nat Genet 2015;47:898-905. https://doi.org/10.1038/ng.3353
  2. 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;44:291-296. https://doi.org/10.1038/ng.1076
  3. Han B, Diogo D, Eyre S, Kallberg H, Zhernakova A, Bowes J, et al. Fine mapping seronegative and seropositive rheumatoid arthritis to shared and distinct HLA alleles by adjusting for the effects of heterogeneity. Am J Hum Genet 2014;94:522-532. https://doi.org/10.1016/j.ajhg.2014.02.013
  4. Jia X, Han B, Onengut-Gumuscu S, Chen WM, Concannon PJ, Rich SS, et al. Imputing amino acid polymorphisms in human leukocyte antigens. PLoS One 2013;8:e64683. https://doi.org/10.1371/journal.pone.0064683
  5. Dilthey AT, Moutsianas L, Leslie S, McVean G. HLA*IMP: an integrated framework for imputing classical HLA alleles from SNP genotypes. Bioinformatics 2011;27:968-972. https://doi.org/10.1093/bioinformatics/btr061
  6. Zheng X, Shen J, Cox C, Wakefield JC, Ehm MG, Nelson MR, et al. HIBAG-HLA genotype imputation with attribute bagging. Pharmacogenomics J 2014;14:192-200. https://doi.org/10.1038/tpj.2013.18
  7. Dunstan SJ, Hue NT, Han B, Li Z, Tram TT, Sim KS, et al. Variation at HLA-DRB1 is associated with resistance to enteric fever. Nat Genet 2014;46:1333-1336. https://doi.org/10.1038/ng.3143
  8. Okada Y, Han B, Tsoi LC, Stuart PE, Ellinghaus E, Tejasvi T, et al. Fine mapping major histocompatibility complex associations in psoriasis and its clinical subtypes. Am J Hum Genet 2014;95:162-172. https://doi.org/10.1016/j.ajhg.2014.07.002
  9. Pillai NE, Okada Y, Saw WY, Ong RT, Wang X, Tantoso E, et al. Predicting HLA alleles from high-resolution SNP data in three Southeast Asian populations. Hum Mol Genet 2014;23:4443-4451. https://doi.org/10.1093/hmg/ddu149
  10. Kim K, Bang SY, Lee HS, Bae SC. Construction and application of a Korean reference panel for imputing classical alleles and amino acids of human leukocyte antigen genes. PLoS One 2014;9:e112546. https://doi.org/10.1371/journal.pone.0112546
  11. International HapMap Consortium. The International HapMap Project. Nature 2003;426:789-796. https://doi.org/10.1038/nature02168
  12. 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;81:559-575. https://doi.org/10.1086/519795
  13. Kim K, Bang SY, Lee HS, Okada Y, Han B, Saw WY, et al. The HLA-$DR{\beta}1$ amino acid positions 11-13-26 explain the majority of SLE-MHC associations. Nat Commun 2014;5:5902. https://doi.org/10.1038/ncomms6902