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MHC*IMP – Imputation of Alleles for Genes in the Major Histocompatibility Complex

David McG. Squire, Allan Motyer, Richard Ahn, Joanne Nititham, Zhi-Ming Huang, Jorge R. Oksenberg, John Foerster, Wilson Liao, Stephen Leslie
doi: https://doi.org/10.1101/2020.01.24.919191
David McG. Squire
1Melbourne Integrative Genomics, The University of Melbourne, Australia
2School of Mathematics and Statistics, The University of Melbourne, Australia
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  • For correspondence: david.squire@unimelb.edu.au
Allan Motyer
1Melbourne Integrative Genomics, The University of Melbourne, Australia
2School of Mathematics and Statistics, The University of Melbourne, Australia
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Richard Ahn
4Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
5Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
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Joanne Nititham
6Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
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Zhi-Ming Huang
6Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
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Jorge R. Oksenberg
7UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
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John Foerster
8Medical School, University of Dundee, Dundee, UK
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Wilson Liao
6Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
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Stephen Leslie
1Melbourne Integrative Genomics, The University of Melbourne, Australia
2School of Mathematics and Statistics, The University of Melbourne, Australia
3School of Biosciences, The University of Melbourne, Australia
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Abstract

We report the development of MHC*IMP, a method for imputing non-classical HLA and other genes in the human Major Histocompatibility Complex (MHC). We created a reference panel for 25 genes in the MHC using allele calls from Whole Genome Sequencing data, combined with SNP data for the same individuals. We used this to construct an allele imputation model, MHC*IMP, for each gene. Cross-validation showed that MHC*IMP performs very well, with allele prediction accuracy 93% or greater for all but two of the genes, and greater than 95% for all but four.

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Posted January 26, 2020.
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MHC*IMP – Imputation of Alleles for Genes in the Major Histocompatibility Complex
David McG. Squire, Allan Motyer, Richard Ahn, Joanne Nititham, Zhi-Ming Huang, Jorge R. Oksenberg, John Foerster, Wilson Liao, Stephen Leslie
bioRxiv 2020.01.24.919191; doi: https://doi.org/10.1101/2020.01.24.919191
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MHC*IMP – Imputation of Alleles for Genes in the Major Histocompatibility Complex
David McG. Squire, Allan Motyer, Richard Ahn, Joanne Nititham, Zhi-Ming Huang, Jorge R. Oksenberg, John Foerster, Wilson Liao, Stephen Leslie
bioRxiv 2020.01.24.919191; doi: https://doi.org/10.1101/2020.01.24.919191

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