articlePLoS ONEJun 6, 2013GOLD OA

Imputing Amino Acid Polymorphisms in Human Leukocyte Antigens

XJXiaoming JiaBHBuhm HanSÖSuna Önengüt-GümüşcüWCWei‐Min ChenPCPatrick Concannon

Massachusetts Institute of Technology · Harvard–MIT Division of Health Sciences and Technology · +7 more institutions

PubMed
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Abstract

DNA sequence variation within human leukocyte antigen (HLA) genes mediate susceptibility to a wide range of human diseases. The complex genetic structure of the major histocompatibility complex (MHC) makes it difficult, however, to collect genotyping data in large cohorts. Long-range linkage disequilibrium between HLA loci and SNP markers across the major histocompatibility complex (MHC) region offers an alternative approach through imputation to interrogate HLA variation in existing GWAS data sets. Here we describe a computational strategy, SNP2HLA, to impute classical alleles and amino acid polymorphisms at class I (HLA-A, -B, -C) and class II (-DPA1, -DPB1, -DQA1, -DQB1, and -DRB1) loci. To characterize…

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Topics & keywords

Topics
Keywords
  • International HapMap Project
  • Genetics
  • Biology
  • Human leukocyte antigen
  • Linkage disequilibrium
  • Tag SNP
  • Imputation (statistics)
  • SNP genotyping
UN Sustainable Development Goals
  • Good health and well-being
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