MHC genotyping from rhesus macaque exome sequences.

 
TitleMHC genotyping from rhesus macaque exome sequences.
Publication TypeJournal Article
Year of Publication2019
AuthorsCaskey, JR, Wiseman, RW, Karl, JA, Baker, DA, Lee, T, Maddox, RJ, Raveendran, M, Harris, RA, Hu, J, Muzny, DM, Rogers, J, O'Connor, DH
JournalImmunogenetics
Date Published2019 Jul 18
ISSN1432-1211
Abstract

Indian rhesus macaque major histocompatibility complex (MHC) variation can influence the outcomes of transplantation and infectious disease studies. Frequently, rhesus macaques are MHC genotyped to identify variants that could account for unexpected results. Since the MHC is only one region in the genome where variation could impact experimental outcomes, strategies for simultaneously profiling variation in the macaque MHC and the remainder of the protein coding genome would be useful. Here we determine MHC class I and class II genotypes using target-capture probes enriched for MHC sequences, a method we term macaque exome sequence (MES) genotyping. For a cohort of 27 Indian rhesus macaques, we describe two methods for obtaining MHC genotypes from MES data and demonstrate that the MHC class I and class II genotyping results obtained with these methods are 98.1% and 98.7% concordant, respectively, with expected MHC genotypes. In contrast, conventional MHC genotyping results obtained by deep sequencing of short multiplex PCR amplicons were only 92.6% concordant with expectations for this cohort.

DOI10.1007/s00251-019-01125-w
Alternate JournalImmunogenetics
PubMed ID31321455
Grant ListP51OD011106 / GF / NIH HHS / United States
R24-OD011173 / GF / NIH HHS / United States
RR15459-01 / GF / NIH HHS / United States
RR020141-01 / GF / NIH HHS / United States
HHSN272201600007C / AI / NIAID NIH HHS / United States