MHC genotyping from rhesus macaque exome sequences.
Immunogenetics
; 71(8-9): 531-544, 2019 09.
Article
in En
| MEDLINE
| ID: mdl-31321455
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.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Polymorphism, Genetic
/
Histocompatibility Antigens Class I
/
Histocompatibility Antigens Class II
/
Exome
/
Macaca mulatta
Limits:
Animals
Language:
En
Journal:
Immunogenetics
Year:
2019
Document type:
Article
Affiliation country:
United States