title: Major histocompatibility complex haplotyping and long-amplicon allele discovery in cynomolgus macaques from Chinese breeding facilities.
abstract: Very little is currently known about the major histocompatibility complex (MHC) region of cynomolgus macaques (Macaca fascicularis; Mafa) from Chinese breeding centers. We performed comprehensive MHC class I haplotype analysis of 100 cynomolgus macaques from two different centers, with animals from different reported original geographic origins (Vietnamese, Cambodian, and Cambodian/Indonesian mixed-origin). Many of the samples were of known relation to each other (sire, dam, and progeny sets), making it possible to characterize lineage-level haplotypes in these animals. We identified 52 Mafa-A and 74 Mafa-B haplotypes in this cohort, many of which were restricted to specific sample origins. We also characterized full-length MHC class I transcripts using Pacific Biosciences (PacBio) RS II single-molecule real-time (SMRT) sequencing. This technology allows for complete read-through of unfragmented MHC class I transcripts (~1100 bp in length), so no assembly is required to unambiguously resolve novel full-length sequences. Overall, we identified 311 total full-length transcripts in a subset of 72 cynomolgus macaques from these Chinese breeding facilities; 130 of these sequences were novel and an additional 115 extended existing short database sequences to span the complete open reading frame. This significantly expands the number of Mafa-A, Mafa-B, and Mafa-I full-length alleles in the official cynomolgus macaque MHC class I database. The PacBio technique described here represents a general method for full-length allele discovery and genotyping that can be extended to other complex immune loci such as MHC class II, killer immunoglobulin-like receptors, and Fc gamma receptors.
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA.
authors.forename: Julie A
authors.initials: JA
authors.lastname: Karl
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Graham
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA.
authors.forename: Roger W
authors.initials: RW
authors.lastname: Wiseman
authors.affiliation: Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA.
authors.forename: Katelyn E
authors.initials: KE
authors.lastname: Heimbruch
authors.affiliation: Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA.
authors.forename: Samantha M
authors.initials: SM
authors.lastname: Gieger
authors.affiliation: Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.
authors.forename: Gaby G M
authors.initials: GG
authors.lastname: Doxiadis
authors.affiliation: Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.
authors.forename: Ronald E
authors.initials: RE
authors.lastname: Bontrop
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA. doconnor@primate.wisc.edu.|Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA. doconnor@primate.wisc.edu.|Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 585 Science Drive, Madison, WI, 53711, USA. doconnor@primate.wisc.edu.
authors.forename: David H
authors.initials: DH
authors.lastname: O'Connor
mesh_terms: D000483:Alleles; D000818:Animals; D001947:Breeding; D002681:China; D005787:Gene Frequency; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D008252:Macaca fascicularis / Q000235:genetics*; D008285:Major Histocompatibility Complex / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: MHC class I; Macaca fascicularis; PacBio long-amplicon sequencing; RNA transcript-based haplotypes