RT Journal Article
SR Electronic
T1 Major histocompatibility complex haplotyping and long-amplicon allele discovery in cynomolgus macaques from Chinese breeding facilities
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 084947
DO 10.1101/084947
A1 Julie A. Karl
A1 Michael E. Graham
A1 Roger W. Wiseman
A1 Katelyn E. Heimbruch
A1 Samantha M. Gieger
A1 Gaby G. M. Doxiadis
A1 Ronald E. Bontrop
A1 David H. O’Connor
YR 2016
UL http://biorxiv.org/content/early/2016/11/02/084947.abstract
AB 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 (~1,100 bp in length), so no assembly is required to unambiguously resolve novel full-length sequences. Overall, we identified 313 total full-length transcripts in a subset of 72 cynomolgus macaques from these Chinese breeding facilities; 131 of these sequences were novel and an additional 116 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.