Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques.
Killer cell immunoglobulin-like receptors (KIRs) modulate disease progression of pathogens including HIV, malaria, and hepatitis C. Cynomolgus and rhesus macaques are widely used as nonhuman primate models to study human pathogens, and so, considerable effort has been put into characterizing their KIR genetics. However, previous studies have relied on cDNA cloning and Sanger sequencing that lack the throughput of current sequencing platforms. In this study, we present a high throughput, full-length allele discovery method utilizing Pacific Biosciences circular consensus sequencing (CCS). We also describe a new approach to Macaque Exome Sequencing (MES) and the development of the Rhexome1.0, an adapted target capture reagent that includes macaque-specific capture probe sets. By using sequence reads generated by whole genome sequencing (WGS) and MES to inform primer design, we were able to increase the sensitivity of KIR allele discovery. We demonstrate this increased sensitivity by defining nine novel alleles within a cohort of Mauritian cynomolgus macaques (MCM), a geographically isolated population with restricted KIR genetics that was thought to be completely characterized. Finally, we describe an approach to genotyping KIRs directly from sequence reads generated using WGS/MES reads. The findings presented here expand our understanding of KIR genetics in MCM by associating new genes with all eight KIR haplotypes and demonstrating the existence of at least one KIR3DS gene associated with every haplotype.
Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA.
Trent M
TM
Prall
Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA.
Michael E
ME
Graham
Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA.
Julie A
JA
Karl
Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA.|Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA.
Roger W
RW
Wiseman
Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA.
Adam J
AJ
Ericsen
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
Muthuswamy
M
Raveendran
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
R
R
Alan Harris
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
Donna M
DM
Muzny
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
Richard A
RA
Gibbs
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Jeffrey
J
Rogers
Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA. doconnor@primate.wisc.edu.|Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA. doconnor@primate.wisc.edu.
David H
DH
O'Connor
D000818:Animals; D059472:Exome; D005787:Gene Frequency; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008252:Macaca fascicularis / Q000235:genetics* / Q000276:immunology; D054340:Receptors, KIR / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods
D054340:Receptors, KIR
Killer cell immunoglobulin-like receptors; Mauritian cynomolgus macaques; PacBio long-amplicon sequencing; Whole Genome and Macaque Exome Sequencing