Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes

We genotyped a Chinese and an Indian-origin rhesus macaque using the Affymetrix Genome-Wide Human SNP Array 6.0 and cataloged 85,473 uniquely mapping heterospecific SNPs. These SNPs were assigned to rhesus chromosomes according to their probe sequence alignments as displayed in the human and rhesus reference sequences. The conserved gene order (synteny) revealed by heterospecific SNP maps is in concordance with that of the published human and rhesus macaque genomes.Using these SNPs' original human rs numbers, we identified 12,328 genes annotated in humans that are associated with these SNPs, 3674 of which were found in at least one of the two rhesus macaques studied. Due to their density, the heterospecific SNPs allow fine-grained comparisons, including approximate boundaries of intra- and extra-chromosomal rearrangements involving gene orthologs, which can be used to distinguish rhesus macaque chromosomes from human chromosomes.

► Rhesus macaques are relevant animal models for post-genomic era biomedical research.
► Chromosomal rearrangements can confound candidate gene identification in macaques.
► Heterospecific SNPs allow fine-grained comparisons of human and macaque chromosomes.
► Synteny maps based on heterospecific SNPs can enable localization of gene orthologs.