Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes

Sree Kanthaswamy, Jillian Ng, Cody T. Ross, Jessica Satkoski Trask, David Glenn Smith, Vince S. Buffalo, Joseph N. Fass, Dawei Lin

Research output: Contribution to journalArticle

8 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)30-37
Number of pages8
JournalGenomics
Volume101
Issue number1
DOIs
StatePublished - Jan 1 2013
Externally publishedYes

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Keywords

  • Heterospecific sequence maps
  • Homo sapiens
  • Macaca mulatta
  • Single nucleotide polymoprhisms (SNPs)

ASJC Scopus subject areas

  • Genetics

Cite this

Kanthaswamy, S., Ng, J., Ross, C. T., Trask, J. S., Smith, D. G., Buffalo, V. S., Fass, J. N., & Lin, D. (2013). Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes. Genomics, 101(1), 30-37. https://doi.org/10.1016/j.ygeno.2012.09.001