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

doi:10.1016/j.ygeno.2012.09.001

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 journal › Article › peer-review

13 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 language	English (US)
Pages (from-to)	30-37
Number of pages	8
Journal	Genomics
Volume	101
Issue number	1
DOIs	https://doi.org/10.1016/j.ygeno.2012.09.001
State	Published - Jan 2013
Externally published	Yes

Keywords

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

ASJC Scopus subject areas

Genetics

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10.1016/j.ygeno.2012.09.001

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title = "Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes",

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.",

keywords = "Heterospecific sequence maps, Homo sapiens, Macaca mulatta, Single nucleotide polymoprhisms (SNPs)",

author = "Sree Kanthaswamy and Jillian Ng and Ross, {Cody T.} and Trask, {Jessica Satkoski} and Smith, {David Glenn} and Buffalo, {Vince S.} and Fass, {Joseph N.} and Dawei Lin",

note = "Funding Information: We thank Ryan Davis at the UC Davis MIND Institute for his helpful advice and contributions to this manuscript. This study was supported by the California National Primate Research Center base grant (No. RR000169-48 ), by an ARRA supplement awarded to SK and Nick Lerche, CNPRC (No. RR018144-07 ) and NIH grants RR005090 and RR025871 to DGS. Animals used in this research were managed in compliance with Institutional Animal Care and Use Committee (IACUC) regulations or in accordance with the National Institutes of Health guidelines or the US Department of Agriculture regulations prescribing the humane care and use of laboratory animals. ",

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AU - Trask, Jessica Satkoski

AU - Smith, David Glenn

AU - Buffalo, Vince S.

AU - Fass, Joseph N.

AU - Lin, Dawei

N1 - Funding Information: We thank Ryan Davis at the UC Davis MIND Institute for his helpful advice and contributions to this manuscript. This study was supported by the California National Primate Research Center base grant (No. RR000169-48 ), by an ARRA supplement awarded to SK and Nick Lerche, CNPRC (No. RR018144-07 ) and NIH grants RR005090 and RR025871 to DGS. Animals used in this research were managed in compliance with Institutional Animal Care and Use Committee (IACUC) regulations or in accordance with the National Institutes of Health guidelines or the US Department of Agriculture regulations prescribing the humane care and use of laboratory animals.

PY - 2013/1

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N2 - 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.

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Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes

Abstract

Keywords

ASJC Scopus subject areas

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