4040 SNPs for genomic analysis in the rhesus macaque (Macaca mulatta)

J. Satkoski Trask, W. T. Garnica, Sreetharan Kanthaswamy, R. S. Malhi, D. G. Smith

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Although the rhesus macaque (Macaca mulatta) is commonly used for biomedical research and becoming a preferred model for translational medicine, quantification of genome-wide variation has been slow to follow the publication of the genome in 2007. Here we report the properties of 4040 single nucleotide polymorphisms discovered and validated in Chinese and Indian rhesus macaques from captive breeding colonies in the United States. Frequency-matched measures of linkage disequilibrium were much greater in the Indian sample. Although the majority of polymorphisms were shared between the two populations, rare alleles were over twice as common in the Chinese sample. Indian rhesus had higher rates of heterozygosity, as well as previously undetected substructure, potentially due to admixture from Burma in wild populations and demographic events post-captivity.

Original languageEnglish (US)
Pages (from-to)352-358
Number of pages7
JournalGenomics
Volume98
Issue number5
DOIs
StatePublished - Nov 2011
Externally publishedYes

Fingerprint

Macaca mulatta
Single Nucleotide Polymorphism
Genome
Myanmar
Translational Medical Research
Linkage Disequilibrium
Population
Breeding
Publications
Biomedical Research
Alleles
Demography

Keywords

  • Linkage disequilibrium
  • Macaca mulatta
  • Nonhuman primate
  • SNP

ASJC Scopus subject areas

  • Genetics

Cite this

4040 SNPs for genomic analysis in the rhesus macaque (Macaca mulatta). / Trask, J. Satkoski; Garnica, W. T.; Kanthaswamy, Sreetharan; Malhi, R. S.; Smith, D. G.

In: Genomics, Vol. 98, No. 5, 11.2011, p. 352-358.

Research output: Contribution to journalArticle

Trask, J. Satkoski ; Garnica, W. T. ; Kanthaswamy, Sreetharan ; Malhi, R. S. ; Smith, D. G. / 4040 SNPs for genomic analysis in the rhesus macaque (Macaca mulatta). In: Genomics. 2011 ; Vol. 98, No. 5. pp. 352-358.
@article{3c978399f6044c4586bd45dad5fb1197,
title = "4040 SNPs for genomic analysis in the rhesus macaque (Macaca mulatta)",
abstract = "Although the rhesus macaque (Macaca mulatta) is commonly used for biomedical research and becoming a preferred model for translational medicine, quantification of genome-wide variation has been slow to follow the publication of the genome in 2007. Here we report the properties of 4040 single nucleotide polymorphisms discovered and validated in Chinese and Indian rhesus macaques from captive breeding colonies in the United States. Frequency-matched measures of linkage disequilibrium were much greater in the Indian sample. Although the majority of polymorphisms were shared between the two populations, rare alleles were over twice as common in the Chinese sample. Indian rhesus had higher rates of heterozygosity, as well as previously undetected substructure, potentially due to admixture from Burma in wild populations and demographic events post-captivity.",
keywords = "Linkage disequilibrium, Macaca mulatta, Nonhuman primate, SNP",
author = "Trask, {J. Satkoski} and Garnica, {W. T.} and Sreetharan Kanthaswamy and Malhi, {R. S.} and Smith, {D. G.}",
year = "2011",
month = "11",
doi = "10.1016/j.ygeno.2011.08.004",
language = "English (US)",
volume = "98",
pages = "352--358",
journal = "Genomics",
issn = "0888-7543",
publisher = "Academic Press Inc.",
number = "5",

}

TY - JOUR

T1 - 4040 SNPs for genomic analysis in the rhesus macaque (Macaca mulatta)

AU - Trask, J. Satkoski

AU - Garnica, W. T.

AU - Kanthaswamy, Sreetharan

AU - Malhi, R. S.

AU - Smith, D. G.

PY - 2011/11

Y1 - 2011/11

N2 - Although the rhesus macaque (Macaca mulatta) is commonly used for biomedical research and becoming a preferred model for translational medicine, quantification of genome-wide variation has been slow to follow the publication of the genome in 2007. Here we report the properties of 4040 single nucleotide polymorphisms discovered and validated in Chinese and Indian rhesus macaques from captive breeding colonies in the United States. Frequency-matched measures of linkage disequilibrium were much greater in the Indian sample. Although the majority of polymorphisms were shared between the two populations, rare alleles were over twice as common in the Chinese sample. Indian rhesus had higher rates of heterozygosity, as well as previously undetected substructure, potentially due to admixture from Burma in wild populations and demographic events post-captivity.

AB - Although the rhesus macaque (Macaca mulatta) is commonly used for biomedical research and becoming a preferred model for translational medicine, quantification of genome-wide variation has been slow to follow the publication of the genome in 2007. Here we report the properties of 4040 single nucleotide polymorphisms discovered and validated in Chinese and Indian rhesus macaques from captive breeding colonies in the United States. Frequency-matched measures of linkage disequilibrium were much greater in the Indian sample. Although the majority of polymorphisms were shared between the two populations, rare alleles were over twice as common in the Chinese sample. Indian rhesus had higher rates of heterozygosity, as well as previously undetected substructure, potentially due to admixture from Burma in wild populations and demographic events post-captivity.

KW - Linkage disequilibrium

KW - Macaca mulatta

KW - Nonhuman primate

KW - SNP

UR - http://www.scopus.com/inward/record.url?scp=80055077877&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80055077877&partnerID=8YFLogxK

U2 - 10.1016/j.ygeno.2011.08.004

DO - 10.1016/j.ygeno.2011.08.004

M3 - Article

C2 - 21907785

AN - SCOPUS:80055077877

VL - 98

SP - 352

EP - 358

JO - Genomics

JF - Genomics

SN - 0888-7543

IS - 5

ER -