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Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta).

BMC genomics | Jun 13, 2011

BACKGROUND: Rhesus macaques are the most widely utilized nonhuman primate model in biomedical research. Previous efforts have validated fewer than 900 single nucleotide polymorphisms (SNPs) in this species, which limits opportunities for genetic studies related to health and disease. Extensive information about SNPs and other genetic variation in rhesus macaques would facilitate valuable genetic analyses, as well as provide markers for genome-wide linkage analysis and the genetic management of captive breeding colonies. RESULTS: We used the available rhesus macaque draft genome sequence, new sequence data from unrelated individuals and existing published sequence data to create a genome-wide SNP resource for Indian-origin rhesus monkeys. The original reference animal and two additional Indian-origin individuals were resequenced to low coverage using SOLiDâ„¢ sequencing. We then used three strategies to validate SNPs: comparison of potential SNPs found in the same individual using two different sequencing chemistries, and comparison of potential SNPs in different individuals identified with either the same or different sequencing chemistries. Our approach validated approximately 3 million SNPs distributed across the genome. Preliminary analysis of SNP annotations suggests that a substantial number of these macaque SNPs may have functional effects. More than 700 non-synonymous SNPs were scored by Polyphen-2 as either possibly or probably damaging to protein function and these variants now constitute potential models for studying functional genetic variation relevant to human physiology and disease. CONCLUSIONS: Resequencing of a small number of animals identified greater than 3 million SNPs. This provides a significant new information resource for rhesus macaques, an important research animal. The data also suggests that overall genetic variation is high in this species. We identified many potentially damaging non-synonymous coding SNPs, providing new opportunities to identify rhesus models for human disease.

Pubmed ID: 21668978 RIS Download

Mesh terms: Animals | Genetic Variation | India | Macaca mulatta | Polymorphism, Single Nucleotide | Sequence Analysis, DNA | Species Specificity

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Associated grants

  • Agency: NICHD NIH HHS, Id: P30 HD003352
  • Agency: NIMH NIH HHS, Id: 5R01-MH046729
  • Agency: NHGRI NIH HHS, Id: U54 HG003273
  • Agency: NHGRI NIH HHS, Id: R01 HG004009
  • Agency: NIMH NIH HHS, Id: 5P50-MH84051
  • Agency: NIDA NIH HHS, Id: U01 DA025956
  • Agency: NIMH NIH HHS, Id: 5R01-MH081884
  • Agency: NHGRI NIH HHS, Id: 2 U54 HG003273
  • Agency: NCRR NIH HHS, Id: NIH-R24-RR15383
  • Agency: NIMH NIH HHS, Id: R01 MH046729

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Catholic University of the Sacred Heart; Milan; Italy

An Italian private research university that offers undergraduate, graduate and postdoctoral level degrees in both Italian and English.


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ENCODE - Encyclopedia of DNA Elements

Encyclopedia of DNA elements consisting of a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active, that is freely available as as a fundamental information resource for all biomedical researchers. ENCODE enables the scientific and medical communities to interpret the role of the human genome in biology and disease. ENCODE provides identification of common cell types to facilitate integrative analysis and a new experimental technologies based on high-throughput sequencing. ENCODE data are available for the entire human genome. All ENCODE data are free and available for immediate use.


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