Whole genome sequencing predicts novel human disease models in rhesus macaques

Benjamin N. Bimber, Ranjani Ramakrishnan, Rita Cervera-Juanes, Ravi Madhira, Samuel M. Peterson, Robert B Norgren, Betsy Ferguson

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Rhesus macaques are an important pre-clinical model of human disease. To advance our understanding of genomic variation that may influence disease, we surveyed genome-wide variation in 21 rhesus macaques. We employed best-practice variant calling, validated with Mendelian inheritance. Next, we used alignment data from our cohort to detect genomic regions likely to produce inaccurate genotypes, potentially due to either gene duplication or structural variation between individuals. We generated a final dataset of > 16 million high confidence variants, including 13 million in Chinese-origin rhesus macaques, an increasingly important disease model. We detected an average of 131 mutations predicted to severely alter protein coding per animal, and identified 45 such variants that coincide with known pathogenic human variants. These data suggest that expanded screening of existing breeding colonies will identify novel models of human disease, and that increased genomic characterization can help inform research studies in macaques.

Original languageEnglish (US)
Pages (from-to)214-220
Number of pages7
JournalGenomics
Volume109
Issue number3-4
DOIs
StatePublished - Jul 1 2017

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Macaca mulatta
Genome
Gene Duplication
Macaca
Practice Guidelines
Breeding
Genotype
Mutation
Research
Proteins

Keywords

  • Chinese-origin
  • Genome
  • Indian-origin
  • Macaca mulatta
  • Nonhuman primate
  • SIV
  • SNP
  • Variant discovery

ASJC Scopus subject areas

  • Genetics

Cite this

Bimber, B. N., Ramakrishnan, R., Cervera-Juanes, R., Madhira, R., Peterson, S. M., Norgren, R. B., & Ferguson, B. (2017). Whole genome sequencing predicts novel human disease models in rhesus macaques. Genomics, 109(3-4), 214-220. https://doi.org/10.1016/j.ygeno.2017.04.001

Whole genome sequencing predicts novel human disease models in rhesus macaques. / Bimber, Benjamin N.; Ramakrishnan, Ranjani; Cervera-Juanes, Rita; Madhira, Ravi; Peterson, Samuel M.; Norgren, Robert B; Ferguson, Betsy.

In: Genomics, Vol. 109, No. 3-4, 01.07.2017, p. 214-220.

Research output: Contribution to journalArticle

Bimber, BN, Ramakrishnan, R, Cervera-Juanes, R, Madhira, R, Peterson, SM, Norgren, RB & Ferguson, B 2017, 'Whole genome sequencing predicts novel human disease models in rhesus macaques', Genomics, vol. 109, no. 3-4, pp. 214-220. https://doi.org/10.1016/j.ygeno.2017.04.001
Bimber BN, Ramakrishnan R, Cervera-Juanes R, Madhira R, Peterson SM, Norgren RB et al. Whole genome sequencing predicts novel human disease models in rhesus macaques. Genomics. 2017 Jul 1;109(3-4):214-220. https://doi.org/10.1016/j.ygeno.2017.04.001
Bimber, Benjamin N. ; Ramakrishnan, Ranjani ; Cervera-Juanes, Rita ; Madhira, Ravi ; Peterson, Samuel M. ; Norgren, Robert B ; Ferguson, Betsy. / Whole genome sequencing predicts novel human disease models in rhesus macaques. In: Genomics. 2017 ; Vol. 109, No. 3-4. pp. 214-220.
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