Genetic Management Services

The primary mission of the Genetics Management Services is to provide genetics-related support and resources for colony management and banking of DNA and other samples for investigators. The lab also provides services on a recharge basis to all investigators internal and external to the CNPRC who are interested in incorporating genetic/genomic techniques into their research programs.

Genetic management to preserve maximum variability among colony animals is achieved by integrating several fundamental population genetic approaches. This not only ensures each animal’s value in terms of maintaining biomedical potential but also guarantees the entire population’s survivability and productivities by increasing heterozygosity (and correspondingly reducing the probability of homozygosity for deleterious alleles). Additional goals include a genetic management plan for the titi monkey colony.
• Genetic management includes country of origin testing, parentage testing and other phylogenetic and population genetic analyses
• Analysis of genealogical and demographic data including kinship assessment, pedigree validation, and the management of selective breeding and development of informative pedigrees
• Bioinformatic analysis including whole genome and target region linkage and association analyses and candidate gene evaluation
• Custom DNA extraction and purification, whole genome amplification, SNP, STR and mtDNA assays
• Development of genotyping assays based on conventional fragment size analysis (including STRs and RFLPs), Sanger sequencing, CNV, SNP and real-time qPCR techniques

• Single-nucleotide polymorphism (SNP)-based typing and analysis and ABO phenotyping currently represents major areas of service.
• The objective is to continue to genotype nonhuman primates at the CNPRC using SNPs to provide parentage assessment, ancestry/admixture testing, and genetic management services on a fee-for-service basis.
• The service has identified 5,000-6,000 high quality SNPs in macaques and developed panels of 96 genetic management SNPs and 96 ancestry informative SNP markers for rhesus and long-tailed macaques.

The Genetics Management Services also manage the CNPRC DNA Bank and participates in the National Primate Research Centers (NPRCs) Consortium.
• The DNA bank provides archived and banked samples and functions as a clearinghouse for the CNPRC.
• DNA and other biological samples from this bank are made available to investigators at a variety of research institutions once a proposal is reviewed and approved by the CNPRC Research Advisory Committee.
• The CNPRC’s DNA bank is part of the National Nonhuman Primate DNA Bank network in the NPRC Consortium that has a goal of standardizing resources across the NPRCs.
• Efforts to create an automated sample tracking system are underway in conjunction with the CNPRC Information Technology staff to ensure optimal organization and to improve access.

Selected Publications from Genetics Management Services activities

Kanthaswamy S, Reader R, Tarara R, Oslund K, Allen M, Ng J, Grinberg C, Hyde D, Smith DG, Lerche, N. Large scale pedigree analysis leads to evidence for founder effects of hypertrophic cardiomyopathy in rhesus macaques (Macaca mulatta), J Med Primatol, In Press.

Kanthaswamy S, Elfenbein HA, Ardeshir A, Ng J, Hyde D, Smith DG, Lerche N. Familial aggregation of chronic diarrhea disease (CDD) in rhesus macaques (Macaca mulatta). Am J Primatol 76(3):262-70, 2013. PMID 24532180

Kanthaswamy S, Ng J, Satkoski J, George DA, Kou AJ, Hoffman LN, Doherty TB, Houghton P, Smith DG. The genetic composition of cynomolgus macaque (Macaca fascicularis) populations used in biomedical research. J Med Primatol, 42(3):120-31, 2013. PMCID: PMC3651788, PMID 23480663

Kanthaswamy S, Ng J, Ross C, Trask J, Buffalo V, Smith DG, Fass JN, Lin D. Identifying and cataloguing human-rhesus macaque gene orthologs using heterospecific SNPs. Genomics 101(1), 30–37, 2013. PMCID: PMC3534948, PMID 22982528

Premasuthan A, Ng J, Kanthaswamy S, Trask JS, Houghton P, Farkas T, Sestak K, Smith DG. Molecular ABO phenotyping in cynomolgus macaques using real-time quantitative PCR. Tissue Antigens 80(4):363–367, 2012. PMCID: PMC3470802, PMID 22861170

Kanthaswamy S, Ng J, Penedo MCT, Ward T, Smith DG, Ha JC. Population genetics of the Washington National Primate Research Center’s (WaNPRC) captive pigtailed macaque (Macaca nemestrina) population. Am J Primatol 74(11):1017-27, 2012. PMID 22851336

Kanthaswamy S, Satkoski J, Ross CT, Kou A, Houghton P, Smith DG, Lerche N. A large-scale SNP-based genomic admixture analysis of the captive rhesus macaque colony at the California National Primate Research Center. Am J Primatol 74(8):747-57, 2012. PMID 24436199

Kanthaswamy S, Clarke PM, Kou AJ, Malladi VS, Satkoski JA, Smith DG. Association between hybrid status and reproductive success of captive male and female rhesus macaques (Macaca mulatta) at the California National Primate Research Center (CNPRC). Am J Primatol 73(7):671-8, 2011. PMID 21433046

Kanthaswamy S, Kou A, and Smith DG. Population genetic statistics from the rhesus macaque (Macaca mulatta) in three different housing techniques at the California National Primate Research Center (CNPRC). Journal of the American Association for Laboratory Animal Science (AALAS) 49(5):598-609, 2010. PMCID: PMC2949430

Kanthaswamy S, Satkoski J, Kou A, Malladi V, and Smith DG. Detecting signatures of inter-regional and inter-specific hybridization among the Chinese rhesus macaque specific pathogen-free (SPF) population using single nucleotide polymorphic (SNP) markers. J Med Primatol 39(4):252-65, 2010. PMCID: PMC2906220, PMID 20618591

Kanthaswamy S, Kou A, Satkoski J, Penedo MCT, Ward T. Ng J, Gill L, Lerche NW, Smith DG. Genetic characterization of specific pathogen-free (SPF) rhesus macaque (Macaca mulatta) populations at the California National Primate Research Center (CNPRC). Am J Primatol 72(7):587-99, 2010. PMCID: PMC2941796, PMID 20162538

Kanthaswamy S, Capitanio JP, Dubay CJ, Ferguson B, Folks T, Ha JC, Hotchkiss, CE, Johnson ZP, Katze MG, Kean LS, Kubisch HM, Lank S, Lyons LA, Miller GM, Nylander J, O’Connor DH, Palermo RE, Smith DG, Vallender EJ, Wiseman RW, Rogers J. Resources for genetic management and genomics research on non-human primates at the National Primate Research Centers (NPRCs). J Med Primatol 38(s1):17-23, 2009. PMID 19863674

Kanthaswamy S, Gill L, Satkoski J, Goyal V, Malladi V, Kou A, Basuta K, Sarkisyan L, George D, Smith, DG. The development of a Chinese-Indian hybrid (Chindian) rhesus macaque colony at the California National Primate Research Center (CNPRC) by introgression. J Med Primatol 38(2):86-96, 2009. PMCID: PMC2664393, PMID 18715266

Kanthaswamy S, Satkoski J, George D, Kou A, Erickson BJ, Smith DG. Interspecies hybridization and the stratification of nuclear genetic variation of rhesus (Macaca mulatta) and long-tailed macaques (Macaca fascicularis). International Journal of Primatology 29(5):1295–1311, 2008. PMCID: PMC2583101, PMID 19122840

Kanthaswamy S, Von Dollen A. Kurushima JD, Alminas O, Rogers J, Ferguson B, Lerche NW, Allen PC, Smith DG. Microsatellite markers for standardized genetic management of captive colonies of rhesus macaques (Macaca mulatta). Am J Primatol 68(1):73-95, 2006. PMID 16419121

Kanthaswamy S and Smith DG. Assessment of genetic management at three captive specific-pathogen-free rhesus macaque (Macaca mulatta) colonies. Journal of Comparative Medicine 52(5): 414 – 423. Journal of Comparative Medicine 54(2):414-23, 2002. PMID 12405633