Genetics Management Services

The Genetics Management Services (GMS) provides genetics and genomics support for colony management and the banking of biological samples, including DNA, for investigators. The unit also offers services on a recharge basis to all investigators, internal and external, at the NBRI who want to incorporate genetic and genomic approaches into their research programs.

GMS Research Geneticist: Sreetharan Kanthaswamy, PhD

GMS Lab Manager: Jodie Usachenko

Please email Genetics Management Services with questions about services or for additional information.

Genetics Management of Animal Colonies

Effective genetic management preserves as much variability as possible among colony animals. It protects each animal’s value for biomedical research and supports the colony's long-term health, productivity, and survivability. Maintaining heterozygosity also lowers the probability of homozygosity for deleterious alleles. We achieve this by integrating established population genetic approaches with modern genomic tools.

Colony genetic management includes:

  • Parentage and pedigree validation, using short tandem repeat (STR) and single nucleotide polymorphism (SNP) panels and whole-genome sequencing (WGS) data.
  • Ancestry and country-of-origin testing, along with phylogenetic and population genetic analyses
  • Kinship and relatedness analysis, including mean kinship, genome uniqueness, and inbreeding coefficients to guide selective breeding and the development of informative pedigrees, and including analysis of mixed-origin founder animals
  • MHC haplotyping to characterize immunogenetic diversity relevant to biomedical research
  • Bioinformatic analysis, including whole-genome and targeted-region linkage and association analyses, runs of homozygosity and identity-by-descent analyses, and candidate gene evaluation

Genetic and Genomic Services for Investigators

We provide the following on a recharge basis:

  • Genotyping and ancestry services: SNP-based typing and analysis, parentage assessment, and ancestry and admixture testing for nonhuman primates at the NBRI, including custom projects coordinated across institutions (sample verification, DNA extraction, plate-based genotyping, and data return)
  • Laboratory and assay services: custom DNA extraction and purification, whole-genome amplification, SNP, STR, and mtDNA assays, ABO phenotyping, and assay development based on fragment size analysis, Sanger sequencing, copy number variation (CNV), and real-time qPCR
  • Validated SNP panels: we have identified high-quality genomic SNPs in macaques and developed panels of 96 genetic management SNPs and 96 ancestry-informative SNP markers for rhesus and cynomolgus (long-tailed) macaques

Moving Toward Whole-Genome Sequencing 

The GMS is working with the UC Davis Genome Center to move parentage and relatedness testing for the specific-pathogen-free (SPF) rhesus macaque colony from STR panels toward whole-genome sequencing (WGS)-based approaches. The framework under development includes:

  • A reproducibility and quality assurance framework, with trigger-based reanalysis criteria
  • Statistical power analysis to design pilot and non-inferiority validation studies against existing STR-based results
  • A bioinformatics pipeline built on widely used, community-standard tools (BWA-MEM2, GATK, GLIMPSE, SHAPEIT, and PLINK)

Collaborative Genetic Management Across Primate Research Centers

The GMS contributes to a broader network of genetic management for captive and free-ranging macaque populations. This includes an NIH-funded project on the genetic management of captive rhesus macaque colonies, and advising on the genetic programs of the UC Davis National Biomedical Research Institute (NBRI) and Caribbean Primate Research Center. That advising covers the free-ranging Cayo Santiago colony and the Sabana Seca colony in Puerto Rico, in collaboration with colleagues at the University of Puerto Rico. Current efforts address whether populations are best analyzed together or separately, and the feasibility of a standalone colony management tool for broader use.

NBRI BioBank and Consortium

The GMS also manages the NBRI DNA BioBank and participates in the National Primate Research Centers (NPRC) Consortium.

  • The BioBank serves as a clearinghouse for the NBRI.
  • Samples are made available to investigators at research institutions once a proposal is reviewed and approved by the NBRI Research Advisory Committee.
  • The NBRI BioBank is part of the National Nonhuman Primate BioBank network in the NPRC Consortium, which aims to standardize resources across the NPRCs.
  • Efforts to create an automated sample tracking system are underway with NBRI Information Technology staff to improve organization and access.

Select Publications 

2026

A Comparative Analysis of the Genetic Structures of Rhesus Macaques (Macaca mulatta) Kept in Enclosure-Based Systems and Semi-Natural Settings. Kanthaswamy S. J. Am Assoc Lab Anim Sci. 2026 Feb 1;65(2):1-11. doi: 10.30802/AALAS-JAALAS-25-159. Epub ahead of print. PMID: 41698678; PMCID: PMC13086203. 

Next-Generation Short-Read Sequencing Reveals Impacts on Major Histocompatibility Complex Diversity Resulting From Differences in Captive Rhesus Macaque (Macaca Mulatta) Colony Expansion Strategies. Kanthaswamy S, Wiseman RW, Stauss MR, Ertl MC, Patel DK, Smith DG, Martínez MI, Maldonado E, Sariol CA. Am J Primatol. 2026 Jan;88(1):e70108. doi: 10.1002/ajp.70108. PMID: 41548195; PMCID: PMC12977098.
 

2023

Pedigree data from six rhesus macaque (Macaca mulatta) matrilines at the California National Primate Research Center indicate inbreeding and loss of genetic variation. Oldt RF, Beisner B, Cameron A, Pomerantz O, Kanthaswamy S. J Am Assoc Lab Anim Sci. 2023 Nov 11;62(6):502‑511. PMCID: PMC10772905.

A global catalog of whole‑genome diversity from 233 primate species. Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips‑Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez‑Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KK, Marques‑Bonet T. Science. 2023 Jun 2;380(6648):906‑913. PMCID: PMC12120848.

The landscape of tolerated genetic variation in humans and primates. Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer‑Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips‑Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez‑Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Bataillon T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell‑Luria A, Rehm HL, Xu J, Rogers J, Marques‑Bonet T, Farh KK.  Science. 2023 Jun 2;380(6648):eabn8153. PMCID: PMC10713091.

2016

The population genetic composition of conventional and SPF colonies of rhesus macaques (Macaca mulatta) at the Caribbean Primate Research Center. Kanthaswamy S, Ng J, Hernández‑Pacheco R, Ruiz‑Lambides A, Maldonado E, Martínez MI, Sariol CA. J Am Assoc Lab Anim Sci. 2016 Mar;55(2):147‑151. PMCID: PMC4783631.

2015

Identifying rhesus macaque gene orthologs using heterospecific human CNV probes. Ng J, Fass JN, Durbin‑Johnson B, Smith DG, Kanthaswamy S. Genom Data. 2015 Dec;6:202‑207. PMCID: PMC4664757.

Population genetics of the California National Primate Research Center’s (CNPRC) captive Callicebus cupreus colony. Mendoza A, Ng J, Bales KL, Mendoza SP, George DA, Smith DG, Kanthaswamy S. Primates. 2015 Jan;56(1):37‑44. PMCID: PMC4289022.

2014

Development and validation of a SNP‑based assay for inferring the genetic ancestry of rhesus macaques (Macaca mulatta). Kanthaswamy S, Johnson Z, Trask JS, Smith DG, Ramakrishnan R, Bahk J, Ng J, Wiseman R, Kubisch HM, Vallender EJ, Rogers J, Ferguson B. Am J Primatol. 2014 Nov;76(11):1105‑1113. PMCID: PMC4319213.

Large‑scale pedigree analysis leads to evidence for founder effects of hypertrophic cardiomyopathy in rhesus macaques (Macaca mulatta). Kanthaswamy S, Reader R, Tarara R, Oslund K, Allen M, Ng J, Grinberg C, Hyde D, Glenn DG, Lerche N.J Med Primatol. 2014 Aug;43(4):288‑291. PMCID: PMC4240635. Large-scale pedigree analysis leads to evidence for founder effects of hypertrophic cardiomyopathy in rhesus macaques (Macaca mulatta), J Med Primatol, In Press.