OHSU

Primate Genetics Program

Primate GeneticsThis program is composed of three individual units providing different areas of expertise within the overall field of genetics: Collaborative Genetic Resources, Colony Demographics and Informatics, and Biostatistics.
 

Collaborative Genetics Resource Unit

The Collaborative Genetics Resource Unit (CGR) provides research expertise to support macaque genotyping and phenotyping efforts. This group is highly interactive with the research staff, supporting the design of genetic studies, identifying and addressing DNA resources and genotyping needs, and facilitating phenotype collection within and between primate centers. This unit also addresses research needs for improved colony management,such as by establishing methods to discern macaque ancestry (Indian or Chinese) to ensure that animals are not unknowingly intermixed. In addition, the CGR maintains a comprehensive ONPRC DNA Bank to facilitate access to NHP genetic materials for present and future research purposes.

Betsy Ferguson, Ph.D., Head
Summer Street, M.P.H., Research Associate
Jason Bahk, M.S., Research Assistant II
 

Services

Rhesus ancestry SNP assay.The SNP assay includes 64 Ancestral Informative Markers (AIMs) from 53 genes. The array is equally represented by SNPs exclusive to Indian or Chinese rhesus. A Sequenom iPLEX platform is used, with multiplexed reactions analyzed on a MassARRAY Compact system. This approach provides maximum design flexibility while minimizing cost and labor requirements.

DNA bank.Whole blood and liver samples are collected from all rhesus and Japanese macaques for processing and archiving for genetic research use. Buffy coat cells are isolated from blood samples, liver samples are obtained at necropsy, and DNA samples are extracted from these tissues as needed. All samples are stored in ultra-low freezers and made available to investigators for a fee. Currently the Bank includes over 9,000 archived samples from more than 4,800 NHPs.

Quality control

Quality control is incorporated into each procedure. For the SNP array, confidence scores for each individual genotype is determined by MassARRAY output and these are reported along with the results. Eight characterized Indian and Chinese rhesus DNA controls are included in each assay to insure the reproducibility of genotype calls in each run. The DNA Bank evaluates DNA samples by UV absorbance to ensure the 260/280 ratio is between1.7-2.0 and that the DNA concentration is between 50-250 ng/μl.

Chargebacks

Charges for rhesus ancestral SNP array analysis are $20/DNA (internal) and $40/DNA (external). Charges for obtaining DNA from the DNA bank is $2/ug DNA for internal use ($4/ug, external). If DNA extraction from a buffy coat or liver sample is required, a $20 fee is charged directly to the investigator by the MCBSC. That core facility extracts the DNA, with the agreement that 10 μg will be delivered to the investigator and the remaining DNA sample will be retained by the Bank.
 

Colony Demographics and Informatics Unit

The Colony Demographics and Informatics Unit (CDI) oversees the ONPRC colony genotyping program, validating parentage and pedigree assignments and monitoring population diversity metrics (founder representation, mean kinship values, genetic drift). These analyses inform and support the healthy management of the macaque breeding colonies by providing accurate information to achieve increased reproductive success and genetic balance in the colony. These efforts also generate the extensive colony pedigree that is the critical foundation for both genetic research investigations and animal model development at the ONPRC.

Christopher J. Dubay, Ph.D., Head
Samone Khouangsathiene, M.S., Research Associate

Services provided

Parentage determination and population analyses.All ONPRC macaques are genotyped to determine familial relationships and to establish population-based genetic statistics for the breeding colony as a whole. Blood samples are routinely collected from all newborn macaques during the annual round-ups of corrals and shelter-housed groups, or from indoor-housed animals during their annual physical exam. A blood sample is also collected from each rhesus macaque purchased for the breeding program each year. A portion of each blood sample is provided to the Collaborative Genetics Resource (CGR) unit for archiving,while the remainder is submitted for genotype analysis at the UC Davis Veterinary Genetics Laboratory (VGL). The VGL uses a set of 16 unlinked microsatellite markers to infer allele sizes (genotypes) of individual animals. The genotypes are compared to those of potential sires and dams to identify the likely parents. The confirmed genetic relationships are then used to update the ONPRC rhesus macaque pedigrees, which include up to seven generations of family lineages. The parentage analysis panel has been run on 97% the corral and shelter-housed animals, and 65% of indoor-housed animals. Both the marker alleles and the parentage assignments are stored in the GRIPdb, which is a demographic and genetic database that is accessible to all ONPRC staff.

The genotype data is also used to report mean kinship values for each breeding group and to identify genome uniqueness values and founder representation based upon allele distributions. These measures are used to identify animals (typically males) whose genetic contributions are overrepresented among the group, contributing to genetic drift. The reports for each housing group are provided, along with interpretation and recommendations, to DAR for use in colony management decisions. Demographic reports are also generated using both the census data and parentage data to report historical trends in reproductive rates by housing group. Population simulations are run to predict future growth rates for each breeding group, and to test the long-term effects of different management decisions.

Facilitate ONPRC access to colony demographic and genetic information.The analysis tools described below facilitate use of the genetic and demographic data generated from genetic monitoring and colony census data. The information is made available through both website access and specialized reports for DAR or research investigators. When feasible, bioinformatic tools to enhance use of genetic data are also made accessible through web-based portals.

1. GRIPdb: a web-based interface for the ONPRC genetic and phenotypic database. The CDI unit has developed a database system integrating data from the ONPRC Integrated Research Information System (IRIS) database (used for animal colony administration) with data stored in our genetics data repository, GRIPdb. The dynamic connection between IRIS and GRIPdb allows reporting of extended animal information to users via the GRIPdb web interface. This information includes:

  • Genetic relationships for each NHP, based upon microsatellite data.
  • Observed relationships for each NHP, based on data from the IRIS database.
  • Genotype data, including data on genetic markers (e.g., allele frequency, genomic location, etc.).
  • Haplotypes for linked genetic loci when available.
  • Basic information on each animal, including birth and death dates, ancestral origin, and housing location.

2. MonkeySNP: a web-based portal to access NHP SNP genotype data. To maximize the utility of the growing SNP data being generated on animals within our rhesus macaque colony, we developed a Web-interfaced database, “MonkeySNP”, to display SNP genotype data.We anticipate this resource becoming highly populated as SNP genotypes on colony animals are generated more rapidly and in larger arrays. MonkeySNP (http://MonkeySNP.ohsu.edu) currently utilizes the dbSNP database schema and design, and mirrors the data with a more intuitive user interface. The loaded genotypes can be searched by gene, chromosome position or animal poplulation and are displayed either by table or bygraphical genotype diagrams.
 

Biostatistics Unit

The Biostatistics Unit provides committed support from the OHSU Division of Biostatistics staff to meet the growing statistical needs at the ONPRC. Collectively, the OHSU Biostatistics group represents a wide range of expertise, including the analysis of microarray and other high-throughput genomics data, statistical genetics, complex sample survey, meta-analysis, Bayesian data analysis, longitudinal data analysis, and survival analysis. Biostatistics workshops are scheduled periodically at the ONPRC to maintain the visibility of this Unit, as well as to provide opportunities for educational drop-in sessions.

Motomi Mori, Ph.D., Professor
Kemal Sonmez, Ph.D., Associate Professor
Byung Park, Ph.D., Senior Research Associate