Primate Genetics Program
The goals of this program are to provide state-of-the-art genetic and genomic resources that support both NHP research and optimal colony management.
COLONY GENETICS UNIT
The Colony Genetics Unit oversees the parentage analysis of all non-human primates (NHPs) at the ONPRC, in order to insure accuracy of all dam and sire assignments, characterize extended colony pedigrees, and monitor colony genetic diversity. These extended pedigrees form a critical foundation for genetic research and animal model development at the ONPRC. Analyses based on these pedigrees are also used to support colony management decisions related to the formation of breeding groups, and to inform other management strategies that impact the genetic health and diversity of NHP colonies at the ONPRC.
Michael Raboin, Ph.D., Research Associate
Parentage determination and population genetic analyses: All ONPRC macaques are genotyped to validate parentage and to establish population genetic indices for the colony as a whole. Blood samples are collected from all newborn macaques during regular physical exams, usually conducted during the "round-ups" of outdoor corrals and shelter-houses, or as a routine part of veterinary care for indoor-housed animals. The blood samples provide DNA both for archiving with the Collaborative Genetics Resource (CGR) unit, and for genotype analysis of new infants and potential parents. Relationships supported by genetic analysis are then used to update pedigrees, which span multiple families and generations. Parentage analysis has been conducted on 97% of animals housed in outdoor corrals and shelter-housing, and on 75% of indoor-housed animals. Both genotypes and parentage assignments are stored in the Genetic Relationships & Information on Primates database (GRIPdb), which is accessible to all ONPRC staff (see below for a description of GRIPdb) and in PRIMe.
Population genetic indices include mean kinship values for breeding groups, estimates of relatedness between individuals and groups, and individual measures of genome uniqueness and founder representation. These measures are used to identify animals (typically males) whose genetic contributions are overrepresented within groups, potentially contributing to loss of genetic diversity within the colony. The reports for each housing group are provided, along with interpretation and recommendations, to DCM for use in colony management decisions.
Maintenance of colony genetic and demographic information: The database tools described below were designed to facilitate use of available data produced by ongoing genetic and demographic analysis within the ONPRC colony. The information is available through the internal websites listed below, or may be summarized in specialized reports requested by colony management personnel or by research investigators. The data available on GRIPdb is also being transitioned to the PRIMe database.
GRIPdb, a web-based interface for ONPRC genetic, demographic and phenotypic data: The GRIP database (http://grip.ohsu.edu) integrates data from the ONPRC colony records with available genetic demographic data. The dynamic connection between IRIS and GRIPdb allows reporting of extended animal information to users of the GRIPdb interface. This information includes:
- Confirmed (genetic) relationships between NHP parents and offspring, based on genotype information at multiple microsatellite markers;
- Observed relationships between NHP parents and offspring, based on records obtained from IRIS;
- Genotype data (allele frequency, genomic location, etc.);
- Haplotypes data for linked genetic loci;
- Basic information on each animal, including birth and death dates, ancestral origin, and housing location.
COLLABORATIVE GENETICS RESOURCE UNIT
The Collaborative Genetics Resource Unit (CGR) provides research expertise to support macaque genotype discovery and analysis. The CGR manages an extensive ONPRC non-human primate DNA Bank, which is available to support both research and colony management needs. The CGR also develops and implements high through-put genotyping assays for the comparative analysis of NHPs. Current genotyping services include the rhesus macaque SNP parentage assay, rhesus macaque SNP ancestry assay, MHC expressed allele assays. Custom genotyping assays are available upon request.
Rita Cervera Juanes, Ph.D., Research Associate
Julie Hollister-Smith, Ph.D., Research Associate
Elizabeth Swanson, B.S., Research Assistant II
Molecular Services Provided
Rhesus macaque SNP parentage assay: This is a 96 SNP assay developed in partnership with the NPRC Genetics and Genomics Working Group Consortium to enable consistent genotyping and comparison of rhesus macaques across all NPRCs. The SNPs were selected for high heterozygosity values and broad chromosomal distribution. The assay makes use of the Illumina BeadExpress technology to identify genotypes, and parentage relationships are evaluated using the NPRC Consortium parentage analysis pipeline.
Rhesus macaque SNP ancestry assay: This SNP assay includes 125 Ancestral Informative Markers (AIMs) selected for high information content and broad genomic representation. The array is run on a LifeTech QuantStudio platform, and Structure analysis (Pritchard et al., 2000) is used to distinguish rhesus macaque ancestral populations. The analysis is performed using the NPRC Consortium ancestry analysis pipeline. Pure bred Indian, Chinese and hybrid animals are identified with this assay.
MHC expressed allele assay: This is an RNA-based assay used to detect expressed MHC class I alleles in rhesus macaques, as described by Wiseman et al., 2009. Targeted polymorphic MHC regions are amplified, multiplexed and sequenced on an Illumina miSeq sequencer. The resulting reads are compared against all defined MHC alleles to identify alleles and haplotypes.
VNTR genotype assay: VNTR assays are available to genotype commonly studied alleles in SLC6A4, MAOA and TPH2. These loci are amplified using fluorescently labeled primers, and then allele size is evaluated using the ABI 3730XL genetic analyzer and Gene Mapper software. Other research-based assays are developed by request.
DNA bank: Whole blood and liver samples are collected from all rhesus and Japanese macaques for processing and archiving for genetic analysis. 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 22,000 archived samples from more than 6,600 NHPs, including 11 different species.
Quality control is incorporated into each service assay. For the SNP parentage assay, two control DNAs are included to monitor the reproducibility of genotype calls. Only genotypes with gentrain scores of 0.6 or higher are reported. For the SNP ancestry array, known Indian and Chinese rhesus DNA controls are included in each assay to monitor the reproducibility of genotype calls. A standardized reference panel of 72 characterized Indian and Chinese rhesus macaques is included in each Structure analysis to insure consistency in population clustering. The 95% confidence intervals for each population fraction are reported for each individual. For the MHC expressed allele assay, RNA from a previously characterized control animal is included in each set of sample, to insure reproducibility and accuracy of allele assignment. Alleles with a minimum of 0.2% sequence representation are reported. Allele call consistency is also evaluated by comparing the deduced alleles among available parent-offspring pairs. For the DNA Bank, DNA samples are evaluated by UV absorbance to ensure the 260/280 ratio is between 1.8-2.0 and that the DNA concentration is between 50-250 ng/ul.
Charges for rhesus ancestral SNP ancestry parentage assays are $50/DNA. The MHC expressed allele assay is $150 per individual. Charges for obtaining DNA from the DNA bank is $2/ug DNA for internal. If DNA extraction from a buffy coat or liver sample is required, a $20 fee is charged, with the agreement that 10 ug is delivered to the investigator and the remaining DNA sample is retained by the Bank.
BIOSTATISTICS AND BIOINFORMATICS UNIT
Byung Park, Ph.D., Research Assistant Professor, Biostatistics
Larry Wilhelm, M.S., Bioinformatics Specialist
Ranjani Ramakrishnan, M.S., Bioinformatics Specialist
Benjamin Popescu, B.S., Bioinformatics Support
Biostatistical support includes a range of analyses, including statistical genetics, comples sample survey, meta analysis, Bayesian data analysis, longitudinal data analysis, survival analysis, microarray analysis, among others. Support for data analysis, study design and manuscript submission are arranged as needed. Drop-In sessions are held weekly to enable opportunity to discuss projects in person. Workshops are held several times a year to provide educational opportunities to learn and discuss commonly used statistical analyses.
Bioinformatic support is offered for next generation sequence analysis, also on a fee/service basis. Whole genome, transcriptome, exome, sequence and structural variation detection, and methylation study analysis are provided. Short-term network storage is made available for large data sets at the OHSU Advanced Computer Center.
Charges for statistical services are $60/hour for junior faculty and $100/hour for senior faculty. Bioinformatics services are priced per project, depending on scale and scope of study, with a base rate of $60/hr.