Primate Genetics Program

 

COLONY GENETICS RESOURCE CORE

The Colony Genetics Resource Core oversees all population genetic analysis of non-human primates (NHPs) at the ONPRC, in order to characterize the large colony pedigree (~23,000 rhesus macaques since 1963), to monitor colony genetic diversity, and to characterize genetic contributions to disease traits in colony macaques. Analyses based on the ONPRC pedigree are 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 NHPs at the ONPRC. With phenotype and genotype data, the ONPRC pedigree is also an immensely valuable resource for discovering genetic contributions to diseases that are conserved between macaques and humans. 

Amanda Vinson, Ph.D., Director
Elizabeth Slikas, Ph.D., Research Associate
Lauren Hales Beck, B.S., Research Asst. 2

Services Provided

  • Parentage Assignment and Other Kinship Analysis:  Blood samples are collected from all newborn macaques during physical exams conducted as a part of routine veterinary care for all animals.  These blood samples provide DNA for parentage analysis and for archiving in the ONPRC DNA Bank to support future genetic research (see below for a description of the ONPRC DNA Bank).  We use a 96 SNP assay based on the Fluidigm platform to assign parentage.  This assay was developed in partnership with the NPRC Genetics and Genomics Working Group Consortium to enable consistent genotyping and comparison of rhesus macaques across all NPRCs. Parentage assignment is evaluated using the NPRC Consortium parentage analysis pipeline.  We also provide analyses of kinship among specified animals based on the overall colony pedigree, as needed by ONPRC investigators.
  • Analysis of Population Genetic Diversity:  All ONPRC macaques are genotyped not only to assign parentage, but to establish population genetic metrics for the colony as a whole.   Population genetic metrics include the estimation of kinship for individuals relative to the rest of the colony, the overall kinship within the colony, and probabilistic measures of allelic diversity for individual animals.These metrics are used to identify animals that are the most genetically valuable to the colony, so that breeding groups can be developed that minimize the loss of genetic diversity from the colony as a whole. To support these efforts, we have developed new software to estimate these metrics, and to aid in developing new breeding groups.  These results are provided, along with recommendations for new breeding groups, to the Division of Comparative Medicine for use in colony management decisions. We also offer assistance to external institutions in the population genetic analysis of their animal colonies 9see charges for consulting services, below).
  • Colony Genetic Epidemiology: We will also work with both internal and external investigators to build pedigree around clinical or research phenotypes of interest in ONPRC macaques, in order to characterize genetic contributions to disease in this valuable animal model. We can provide analyses of trait heritability and gene-by-environment interaction that do not require specific genotype data. With genotype data, we can also conduct linkage analyses, and family-based candidate gene/SNP association to identify specific genetic variants that may contribute to disease traits (see charges for consulting services, below).
  • Maintenance of Colony Genotype Data and the ONPRC DNA biobank:  The PRIMe database is the central electronic health records (EHR) system for all NHPs at the ONPRC. As part of PRIMe, we upload and maintain all marker genotype data collected on individual animals for parentage analysis (both microsatellite and SNP marker genotype data), as well as results of parentage assignment. Additionally, our curation of the ONPRC pedigree permits estimates of mean individual kinship relative to the colony, as well as pairwise kinship between any 2 macaques, to be accessed through PRIMe.  Small pedigrees around a focal animal that extend from grandparents through offspring may also be viewed within PRIMe.

The ONPRC DNA Bank contains whole blood and liver samples collected on an ongoing basis from all rhesus and Japanese macaques to support genetic analysis. DNA is extracted as needed from buffy coat, from whole blood, or from liver samples. All samples and DNA are stored in ultra-low freezers and are available to investigators for a fee. Currently, the DNA Bank includes over 22,000 archived samples from more than 6,600 NHPs, including 11 different species.

Charges 

Charges for obtaining DNA from the DNA bank is $2/ug DNA for internal investigators. 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 DNA Bank.

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. 

Betsy Ferguson, Ph.D., Director
Rita Cervera Juanes, Ph.D., Research Assistant Professor
Rachna Shah, B.S., Research Associate
Gwen Steinbach, B.S., R.N., Research Assistant I

Molecular Services Provided 

  • 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. Geneotypes and haplotypes are deposited into PRIMe. 

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.

Chargebacks

Charges for rhesus ancestral SNP ancestry parentage assays are $50/DNA. The MHC expressed allele assay is $160 per individual.  

BIOSTATISTICS AND BIOINFORMATICS UNIT 

Lucia Carbone, Ph.D., Director
Byung Park, Ph.D., Research Assistant Professor, Biostatistics
Suzanne Fei, Ph.D., Computational Genomics Analyst
Charles Huang, M.S. Bioinformatics Specialist 

Biostatistical support includes a range of analyses, including statistical genetics, meta analysis, Bayesian data analysis, longitudinal data analysis, survival 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.

Bioinformatics support is offered for analysis of next-generation sequence data. Standard analysis including, whole genome (DNA-seq), transcriptome (RNA-seq), exome, proteomics are provided. The BBU also supports analysis of single nucleotide variant (SNV), copy number variations (CNV), and CpG methylation. Consultation with the unit director and her staff about the study design before gathering sequence data is encouraged and free of charge. The BBU will obtain the data directly from the sequencing core and will store it and back it up through the OHSU Advanced Computer Center. Raw and analyzed data will then be released to the investigator in a portable hard-drive together with a final report with the description of the methods and results of the analyses.

Chargebacks

Charges for statistical and bioinformatics services are $60/hour for junior faculty and $100/hour for senior faculty.