Genotyping for parentage validation is performed using a 96 SNP assay, performed on a Fluidigm Biomark HD platform. This SNP 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. Quality Control: two replicate samples are included with each assay to evaluate the reproducibility of genotype calls.

The formally offered, SNP-chip based Rhesus Macaque Ancestry Assay has been discontinued. However, alternative approaches are available which can similarly estimate Chinese and Indian admixture of a rhesus macaque sample based on the genotyping of highly informative Ancestral Informative Markers (AIMs). Please contact the Core for specifics regarding testing capabilities. 

For projects and assays not requiring the high throughput offered by the latest Next-Gen sequencing platforms, the Primate Genetics Core offers MiSeq sequencing, ideal for smaller-scale projects or targeted assays, including those that require read length flexibility or that require rapid turnaround. We specialize in working with researchers to optimize assays to meet research needs in a timely fashion.  

MHC expressed allele assay

Macaque MHC class I genotyping is performed using the RNA-based expressed allele assays, as described by Wiseman et al., 2009. Targeted polymorphic MHC Class I 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. Alleles with a minimum of 0.2% sequence representation are reported. Finalized MHC alleles and haplotypes are reported directly or uploaded into the PRIMe database. Quality Control: A previously analyzed RNA sample is included in each round of library construction to ensure the reproducibility of results. 

Custom genotyping assays

The design of assays to distinguish macaque Single Nucleotide Variants (SNVs) or Variable Number Tandem Repeats (VNTRs) are available for investigators by request. Genotyping based on previously established assay designs (CLN7 c.769delA, 5-HTTLPR, MAOA-LPR, CRH C-2610T, TPH2 A2051C, Mamu-A*01, Mamu-B*08, Mamu-B*17) are also available. DNA samples with known genotypes are included to assure the reproducibility of assay results. 

ONPRC NHP DNA Bank

The ONPRC DNA Bank contains whole blood and liver samples collected on an ongoing basis from all rhesus and Japanese macaques to support internal and external research programs. DNA is extracted as needed from buffy coat, whole blood, or liver samples. Currently, the DNA Bank includes over 60,000 archived samples from more than 19,000 NHPs, including 11 different species.

Most specialized and general equipment maintained and operated by the core is also available for use by individual investigators. Training, supervision, and necessary reagents is supplied. Available equipment includes real-time PCR machines, automated nucleic acid extraction robots, DNA/RNA QC platforms, plate readers, cell counters, and gel imagers. Please inquire about other services or requests.

The Primate Genetics Core has extensive experience extracting DNA and RNA from a variety of tissue sources using standard protocols and automated systems. Quality and quantity of isolated samples is assayed with ThermoFisher Qubit Fluorometer, Nanodrop Spectrophotometer and Agilent Bioanalyzer.

Primate Genetics Support Service Rates

Sample submission

For ONPRC and OHSU users
All materials/samples are supplied either in person or shipped directly to the Genetics Support Services using the inter-campus courier.  Please give notice before shipping and provide the appropriate manifest or submission form at the time of notification.  Please provide billing information with the sample submission.

For external (non-OHSU) users
External billing proceeds through the ONPRC billing office. Please email us with any inquiries and we will generate a quote. ONPRC guidelines require external users to supply us with a purchase order (PO) before initiating services. After the work is completed, external users will receive an invoice for review, and the supplied PO will be billed.

Materials should be submitted by FedEx.  All materials should be packaged according to your institution's biosafety requirements and following IATA guidelines for shipping dangerous goods.  Please give us at least 24 hours of notice, via email, before shipping samples to the Genetics Support Services.  Provide the appropriate manifest or submission form with your notification.  

Results for genotype assays will be provided by email.