Rhesus macaque 96 SNP parentage assay:
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.
Rhesus macaque SNP ancestry assay:
This SNP assay includes 122 Ancestral Informative Markers (AIMs) selected for high information content and broad genomic representation. The genotyping is carried out using the ABI QuantStudioTM 12K Flex System. The genotypes are then compared with 74 animals of known origin (35 Indian rhesus, 35 Chinese rhesus, and 4 hybrid animals of mixed Indian/Chinese origin). STRUCTURE analysis (Pritchard et al., 2000) is used to calculate a statistical probability of assignment into the two populations, with the 90% probability interval reported. Quality Control: Two previously genotype DNAs are included to evaluate consistency of genotype and ancestry calls. Ancestry determination is not made on DNAs with more than 10% missing genotype information.
MHC expressed allele assay:
The RNA-based MHC assay used to detect expressed class I alleles in rhesus macaques, 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 uploaded into the PRIMe database. Quality Control: A previously analyzed RNA sample is included in each round of library construction to insure reproducibility of results. Samples producing fewer than 1,000 reads are not reported.
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. Quality Control: control gDNAs having known genotypes are included to assure reproducbility 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 35,000 archived samples from more than 7,600 NHPs, including 11 different species.