Ancestry Informative Markers and Genetic Management Panels for Rhesus Macaque
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The ancestry informative marker (AIM) and genetic management (GM) panels of genetic polymorphisms described below were developed by the Genomics and Genetics Working Group of the Nonhuman Primate Research Consortium for use by the National Primate Research Centers (NPRCs) to genetically characterize rhesus macaques employed in biomedical research. Both panels comprise single nucleotide polymorphisms (SNPs) most informative for identifying the geographic origin (AIM panel) and managing the genetic structure (GM panel) of rhesus macaque colonies. The locations of SNPs in each panel, their major and minor allele frequencies, heterozygosity and P values for HW erquilibrium in a random sample of Indian and Chinese rhesus macaques at the eight NPRCs and their flanking sequence for constructing primers and probes are shown.
The panels were constructed by selecting the most informative of thousands of SNPs randomly distributed throughout the rhesus macaque genome and genotyping them in several hundred rhesus macaques randomly selected from each of the eight NPRCs. The SNPs were genotyped using Illumina's Bead Array Assay and BeadXpress Reader on a Golden Gate Platform and exhibit Gentran scores at or above 0.6. The AIM panel includes SNPs whose minor allele frequencies (MAF) differ maximally between rhesus macaques originating in India and China, and the GM panel represents SNPs with the highest possible MAF in rhesus macaques originating in both geographic locations. The AIM panel is designed to determine whether a rhesus macaque is of Indian, Chinese or mixed ancestry. The GM panel is designed to determine parentage (sire and dam) of rhesus macaques and provide robust estimates of parameters, such as coefficients of inbreeding and kinship, heterozygosity and genetic subdivision of colonies, useful for colony genetic management.
These panels are more effective than existing panels using microsatellite (STR) markers and can be genotyped at a cost of approximately $50 per panel. As additional more effective SNPs are discovered they will replace the least effective SNPs on each panel and further technological developments are likely to reduce the cost of the panels.
Download the Ancestry Informative Markers Panel (Excel Spreadsheet)
Download the Genetic Management Markers Panel (Excel Spreadsheet)