Nonhuman Primate Genetics and Genomics Working Group
The Genetics and Genomics Working Group within the NPRC Consortium was established to provide a forum for discussion and collaboration among NPRC faculty and staff involved in the genetic analysis of nonhuman primates. The group works to develop and distribute new molecular and software tools that facilitate the genetic analysis of primate models of disease. These resources are now available to the broader research community, for the purpose of increasing the application of primate genetic data in research and to help researchers address questions related to human health and primate biology.
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NHP Genetics and Genomics Resources
Nonhuman Primate Genetic Variant Database
The Nonhuman Primate Genetic Variant Database currently houses around 64 million Single Nucleotide Polymorphisms (SNPs) contributed by researchers at participating NPRCs. Researchers can query for SNPs via chromosome and position, gene name, or SNP name. Returned SNPs can be automatically piped out to the UCSC Genome Browser as a custom track for visualization.
Macaque Genotype and Phenotype Database
The Macaque Genotype and Phenotype Database (mGAP.OHSU.edu) is a free resource with genomic and phenotypic data from a large cohort of rhesus macaques from the Oregon National Primate Research Center. This new resource currently offers includes more than 15 million annotated macaque variants.
National Nonhuman Primate DNA Bank
The National Primate Research Centers maintain and distribute extracted DNA. Samples from contributing institutions are available centrally via a web-based request system. The available species in the DNA bank include: Callithrix jacchus, Callicebus moloch, Chlorocebus aethiops, Macaca fascicularis, Macaca fuscata, Macaca mulatta, Macaca nemestrina, Pan troglodytes, and Papio anubis.
BALDR (BCR Assignment of Lineage by De novo Reconstruction)
BALDR (BCR Assignment of Lineage by De novo Reconstruction) is a pipeline for reconstructing human or rhesus macaque immunoglobulin(Ig)/B cell receptor(BCR) sequences from single cell RNA-Seq data generated by Illumina sequencing.
Ancestry Informative Marker and Genetic Management Panels for Rhesus Macaque
The ancestry informative marker (AIM) and genetic management (GM) panels are curated sets of SNPs that were developed for use by the NPRCs and other macaque research colonies to genetically characterize rhesus macaques employed in biomedical research. The panels are comprised of SNPs that were chosen to be informative for identifying the geographic origin (AIM panel) or managing the genetic structure (GM panel) of rhesus macaque colonies.
Genetic Management of Nonhuman Primate Colonies
This document presents a set of recommendations to aid in making breeding decisions that complement and enhance other existing data-driven husbandry practices and goals. These recommendations are based primarily on the development and use of multigenerational pedigree information for each colony, which facilitates the calculation of genetic relationships between animals.
Publications by Genetics and Genomics Working Group Members
See the latest publications by members of the Genetics and Genomics Working Group.