Genomics Services

MHC genotyping

Genomics Services provides high-throughput MHC genotyping for investigators using nonhuman primates to study cellular immunity and transplantation tolerance.

The MHC region of macaques is much more complex than the human MHC, with each animal expressing a variable number of MHC class I alleles. To distribute animals appropriately depending on experimental goals, we sequence the most polymorphic segments of MHC genes, then group sequences into simplified haplotypes to indicate highly transcribed alleles. These haplotype designations make it possible to identify animals that share multiple MHC alleles. Standard genotyping reports include the full list of detected alleles, in addition to the simplified haplotype designations.

Our MiSeq assay provides lineage-level allelic resolution and is appropriate for balancing experimental and control groups or determining the degree of MHC mismatch for transplant studies.

For more information on our approach to MHC genotyping, please see our MHC white paper (pdf).

Parentage authentication for Mauritian cynomolgus macaques

Genomics Services also provides high-throughput SNP genotyping assays to authenticate parentage for Mauritian-origin cynomolgus macaques. This SNP panel includes  assays for genotyping of ABO histo-blood group antigens that are critical for transplant researchers.

For these assays, we utilized our extensive database of whole exome sequences from Mauritian cynomolgus macaques to identify a custom panel of 96 highly informative SNPs that are widely distributed across the genome. Competitive PCR assays were designed for each SNP with unlabeled allele-specific primers and universal fluorescent probes. Multiplex PCRs are performed in a Standard BioTools Biomark X instrument with integrated fluidics circuits that allow all 96 SNP assays to be evaluated simultaneously with DNAs from 96 animals.

These assays help to ensure access to ethically sourced, purpose-bred cynomolgus macaques for biomedical research.

Other immune loci genotyping

Many investigators studying cellular immunity in nonhuman primates are interested in loci beyond the MHC. We offer the following genotyping services:

• ABO histo-blood group genotyping with Biomark X SNP assays
• TRIM5 genotyping with a MiSeq short amplicon sequence-based assay to detect TRIM5Q, TRIM5TFP, and TRIM5CypA alleles.
• Fc gamma receptor (FcɣR) genotyping via full-length transcript sequencing
• Killer immunoglobulin-like receptor (KIR) genotyping via full-length transcript sequencing
• Natural Killer Group 2 (NKG2) genotyping via full-length transcript sequencing

Though FcɣR, KIR and NKG2 assays are still under development for most nonhuman primate populations, we work with investigators interested in prototyping these assays as “early access” clients.

Fee-for-service consulting

Genomics Services staff are available for hourly fee-for-service consulting on balancing experimental groups based on genomics and assisting with the interpretation of many types of macaque genomics data, including whole genome and exome sequencing.