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 or full-length transcripts, 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.

To balance experimental and control groups or determine the degree of MHC mismatch for transplant studies, lineage-level allelic resolution provided by our standard MiSeq assay (that focuses on the most polymorphic segments of MHC genes) is appropriate.  When full resolution of the specific MHC allelic variant is important to discovery, we recommend PacBio SMRT sequencing of full-length MHC transcripts. If you are unsure of which MHC assay is best for your research, please contact Genomics Services.

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

To request service, please complete the on-line WNPRC Genomics Services Service Request form.

To estimate costs for MHC genotyping, please visit the on-line WNPRC Genomics Services Cost Estimator

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:

• TRIM5 genotyping via a MiSeq short amplicon sequence-based assay to detect TRIM5Q, TRIM5TFP, and TRIM5CypA alleles.
• Fc gamma receptor (FcɣR) genotyping via PacBio Sequel full-length sequencing
• Killer immunoglobulin-like receptor (KIR) genotyping via PacBio Sequel full-length sequencing

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

For more information including current pricing, please see our Other Immune Loci white paper (pdf).

Interested in more information? Contact the Genomics Services Host Genotyping group.

VIRAL PATHOGEN SEQUENCING

We specialize in RNA viral genome sequencing with an emphasis on simian immunodeficiency viruses (e.g., SIVmac239, SIVmac251, and SIVsmE660) and emerging pathogens (e.g., Zika virus). We use Illumina MiSeq technology to sequence the entire coding sequence of RNA viruses, shorter amplicons, and plasmids.

Sequencing data can be produced from various starting materials, including plasma, cell culture, RNA, and DNA. In our method, each genome is molecularly barcoded, and 20-30 viral genomes are pooled together for each MiSeq run. After images are processed and nucleotides are called on the MiSeq instrument, we bin the sequence reads by barcode tag. We routinely provide fastq files for each read. If a reference genome is available, we can also generate BAM or SAM alignments. Additional data analyses may be performed after consultation with Pathogen sequencing lead, Dr. Shelby O’Connor.

Viral pathogen stocks used to infect animals will be deep sequenced  free of charge*  provided investigators agree to make this important information publicly available via the SRA database.

Please see our pathogen sequencing white paper (pdf) for additional details.

To learn more, contact Pathogen sequencing lead, Shelby O’Connor, PhD.

PRICING EXAMPLES:

SERVICE	COST/SAMPLE**
SIV SEQUENCING FROM PLASMA – Qiagen	$213.63
SIV SEQUENCING FROM PLASMA – Maxwell	$197.59
VIRUS SEQUENCING MULTIPLEX TWO POOLS FROM PLASMA	$226.70
VIRUS SEQUENCING FROM CDNA AMPLICONS GENERATED BY CLIENT	$237.16
*UNBIASED SEQUENCING OF INOCULA FROM RANDOM HEXAMERS	$0

**All pricing examples cover the cost of reagents, labor & BAM alignment. Prices shown are cost recovery rates for UW-Madison investigators. Other investigators are charged overhead rates ranging from 38.5% (federal or not-for-profit) to 72.5% (for-profit entities).