Request for applications: Genomic profiling nonhuman primates used in WNPRC research

Co-sponsored by the Wisconsin National Primate Research Center and the Baylor College of Medicine Human Genome Sequencing Center

Number of Applications

Funding for exome sequencing a total of 200 nonhuman primates is anticipated.

Overview

This opportunity solicits applications to perform genomic profiling on nonhuman primates used in biomedical research. The Genetics Services Unit of the Wisconsin National Primate Research Center, in collaboration with the Baylor College of Medicine, anticipates offering combination genomic profiling (high resolution MHC genotyping plus whole exome sequencing) on a fee-for- service basis beginning in 2016. Genomic profiling of nonhuman primates offers the potential to improve experimental design and interpretation. Informal surveys of Principal Investigators at the WNPRC revealed interest in obtaining genomic profiles tempered by concerns about cost and whether this data would offer an immediate benefit to research projects. This RFA seeks to bridge this gap by subsidizing genomic profiling of approximately 200 macaques used in WNPRC research projects.

Key Dates

Posted Date

October 20, 2015

Application Due Date(s)

December 1, 2015

Merit Review

December, 2015

Purpose

The Genetics Services Unit of the Wisconsin National Primate Research Center (WNPRC), in collaboration with the Baylor College of Medicine Human Genome Sequencing Center, intends to offer genomic profiling of nonhuman primates beginning in 2016. Genomic profiles consist of genome-wide exome sequences plus high-resolution major histocompatibility complex (MHC) class I and class II genotypes (since complex immune loci such as the MHC are poorly resolved with current exome sequencing technology). Initially, genomic profiling will be available for macaques (rhesus, pig-tail, and cynomolgus).

Researchers are the target audience for this genomic profiling service. Genetics Services has provided thousands of MHC genotypes to researchers who routinely incorporate this data into their experimental designs and analyses. The purpose of this RFA is to encourage researchers to incorporate similar analyses of the remainder of the genome into their studies.

Objective

Responsive applications will identify specific WNPRC macaques for genomic profiling. Each qualifying animal must have been used in a research study, be in an ongoing research study, or be under consideration for inclusion in planned research studies. Genomic profiling of breeding colony animals is not responsive to this RFA. Investigators will be responsible for coordinating the collection of blood from living animals or obtaining high-quality DNA samples from animals used in retrospective studies. The samples will be shipped by Genetics Services to the Baylor College of Medicine (BCM) Human Genome Sequencing Center. DNA from protein-coding exons and MHC genes will be deep sequenced at BCM. Sequence reads will be mapped multiple reference genomes (human, cynomolgus macaque, and rhesus macaque for macaque samples), sites with high-confidence variation will be identified, and the predicted impact of these variants on protein function will be determined. Investigators will receive curated reports of variants predicted to cause loss of protein function from Genetics Services, as well as the raw sequencing data (FASTQ), read mappings (BAM), and variant calls (g.VCF). Because the sequencing is subsidized by the WNPRC, the genomic data will be incorporated into the WNPRC EHR and available to all WNPRC researchers.

Application process

Applicants are expected to prepare a 1-2 page document describing the research question(s) addressed with the animals proposed for genomic profiling, the type of phenotypic variation hypothesized to have a genetic basis, and, if known, genes or pathways that are hypothesized to vary between these animals. Note that applications do not need to have candidate genes to be responsive to this RFA but preference may be given to applications that have more clearly defined outcomes.

Each application must propose a minimum of ten animals for genomic profiling. There is not a formal maximum, however, since this pilot program is aimed to increase awareness of genomic profiling among investigators smaller (25 or fewer NHP), equally meritorious requests will receive preference. Funding is available to support genomic profiling of 200 total NHP.

In addition to the application, applicants are expected to provide an Appendix Table individually identifying each animal proposed for sequencing and the source of samples that will be used for high-quality DNA extraction.

Successful applicants will be notified by the end of January 2016. Sequencing at BCM is expected to take approximately three months. Data analysis is anticipated to take approximately one month.

Completed applications should be sent to Edi Chan; chan@primate.wisc.edu.

Questions

Please direct any questions to Dave O’Connor; doconnor@primate.wisc.edu.