The purpose of this core is to obtain genotypes for ~5,000 DNA samples derived from rats that are phenotyped by Projects 1, 2, and 3. In addition, we will perform RNA Sequencing (RNASeq) in support of Research Projects 1 and 2. Finally, we use these data to perform genome wide association studies (GWAS) and a number of related analyses.
One of the critical technical advances that made this center possible was our development of genotyping by sequencing (GBS) for use in rats. We are able to obtain ~3.7 million SNPs for less than $50 per sample.
In addition to obtaining genotypes and performing RNASeq, this core will perform genetic analyses, which include GWAS, phenome-wide association analyses (PheWAS), transcriptome wide association analyses (TWAS), heritability estimates, genetic correlations, and a new approach that we call polygenic transcriptomic risk score (PTRS) prediction. All of these analyses are routinely performed in Palmer laboratory and have been the subjects of prior publications that used rats, mice, and humans.
This core may also provide genotyping services to outside investigators on a cost recovery basis. Because the analysis of GBS data requires large numbers of samples, such a service would only be appropriate for investigators who are interested in genotyping at least several hundred samples.