Core C: Sequencing Core

The purpose of this core is to obtain genotypes for 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.
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.

Genotyping services

This core may also provide genotyping services to outside investigators on a cost recovery basis. Because our genotyping technique requires large numbers of samples, such a service would only be appropriate for investigators who are interested in genotyping at least several hundred samples.

Sequencing is performed at the UC San Diego IGM Genomics Center utilizing an Illumina NovaSeq 6000 that was purchased with funding from a National Institutes of Health SIG grant S10 OD026929

Updated 05/06/2020