Core C

Project Summary (Core C: Genotyping, Analysis and eQTL Core) The purpose of this core is to provide genotyping and analysis services for the supported grants. Analysis services will focus on genome wide association studies (GWAS) that are intended to identify the relationships between genotypes and phenotypes with the ultimate goal of implicating specific genes that

influence substance use disorder (SUD) relevant traits. The wet-lab protocols and bioinformatic pipelines used by this core have already been established, but they will continue to be improved over the course of the funding period. We will also continue to provide expression quantitative trait locus (eQTL) mapping, presenting

these results on a public facing website and also incorporating them into the GWAS results. This core will also perform the wet-lab and bioinformatic steps necessary for phenotype prediction in support of RATTACA (RAT Trait Ascertainment using Common Alleles), which is described in Core B. One of the key services that this core will offer is the ability to genotype heterogeneous stock (HS) rats

at millions of polymorphic markers with an accuracy of >99.75% at an extremely low cost. We will accomplish this by performing low coverage whole genome sequencing (lcWGS) followed by an imputation step that uses the deep sequence data that are available from the 8 inbred founders of the HS population. This approach has

undergone multiple improvements over the past decade. We have used this approach to genotype HS rats, Sprague Dawley rats, various outbred mouse populations and most recently zebrafish; however, the purpose of this core is to genotype HS rats for supported grants. We will continue to improve this pipeline by inputting

tandem repeats and structural variants and by calling genotypes on the Y and mitochondrial chromosomes. In addition to genotyping HS rats, this core will perform genetic analyses, which include GWAS, phenome-wide association studies (PheWAS), heritability estimates, genetic correlations and related approaches. We have already demonstrated our ability to perform these analyses and will offer them as a

service to supported grants. Results are summarized in “reports'' that provide figures and tables that can be incorporated directly into publications. These reports are one of the primary outputs of this core and would be extremely difficult for the supported grants to develop independently because they require substantial

statistical and computational expertise. Finally, this core will support two public facing websites. The first provides the only available eQTL resource for rats. The second will introduce, for the first time, a public facing transcriptome wide association studies (TWAS) portal, allowing investigators to query individual genes and discover correlations between the

genetically determined expression of that gene and all of the phenotypes in our HS rat database; the database, which is supported by Core A, currently contains phenotype and genotype data for more than 15,000 HS rats and will continue to grow over the course of this award.