UC San Diego

The “replication crisis” has highlighted the apparent lack of replication across scientific fields. Assessing the true effect size of a genetic variant and designing an adequately powered study remain difficult when replicating genome-wide association studies (GWAS) results. Functional replication studies that validate the identified loci have also been scarce. Given the importance of replication, my thesis focuses on the computational and the functional aspects of replication. In chapter 1, I explored replication in a mouse model using an advanced intercross line (AIL), which is a multigenerational intercross between two inbred strains. I used genotyped and re-genotyped data from two cohorts of the LG/J x SM/J AIL mice (F34, n=428; F39-43, n=600). For the subset of traits that were measured in both cohorts (locomotor activity, body weight, and coat color), I attempted to replicate loci identified in either F34 or F39-43 in the other cohort. Coat color was robustly replicated; locomotor activity and body weight were only partially replicated, which was inconsistent with our power simulations. We used a random effects model to show that the partial replications could not be explained by Winner’s Curse but could be explained by study-specific heterogeneity. Despite this heterogeneity, I performed a mega-analysis by combining F34 and F39-43 cohorts (n=1,028). In chapter 2, I followed up on a candidate gene, Azi2, which had previously been identified in a GWAS for locomotor response to methamphetamine using an outbred Carworth Farms White (CFW) population. To validate Azi2 as a putative causal gene for methamphetamine sensitivity, I created an Azi2 knockout mouse line using CRISPR/Cas9 and established the mutant phenotype of locomotor response to methamphetamine. In addition, I investigated a published hypothesis that an independent transcript that matches to the second half of the 3’UTR sequence of Azi2 is a downregulator of Slc6a3, which encodes the dopamine transporter (DAT), in the ventral tegmental area (VTA) region of midbrain. To test this hypothesis, I examined the possible correlations among Azi2, Azi2 3’UTR, and Slc6a3 expression in the Azi2 KO line and in naïve CFW mice.