Sample duplicate and pedigree mix-up QCs use genetic kinship. There is a base level of relatedness among all HS rats from shared genetic history: outbred from eight inbred strains (Hansen and Spuhler 1984), then maintained as an intrabreeding population. Put blithely, everyone is everyone’s second cousin. Herein two methods to calculate genetic kinship are considered: KING robust coefficients and GRM off-diagonal values. Then, sample duplicates and pedigree discordance QCs for HS rats are developed.

High loadings in principal component analysis and unusual patterns of long-range linkage disequilibrium suggest that Chromosome 13 has a recombination desert, possibly due to an inversion on HS chr13. Large inversions prevent recombination between the inversion and non-inversion haplotypes (Li et al. 2023). We aim to find the location and cause of the recombination desert.

Regional association plots require the positions of genes to plot. We use the refFlat format, as required by LocusZoom. However, the Rat Genome Database (RGD) releases genome annotations in GFF3 format. Thus, we need to convert from one format to the other.

This project seeks to introduce and verify an “albinism QC”. Coat color is easy to phenotype and the genetic basis of albinism in rats is known. An albinism QC compares phenotyped coat color (albino vs. not albino) to genotyped albinism (homozygous recessive vs. others).

Best practice in human GWAS is to include the top principal components (PCs) as covariates. This project evaluated the use of PCs as covariates in GWAS using HS rat data. Does using PC covariates have a significant and/or positive effect on GWAS results?

It is of interest to know the locations and causes of HS rat genotype gaps. For example, little can be done to address a gap due to a lack of founder variation, but a gap due to poor genotyping may be amenable to improved genotyping methods. This project set out to discover gap locations in the context of minor allele frequency (MAF), both in founders and the modern population.

Ties are a problem for rank-based normalization. All samples must be assigned distinct ranks. Therefore, all ties must be broken in some way. Tie-breaking methods include the order samples appear, the alphanumerical order of sample identifiers, or randomly by a pre-determined seed number. We seek to determine the extent to which particular tie-break choices affect the GWAS results.

The manuscript titled ”Genome-wide association study of delay discounting in Heterogenous Stock rats” was accepted in Genes, Brain and Behavior.

Authors include current Palmer Lab members: Montana Lara, Apurva Chitre, Denghui Chen, Benjamin Johnson, Khai-Minh Nguyen, Sakina Muckadam, Thiago Sanches, Oksana Polesskaya, and Abraham Palmer.

Nina joined the Palmer Lab in July 2024 as a laboratory/animal assistant.

She graduated from UC Santa Barbara with a bachelor of science degree in Microbiology, and she plans to pursue graduate school.

Welcome, Nina!

Michael Rempel joined the Palmer Lab in July 2024 for a five-week internship on the Wet Lab team. His work focuses on genotyping Cadm2 transgenic rats which were created as an animal model to study the effect of mutations on the recursive splice site in Cadm2, which is known to be strongly associated with ADHD in humans.

Michael is a high school student at SET High. He is interested in modern biotechnology, including computational biology. Outside of school, Michael spends time with friends, volunteers at concerts, and helps with native habitat restoration in Rose Canyon.

Welcome, Michael!