Joel Leal accepts Assistant Professor position at Lincoln University of Missouri
Joel will work on understanding the genetic architecture of complex phenotypes using sheep as animal models.
Congratulations, Joel!
10th Annual P50/P30 Center Retreat
The 10th Annual P50/P30 Retreat was held on Friday, September 6, 2024 at the University of California San Diego.
Thank you to all who attended in person and remotely! We hope you found the talks and discussions informative and made connections with new HS rats/GWAS colleagues.
Presenters, talk recordings, and photos are available on the P50/P30 Center website. (ratgenes.org)
Dr. Palmer attends GRC 2024 in Maine
Dr. Palmer was invited to present at the third Gordon Research Conference (GRC) in Newry, Maine on August 18-23, 2024.
He gave a talk titled “Studying Intermediate Phenotypes to Elucidate the Genetic Basis of Substance Use Disorders” during the concurrent Neurobiology of Drug Addiction meeting.
NIDA P30 Grant Awarded
The NIDA Core Center of Excellence grant titled, “Center for Genetics, Genomics, and Epigenetics of Substance Use Disorders in Outbred Rats,” has been awarded to Drs. Abraham Palmer, Pejman Mohammadi, Oksana Polesskaya, and Leah Solberg Woods.
Congratulations!
Rudy Avila joins the Palmer Lab
Rudy started at the Palmer Lab as a Lab Assistant in August 2024.
Prior, he obtained a BS in Molecular and Cellular Biology from Johns Hopkins University.
Welcome, Rudy!
Detecting errors by using genotype kinships
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.
Recombination desert on HS rat Chromosome 13
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.
Converting GFF3 to refFlat
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.
Detecting errors by using albinism
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).
Should GWAS in HS rats use PCs as covariates?
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?
