* Double Digest Genotyping-by-Sequencing (ddGBS) Protocol
Double digest genotyping-by-sequencing (ddGBS) is a reduced representation genotyping method for sequencing on the Illumina platform. ddGBS libraries are prepared by digesting gDNA with two restriction enzymes and annealing oligonucleotide adapters to the resulting overhangs. By focusing sequencing efforts onto restriction sites, ddGBS achieves higher coverage than if the entire genome was sequenced at random.
This protocol was adapted from the original approach using a single restriction enzyme (Elshire et al. 2011) and is optimized for use in rodents. It details how to construct sequencing libraries using a set of 48 indexed adapters (designed by Grabowski et al. 2014). Specifications vary according to the needs of individual projects. It is strongly recommended to contact the Palmer Lab before use to ensure proper concentrations of all adapter stocks and that sample multiplexing will achieve the desired depth of coverage.
QTLRel is an R package for mapping quantitative trait loci (QTLs) in experimental crosses such as advanced intercross lines (AILs) where relatedness among individuals should not be ignored.
QTLRel includes functions to estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for quantitative trait loci, and plot the mapping results.
R code to select breeders from an advanced intercross line so that they minimize inbreeding in the offspring.
QTL mapping for craniofacial morphology traits in Swiss Webster (CFW) mice using GEMMA. Contains genotype & phenotype data and R code to reproduce results of upcoming PLoS Genetics article. This project was a collaboration with Luisa F Pallares and Diethard Tautz, Max Planck Institute for Evolutionary Biology in Germany.
Demonstration of QTL mapping for fear conditioning traits in LG/J x SM/J mouse advanced intercross line. Contains data and R code to reproduce results of a forthcoming Genetics article.
QTL mapping for prepulse inhibition phenotypes in F1 panel derived from common inbred mouse strains using a linear mixed model (GEMMA). Contains data and R code to reproduce results of upcoming GWAS manuscript.
* dbGaP Study: “Sensitivity to the Subjective Effects of Amphetamine”
Study results and data sets available for examination and analysis.
The goal of this study was to identify SNPs associated with subjective, physiological, and behavioral responses to d-amphetamine. Molecular data included whole-genome genotyping (AFFY_6.0 platform) and imputation (1000 Genomes Project). This project was a collaboration with Harriet de Wit, Director of the Human Behavioral Pharmacology Lab at the University of Chicago.
Files: readme, Linear4PGC.zip, Multi4PGC.zip, Cacr4PGC.zip
Summary statistics of GWAS for loneliness in humans (Gao et al., Neuropsychopharmacology, 2016). All genotype and phenotype data were collected as part of the Health and Retirement Study at the University of Michigan. This project was a collaboration with John Cacioppo at the University of Chicago.
* WIPO Patent: Methods and Compositions for Inhibiting Glyoxalase 1 (GLO1)
Palmer A, Distler M. Methods and compositions for inhibiting Glyoxalase 1 (GLO1). International Patent Number WO2014/159720. Date Issued: October 2, 2014.