Physiological trait and genotype data for 1,038 outbred CFW mice

R data set containing physiological trait data and genotype data for 1,038 mice from the Carworth Farms White (CFW) outbred mouse stock. These data were collected as part of a large study to assess the viability of using Carworth Farms White (CFW) mice for mapping genes and genetic loci underlying complex traits relevant to the study of human disease and psychology. The data accompany the following publication:

Parker CC, Gopalakrishnan G, Carbonetto P, Gonzales NM, Leung E, Park YJ, Aryee E, Davis J, Blizard DA, Ackert-Bicknell CL, Lionikas A, Pritchard JK, Palmer AA. Genome-wide association study of behavioral, physiological and gene expression traits in commercially available outbred CFW mice. Nature Genetics 48: 919–926.

To use these data for your research, please cite this Zenodo resource, as well as the paper published in Nature Genetics.

After loading these data into the R environment, e.g., by running "load(cfw.RData)", you will find R objects including:

"pheno"—a 1,038 x 7 matrix containing the quantitative trait, or "phenotype", data. Traits include body weight, tibia length, muscle weights (EDL and soleus), and a binary indicator for abnormal bone health.

"map"—a data frame containing information for 79,748 single nucleotide polymorphisms (SNPs) on chromosomes 1–19 genotyped in the CFW mice. All genomic positions are based on Mouse Genome Assembly 38 from the NCBI database (mm10, December 2011).

"geno"—a 1,038 x 79,748 matrix containing genotype data for 1,038 mice at 79,748 SNPs.

For more information on these data, please refer to the Data Dryad repository: http://dx.doi.org/10.5061/dryad.2rs41

For code implementing QTL mapping of physiological, behavioral and gene expression phenotypes, and other analyses of these data, see: http://github.com/pcarbo/cfw