Diversity Outcross (DO) QTL Mapping data - high fat diet, multiple phenotypes

Description

A panel of 150 Diversity Outbred (DO) mice were phenotyped over a period of 24 weeks. 100 of the mice received a chow diet and 50 received a high fat diet from weaning until sacrifice. The mice were genotyped at 7,854 SNPs on the Mouse Universal Genotyping Array (MUGA) and quantitative trait locus (QTL) mapping was performed on the phenotypes. Animals were subject to a battery of noninvasive physiological measurements to obtain clinical parameters, including: serum cholesterol (at 8 and 24 weeks), early and late measurements of clinical plasma chemistries (lipids, glucose, insulin) and body composition (weight, percent fat, lean tissue mass). Coat color was also recorded. The genotypes were reconstructed using a hidden Markov model that produced genotype probabilities for each sample at each SNP. These were then condensed down to eight founder allele dosages that were used to map each trait. Mapping was carried out with QTLRel, which accounts for the complex genetic relationships between mice.

Reference

Use of these data should cite the following references:

High-Resolution Genetic Mapping Using the Mouse Diversity Outbred Population
Svenson KL, Gatti DM, Valdar W, Welsh CE, Cheng R, Chesler EJ, Palmer AA, McMillan L, Churchill GA.
Genetics. 2012 Feb;190(2):437-47. PMCID: PMC3276626 [Available on 2013/2/1]

The Diversity Outbred Mouse Population
Churchill GA, Gatti DM, Munger SC, Svenson KL
Mammalian Genome 2012 Aug 15. [Epub ahead of print]

Datasets

 

Phenotype Data

Array Genotype Data

Reconstructed Genotype Data for Svenson et al. Genetics 2012

Reconstructed Genotype Data for Churchill et al. Mammalian Genome 2012

  • This zip file contains 143 files, one for each sample that could be genotyped. 7 samples were not genotyped due to technical reasons. Each file is a tabular, comma separated file with 36 columns and 7,854 rows. Each column represents one unphased genotype. Each row represents a single SNP. Each cell contains the posterior probability that the sample contains the genotype of that column at the SNP for that row. There is also a “SNP_Map.txt” file that contains the SNP locations.
    Churchill.Mamm.Gen.2012.genotype.probs.zip

QTL Results for Svenson et al. Genetics 2012

QTL Results for Churchill et al. Mammalian Genome 2012

  • This zip file contains the QTL results. Text files are tab delimited. The LOD scores are in files called *.QTLRel.LOD.txt. The model coefficients are in files called *.QTLRel.coef.txt. The maximum LOD score over 1,000 permutations is in files called *.QTLRel.perms.txt. Each phenotype contains a PDF with a QTL plot and coefficient and effect plots for significant QTL.
    Churchill.Mamm.Gen.2012.QTL.zip