mice: Heterogenous stock mice population

Description Usage Format Source References Examples


Data set comprises public available data of 2527 (1293 males and 1234 females) heterogenous stock mice derived from eight inbred strains (A/J, AKR/J, BALBc/J, CBA/J, C3H/HeJ, C57BL/6J, DBA/2J and LP/J) followed by 50 generations of pseudorandom mating. All individuals are labeled with a unique ID, starting with A048005080. For all individuals, family, sex (females=0, males=1), month of birth (1-12), birthyear, coat color, cage density and litter is available and stored in covar.

The measured traits are described in Solberg et al. (2006). Here, the body weight at age of 6 weeks [g] and growth slope between 6 and 10 weeks age [g/day] are available. The heritabilities of these traits are reported as 0.74 and 0.30, respectively (Valdar et al, 2006b). Phenotypic data was taken from http://mus.well.ox.ac.uk/GSCAN/HS_PHENOTYPES/Weight.txt.

Genotypic data consists of 12545 biallelic SNP markers and is available for 1940 individuals. Raw genotypic data from http://mus.well.ox.ac.uk/GSCAN/HS_GENOTYPES/ is given in the Ped-File Format with two columns for each marker. Both alleles were combined to a single genotype for each marker in mice data. The SNPs are mapped in a sex-averaged genetic map with distances given in centimorgan (Shifman et al. (2006)). SNPs are mapped across all 19 autosomes and X-chromosome where distances between adjacent markers vary form 0 to 3 cM.




Object of class gpData


Welcome Trust Centre for Human Genetics, Oxford University, data available from http://gscan.well.ox.ac.uk


Shifman S, Bell JT, Copley RR, Taylor MS, Williams RW, et al. (2006) A High-Resolution Single Nucleotide Polymorphism Genetic Map of the Mouse Genome. PLoS Biol 4(12)

Solberg L.C. et al. (2006), A protocol for high-throughput phenotyping, suitable for quantitative trait analysis in mice. Mamm. Genome 17, 129-146

Valdar W, Solberg LC, Gauguier D, Burnett S, Klenerman P, Cookson WO, Taylor MS, Rawlins JN, Mott R, Flint J. (2006a) Genome-wide genetic association of complex traits in heterogeneous stock mice. Nat Genet. 8, 879-887.

Valdar W, Solberg LC, Gauguier D, Cookson WO, Rawlins NJ, Mott R, Flint J.(2006b) Genetic and environmental effects on complex traits in mice. Genetics 175, 959-984


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synbreedData documentation built on May 1, 2019, 6:51 p.m.