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  • Review Article
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Genome-wide association studies in mice

Nature Reviews Genetics volume 13, pages 807–817 (2012)Cite this article

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Key Points

  • Genome-wide association studies (GWASs) have transformed the field of human genetics and have led to the discovery of hundreds of genes that are implicated in human disease. The technological advances that drove this revolution are now poised to transform genetic studies in model organisms, including mice.

  • Until recently, most mouse genetic studies used a standard genetic cross, which has the drawback that the regions implicated in the cross are very large and contain hundreds of genes.

  • Several recently proposed mouse GWAS strategies include those using the Hybrid Mouse Diversity Panel, the Collaborative Cross and heterogeneous and commercially available outbred stocks. Each of these strategies has advantages and disadvantages relative to the others, yet all improve resolution by an order of magnitude over the classic genetic cross.

  • The design of GWASs in mouse strains is fundamentally different from those carried out on humans, creating new challenges and opportunities. The development of modern mouse GWAS strategies is an active research area.

  • Using these strategies, many groups are rapidly identifying regions in the mouse genome that associate with complex traits that are relevant to human disease. This has led to the discovery of additional genes involved in human disease.

  • Mouse GWASs have advantages over human studies in their ability to functionally characterize implicated genes to understand mechanisms. These advantages include the accessibility of relevant tissues and the ability to carry out genetic manipulations, such as knockouts, which are impossible in human studies.

Abstract

Genome-wide association studies (GWASs) have transformed the field of human genetics and have led to the discovery of hundreds of genes that are implicated in human disease. The technological advances that drove this revolution are now poised to transform genetic studies in model organisms, including mice. However, the design of GWASs in mouse strains is fundamentally different from the design of human GWASs, creating new challenges and opportunities. This Review gives an overview of the novel study designs for mouse GWASs, which dramatically improve both the statistical power and resolution compared to classical gene-mapping approaches.

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Figure 1: Breeding schemes for mouse genome-wide association study populations.
Figure 2: Overview of mouse GWASs.
Figure 3: Comparison of mouse GWASs for HDL cholesterol.

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Acknowledgements

J.F. is supported by the Wellcome Trust. E.E. is supported by US National Science Foundation grants 0513612, 0731455, 0729049, 0916676 and 1065276, and US National Institutes of Health grants K25-HL080079, U01-DA024417, P01-HL30568 and PO1-HL28481. This research was supported in part by the University of California, Los Angeles, subcontract of contract N01-ES-45530 from the National Toxicology Program and the National Institute of Environmental Helath Sciences to Perlegen Sciences.

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Authors and Affiliations

  1. The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK

    Jonathan Flint

  2. Department of Computer Science, Department of Human Genetics, University of California, Los Angeles, 3532-J Boelter Hall, Los Angeles, 90095–91596, California, USA

    Eleazar Eskin

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Correspondence to Eleazar Eskin.

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FURTHER INFORMATION

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GeneNetwork

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MGI — Mouse Genome Informatics

Mouse Genome Variation Identifier

Mouse Phenome Database

Nature Reviews Genetics Series on Genome-wide association studies

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Glossary

Inbred strains

Mouse strains that have been sibling-mated for at least 20 generations to the point that both alleles at each locus are expected to be identical.

Linkage analysis

A statistical method for identifying a region of the genome that is implicated in a trait by observing which region is inherited from the parental strain carrying the trait in offspring that carry the trait.

Quantitative trait loci

(QTLs). Regions of the genome that are implicated in a quantitative trait.

Recombinant inbred strains

Inbred strains that are generated by sibling-mating the offspring of a genetic cross until the progenies are inbred.

Collaborative Cross project

A large panel of inbred mouse strains that are currently being developed through a community effort. The strains are derived from an eight-way cross using a set of founder strains that include three wild-derived strains.

Population structure

Differences in levels of genetic similarity between individuals in the study population. Population structure can cause spurious associations in genetic studies.

Imputation

A statistical procedure to predict the values of genetic variation which was not collected using observed genetic variation and genetic reference data sets.

Heritability

A measure of the genetic component of phenotypic variance of a trait.

Linkage disequilibrium decay

The decrease in the correlation between genetic variants as the distance between the variants increases.

Private variants

Genetic variants that are confined to single individuals, families or populations.

Multiple testing

A statistical problem that arises from carrying out many (in the order of thousands) hypothesis tests together. The significance threshold must be appropriately corrected to avoid false positives: for example, by using the Bonferroni correction.

F1 strains

Mouse strains that are generated by breeding two inbred strains together. An F1 mouse has one chromosome from each of the parental strains.

Co-isogenic wild-type strain

A strain that differs from the wild-type strain at only a single locus through a mutation occurring in the wild-type strain.

Congenic strains

Strains that are produced by a breeding strategy in which recombinants between two inbred strains are backcrossed to produce a strain that carries a single genomic segment from one strain on the genetic background of the other.

Additive

In the context of a genetic effect, the linear relationship between the replacement of an allele and its effect on the phenotype.

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Flint, J., Eskin, E. Genome-wide association studies in mice. Nat Rev Genet 13, 807–817 (2012). https://doi.org/10.1038/nrg3335

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