Haplotype Association Mapping Identifies a Candidate Gene Region in Mice Infected With Staphylococcus aureus.

Abstract

Exposure to Staphylococcus aureus has a variety of outcomes, from asymptomatic colonization to fatal infection. Strong evidence suggests that host genetics play an important role in susceptibility, but the specific host genetic factors involved are not known. The availability of genome-wide single nucleotide polymorphism (SNP) data for inbred Mus musculus strains means that haplotype association mapping can be used to identify candidate susceptibility genes. We applied haplotype association mapping to Perlegen SNP data and kidney bacterial counts from Staphylococcus aureus-infected mice from 13 inbred strains and detected an associated block on chromosome 7. Strong experimental evidence supports the result: a separate study demonstrated the presence of a susceptibility locus on chromosome 7 using consomic mice. The associated block contains no genes, but lies within the gene cluster of the 26-member extended kallikrein gene family, whose members have well-recognized roles in the generation of antimicrobial peptides and the regulation of inflammation. Efficient mixed-model association (EMMA) testing of all SNPs with two alleles and located within the gene cluster boundaries finds two significant associations: one of the three polymorphisms defining the associated block and one in the gene closest to the block, Klk1b11. In addition, we find that 7 of the 26 kallikrein genes are differentially expressed between susceptible and resistant mice, including the Klk1b11 gene. These genes represent a promising set of candidate genes influencing susceptibility to Staphylococcus aureus.

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Published Version (Please cite this version)

10.1534/g3.112.002501

Publication Info

Johnson, Nicole V, Sun Hee Ahn, Hitesh Deshmukh, Mikhail K Levin, Charlotte L Nelson, William K Scott, Andrew Allen, Vance G Fowler, et al. (2012). Haplotype Association Mapping Identifies a Candidate Gene Region in Mice Infected With Staphylococcus aureus. G3 (Bethesda), 2(6). pp. 693–700. 10.1534/g3.112.002501 Retrieved from https://hdl.handle.net/10161/13318.

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Allen

Andrew Scott Allen

Professor of Biostatistics & Bioinformatics

My research focuses on developing new statistical methods for identifying susceptibility loci involved in complex human disease.  It involves a mix of genetics, statistics, and computer science and is motivated by the complexities of real data encountered in collaborative disease-gene mapping projects.


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