Genomics

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Strains for eQTL CNV Analysis


ABSTRACT: Background Haplotype association mapping is a recently developed method that can be used to identify expression Quantitative Trait Loci (eQTLs). The underlying genomic structure of the haplotype can be defined by single nucleotide polymorphisms (SNPs), variable number tandem repeats (VNTRs) and copy number variations (CNVs). Microarray genotyping platforms are able to interrogate all three genomic polymorphisms simultaneously. Combined with gene expression data, these data allow for the elucidation of sites responsible for the regulation of transcription. Results Thirty three inbred strains were genotyped on a microarray platform to assess possible contributions of polymorphic regions to gene expression. Over one hundred million statistical correlations were made between probe performance on genotyping and gene expression microarrays. This analysis provided 10,655 trans associations and 31 cis associations. Further investigation of one of the cis associations revealed that a 84kb region of MMU3 acts as a haplotype-specific locus control region for the glutathione-S-transferase mu family in multiple tissues. In the strains that share the minor haplotype, reductions in mRNA levels in members of the Gst mu family are observed. Conclusions We have identified a haplotype containing a putative locus control region for the Gst mu family gene cassette. In the strains with affected haplotype, Gst mu expression is drastically reduced. The reduction in Gst mu levels has important relevance for pharmacology and toxicology studies. The reduction of Gst mu levels in general, and Gstm5 in particular, has implication in models of dopamine metabolism, Parkinson’s disease, and chemical neurotoxicity. Keywords: Liver gene expression, no treatment

ORGANISM(S): Mus musculus

PROVIDER: GSE10377 | GEO | 2008/10/31

SECONDARY ACCESSION(S): PRJNA108115

REPOSITORIES: GEO

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