Genomics

Dataset Information

16

CGH analysis of inbred mouses strains


ABSTRACT: The contribution to genetic diversity of genomic segmental copy number variations (CNVs) is less well understood than that of single-nucleotide polymorphisms (SNPs). While less frequent than SNPs, CNVs have greater potential to affect phenotype. In this study, we have performed the most comprehensive survey to date of CNVs in mice, analyzing the genomes of 42 Mouse Phenome Consortium priority strains. This microarray comparative genomic hybridization (CGH)-based analysis has identified 2094 putative CNVs, with an average of 10 Mb of DNA in 51 CNVs when individual mouse strains were compared to the reference strain C57BL/6J. This amount of variation results in gene content that can differ by hundreds of genes between strains. These genes include members of large families such as the major histocompatibility and pheromone receptor genes, but there are also many singleton genes including genes with expected phenotypic consequences from their deletion or amplification. Using a whole-genome association analysis, we demonstrate that complex multigenic phenotypes, such as food intake, can be associated with specific copy number changes. Keywords: comparative genomic hybridization Overall design: DNA from two individual mice per strain, for each of 42 strains was hybridized onto Agilent CGH arrays along with DNA from a reference C57BL/6J sample. One replicate per strain was labeled with Cy5 and one with Cy3, so each biological replicate is also a dye-flip replicate.

INSTRUMENT(S): Agilent-014695 Mouse Genome CGH Microarray 244A (G4415A) (Feature Number version)

SUBMITTER: Gene Cutler  

PROVIDER: GSE9186 | GEO | 2007-11-06

SECONDARY ACCESSION(S): PRJNA102755

REPOSITORIES: GEO

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Publications

Significant gene content variation characterizes the genomes of inbred mouse strains.

Cutler Gene G   Marshall Lisa A LA   Chin Ni N   Baribault Helene H   Kassner Paul D PD  

Genome research 20071107 12


The contribution to genetic diversity of genomic segmental copy number variations (CNVs) is less well understood than that of single-nucleotide polymorphisms (SNPs). While less frequent than SNPs, CNVs have greater potential to affect phenotype. In this study, we have performed the most comprehensive survey to date of CNVs in mice, analyzing the genomes of 42 Mouse Phenome Consortium priority strains. This microarray comparative genomic hybridization (CGH)-based analysis has identified 2094 puta  ...[more]

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