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Sequence divergence of Mus spretus and Mus musculus across a skin cancer susceptibility locus
- Source :
- BMC Genomics, Mahler, KL; Fleming, JL; Dworkin, AM; Gladman, N; Cho, HY; Mao, JH; et al.(2008). Sequence divergence of Mus spretus and Mus musculus across a skin cancer susceptibility locus. BMC Genomics, 9. doi: 10.1186/1471-2164-9-626. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/18f3b97h, BMC Genomics, Vol 9, Iss 1, p 626 (2008), BMC genomics, vol 9, iss 1
- Publication Year :
- 2008
-
Abstract
- Background Mus spretus diverged from Mus musculus over one million years ago. These mice are genetically and phenotypically divergent. Despite the value of utilizing M. musculus and M. spretus for quantitative trait locus (QTL) mapping, relatively little genomic information on M. spretus exists, and most of the available sequence and polymorphic data is for one strain of M. spretus, Spret/Ei. In previous work, we mapped fifteen loci for skin cancer susceptibility using four different M. spretus by M. musculus F1 backcrosses. One locus, skin tumor susceptibility 5 (Skts5) on chromosome 12, shows strong linkage in one cross. Results To identify potential candidate genes for Skts5, we sequenced 65 named and unnamed genes and coding elements mapping to the peak linkage area in outbred spretus, Spret/EiJ, FVB/NJ, and NIH/Ola. We identified polymorphisms in 62 of 65 genes including 122 amino acid substitutions. To look for polymorphisms consistent with the linkage data, we sequenced exons with amino acid polymorphisms in two additional M. spretus strains and one additional M. musculus strain generating 40.1 kb of sequence data. Eight candidate variants were identified that fit with the linkage data. To determine the degree of variation across M. spretus, we conducted phylogenetic analyses. The relatedness of the M. spretus strains at this locus is consistent with the proximity of region of ascertainment of the ancestral mice. Conclusion Our analyses suggest that, if Skts5 on chromosome 12 is representative of other regions in the genome, then published genomic data for Spret/EiJ are likely to be of high utility for genomic studies in other M. spretus strains.
- Subjects :
- Skin Neoplasms
lcsh:QH426-470
Genotype
Evolution
Bioinformatics
Mus spretus
Genetic Linkage
lcsh:Biotechnology
Locus (genetics)
Biology
Quantitative trait locus
Medical and Health Sciences
Genome
Evolution, Molecular
Mice
Genetic
Species Specificity
Genetic linkage
Information and Computing Sciences
lcsh:TP248.13-248.65
Genetics
2.1 Biological and endogenous factors
Animals
Genetic Predisposition to Disease
Aetiology
Polymorphism
Gene
Chromosome 12
Phylogeny
Cancer
Polymorphism, Genetic
Phylogenetic tree
Human Genome
Molecular
Chromosome Mapping
DNA
Sequence Analysis, DNA
Biological Sciences
biology.organism_classification
lcsh:Genetics
Amino Acid Substitution
Sequence Analysis
Sequence Alignment
Biotechnology
Research Article
Subjects
Details
- ISSN :
- 14712164
- Volume :
- 9
- Database :
- OpenAIRE
- Journal :
- BMC genomics
- Accession number :
- edsair.doi.dedup.....9c55d529ef71146a3c99814082f80d29