An integrated in silico gene mapping strategy in inbred mice

Alessandra C.L. Cervino, Ariel Darvasi, Mohammad Fallahi, Christopher C. Mader, Nicholas F. Tsinoremas

Research output: Contribution to journalArticle

39 Scopus citations

Abstract

In recent years in silico analysis of common laboratory mice has been introduced and subsequently applied, in slightly different ways, as a methodology for gene mapping. Previously we have demonstrated some limitation of the methodology due to sporadic genetic correlations across the genome. Here, we revisit the three main aspects that affect in silico analysis. First, we report on the use of marker maps: we compared our existing 20,000 SNP map to the newly released 140,000 SNP map. Second, we investigated the effect of varying strain numbers on power to map QTL. Third, we introduced a novel statistical approach: a cladistic analysis, which is well suited for mouse genetics and has increased flexibility over existing in silico approaches. We have found that in our examples of complex traits, in silico analysis by itself does fail to uniquely identify quantitative trait gene (QTG)-containing regions. However, when combined with additional information, it may significantly help to prioritize candidate genes. We therefore recommend using an integrated work flow that uses other genomic information such as linkage regions, regions of shared ancestry, and gene expression information to obtain a list of candidate genes from the genome.

Original languageEnglish (US)
Pages (from-to)321-333
Number of pages13
JournalGenetics
Volume175
Issue number1
DOIs
StatePublished - Jan 1 2007

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ASJC Scopus subject areas

  • Genetics

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