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Bioinformatics Advance Access originally published online on January 31, 2007
Bioinformatics 2007 23(7):785-788; doi:10.1093/bioinformatics/btm003
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Large scale genotype–phenotype correlation analysis based on phylogenetic trees

Farhat Habib 1,*, Andrew D. Johnson 2, Ralf Bundschuh 1 and Daniel Janies 3

1Department of Physics, 2Department of Pharmacology and 3Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA

*To whom correspondence should be addressed.


  Abstract

We provide two methods for identifying changes in genotype that are correlated with changes in a phenotype implied by phylogenetic trees. The first method, VENN, works when the number of branches over which the change occurred are modest. VENN looks for genetic changes that are completely penetrant with phenotype changes on a tree. The second method, CCTSWEEP, allows for a partial matching between changes in phenotypes and genotypes and provides a score for each change using Maddison's concentrated changes test. The mutations that are highly correlated with phenotypic change can be ranked by score. We use these methods to find SNPs correlated with resistance to Bacillus anthracis in inbred mouse strains. Our findings are consistent with the current biological literature, and also suggest potential novel candidate genes.

Contact: farhat{at}pacific.mps.ohio-state.edu for software requests.

Associate Editor: Joaquin Dopazo

Received on August 23, 2006; revised on December 22, 2006; accepted on January 9, 2007

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