Large scale genotype-phenotype correlation analysis based on phylogenetic trees.
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.
Habib
Farhat
F
Department of Physics, The Ohio State University, Columbus, OH 43210, USA. farhat@pacific.mps.ohio-state.edu
Johnson
Andrew D
AD
Bundschuh
Ralf
R
Janies
Daniel
D
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004247:DNA / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods; D014644:Genetic Variation / Q000235:genetics; D005838:Genotype; D008969:Molecular Sequence Data; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012984:Software; D013223:Statistics as Topic
D004247:DNA