title: CanPredict: a computational tool for predicting cancer-associated missense mutations.
abstract: Various cancer genome projects are underway to identify novel mutations that drive tumorigenesis. While these screens will generate large data sets, the majority of identified missense changes are likely to be innocuous passenger mutations or polymorphisms. As a result, it has become increasingly important to develop computational methods for distinguishing functionally relevant mutations from other variations. We previously developed an algorithm, and now present the web application, CanPredict (http://www.canpredict.org/ or http://www.cgl.ucsf.edu/Research/genentech/canpredict/), to allow users to determine if particular changes are likely to be cancer-associated. The impact of each change is measured using two known methods: Sorting Intolerant From Tolerant (SIFT) and the Pfam-based LogR.E-value metric. A third method, the Gene Ontology Similarity Score (GOSS), provides an indication of how closely the gene in which the variant resides resembles other known cancer-causing genes. Scores from these three algorithms are analyzed by a random forest classifier which then predicts whether a change is likely to be cancer-associated. CanPredict fills an important need in cancer biology and will enable a large audience of biologists to determine which mutations are the most relevant for further study.
authors.affiliation: Department of Bioinformatics, Genentech, Inc., South San Francisco, CA 94080, USA.
authors.forename: Joshua S
authors.initials: JS
authors.lastname: Kaminker
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Colin
authors.initials: C
authors.lastname: Watanabe
authors.forename: Zemin
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D000483:Alleles; D000596:Amino Acids / Q000737:chemistry; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods; D004273:DNA, Neoplasm / Q000235:genetics; D020224:Expressed Sequence Tags; D020022:Genetic Predisposition to Disease; D006801:Humans; D020407:Internet; D020125:Mutation, Missense; D009369:Neoplasms / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D014584:User-Computer Interface
chemical_list: D000596:Amino Acids; D004273:DNA, Neoplasm