SNVBox – UPDATE

Unmet Need

In the new “post-genome” era of personalized medicine, many variants critical to disease susceptibilities and drug sensitivities will be identified and increased numbers of people will undergo genetic testing. The Karchin group is developing algorithms and tools to facilitate this process. These models are being applied to cancer genomics, unclassified variants in Mendelian disease genes, and complex disease genetics.

Technology Overview
CHASM AND VEST
A machine learning method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give cells selective advantage (CHASM) or impair protein activity (VEST).

SNVBox & SNVBox Update
A MySQL database that contains pre-computed features for all codons in the human exome. SNVBox can be used as a tool for those developing new computational algorithms to classify amino acid substitutions.

BOMP
A novel hybrid likelihood model to identify phenotype-associated genes from sequencing data in case/control study designs.

SCHISM
A computational framework that reconstructs tumor subcolonal phylogenies using somatic mutation cellularities in patients’ tumor samples.

Stage of Development
Current software releases are available online and are available at no cost for non-commercial use; commercial use will require a license.

Publications