SCHISM combines information about somatic mutation cellularity (aka mutation cancer cell fraction) across all tumor sample(s) available from a patient in a hypothesis testing framework to identify the statistical support for the lineage relationship between each pair of mutations or mutation clusters. The results of the hypothesis test are represented as Cluster Order Precedence Violation (CPOV) matrix which informs the subsequent step in SCHISM and ensures compliance of candidate tree topologies with lineage precedence rule.
Finally, an implementation of genetic algorithm (GA) based on a fitness function that incorporates considerations for both lineage precedence (CPOV) rule and lineage divergence rule explores the space of tree topologies and returns a prioritized list of candidate subclonal phylogenetic trees, most compatible with observed cellularity data.
SCHISM is free for non-commercial use. For more details please refer to our Software License. Commercial users should contact the Johns Hopkins Technology Transfer office.
Current stable release is SCHISM.1.1.2, last updated on 05/11/2016.
SCHISM-1.1.2.tar.gz 05/11/2016 Better color handling in cellularity plots. Dockerfile added.
SCHISM-1.1.1.tar.gz 02/19/2016 POV and cellularity visualization added.
SCHISM-1.1.0.tar.gz 01/26/2016 Mutation clustering module added.
SCHISM-1.0.1.tar.gz 01/01/2016 Initial release with the manuscript, with minor visualization update
SCHISM-1.0.1.tar.gz 03/15/2015 Initial release with the manuscript
Please consult the project wiki page for installation and usage details.
Niknafs N, Beleva-Guthrie V, Naiman DQ, Karchin R (2015) SubClonal Hierarchy Inference from Somatic Mutations: automatic reconstruction of cancer evolutionary trees from multi-region next generation sequencing. PLoS Computational Biology 11(10):e1004416 Abstract
Noushin Niknafs: niknafs at jhu dot edu