Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing
To determine whether the sampled tree will be accepted
To get BIC as a model selection criterion
E-step of EM algorithm for multivariate clustering of SNAs
M-step of EM algorithm for multivariate clustering of SNAs
EM algorithm for multivariate clustering of SNAs
To generate a posterior tree
To plot tree inferred by Canopy
Posterior evaluation of MCMC sampled trees
MCMC sampling in tree space with pre-clustering of SNAs
MCMC sampling in tree space with pre-clustering of SNAs
MCMC sampling in tree space
MCMC sampling in tree space
To get clonal composition
To get major and minor copy per clone
To get CNA genotyping matrix CZ
To get likelihood of the tree
To get SNA likelihood of the tree
To get SNA-CNA genotyping matrix
To get variant allele frequency (VAF)
To get SNA genotyping matrix
To initialize positions of CNAs
To initialize major and minor copies of CNAs
To initialize clonal frequency matrix
To initialize positions of SNAs
To sample CNA positions
To sample major and minor copies of CNAs
To sample clonal frequency
To sample positions of SNA clusters
To sample SNA positions
To sort identified overlapping CNAs.
A statistical framework and computational procedure for identifying the sub-populations within a tumor, determining the mutation profiles of each subpopulation, and inferring the tumor's phylogenetic history. The input are variant allele frequencies (VAFs) of somatic single nucleotide alterations (SNAs) along with allele-specific coverage ratios between the tumor and matched normal sample for somatic copy number alterations (CNAs). These quantities can be directly taken from the output of existing software. Canopy provides a general mathematical framework for pooling data across samples and sites to infer the underlying parameters. For SNAs that fall within CNA regions, Canopy infers their temporal ordering and resolves their phase. When there are multiple evolutionary configurations consistent with the data, Canopy outputs all configurations along with their confidence assessment.