Type Package Title ExPANdS Version 1.4 Date 2014-03-01

terizes coexisting subpopulations (SPs) in a tumor using copy number and allele frequencies de-rived from exome- or whole genome sequencing input data. The model amplifies the statisti-cal power to detect coexisting genotypes, by fully exploiting run-specific tradeoffs be-tween depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal ex-pansions, the size of the resulting SPs in the tumor bulk, the mutations specific to each SP and tu-mor purity. The main function runExPANdS provides the complete functionality needed to pre-dict coexisting SPs from single nucleotide variations (SNVs) and associated copy num-bers. The robustness of the subpopulation predictions by ExPANdS increases with the num-ber of mutations provided. It is recommended that at least 200 mutations are used as an in-put to obtain stable results. Updates include (1)Phylogeny reconstruction based on SP spe-cific copy number profiles. (2) Additional optional parameter ``maxN' ' provided for function run-ExPANdS, specifying the maximal number of SNVs to be used for the clustering step. Restric-tion imposed by ``maxN' ' is now used only for SP detection, not also for mutation assign-ment to SPs. (3) Relevant for whole genome sequencing (WGS) data: additional optional param-eter ``region' ' provided for function runExPANdS, specifying the re-gion within which SNVs are to be used during clustering