EXPANDS

Overview

EXPANDS (Expanding Ploidy and Allele Frequency on Nested Subpopulations) is a computational method for inferring clonal population structure from bulk tumor sequencing data. It integrates somatic SNV allele frequencies and copy-number information to reconstruct the number and composition of co-existing tumor subclones, estimate their prevalence, and build phylogenetic relationships between subpopulations.

Used by

• Used alongside PyClone for clonal-prevalence inference in 14 germline-matched medulloblastoma WGS pairs; EXPANDS modelling confirmed branched clonal evolution in all 14 cases and detected increased clonal-population counts post-therapy in 71.4% of patients PMID:26760213.

Notes

• Operates on paired SNV and copy-number segmentation data from bulk tumor sequencing.
• Returns estimates of subclonal population frequencies and a phylogenetic tree of clonal populations.
• Validated for use with WGS and WES data; sensitivity is limited by sequencing depth and purity.

Sources

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