CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples

Genome Biol. 2023 Jun 20;24(1):144. doi: 10.1186/s13059-023-02983-0.

Abstract

Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies from such data. CNETML is the first program to jointly infer the tree topology, node ages, and mutation rates from total copy numbers of longitudinal samples. Our extensive simulations suggest CNETML performs well on copy numbers relative to ploidy and under slight violation of model assumptions. The application of CNETML to real data generates results consistent with previous discoveries and provides novel early copy number events for further investigation.

Keywords: Copy number alteration; Low-coverage sequencing; Maximum likelihood; Model of evolution; Phylogeny inference.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • DNA Copy Number Variations*
  • Humans
  • Mutation Rate
  • Neoplasms*
  • Phylogeny