Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations.

ABSTRACT:

Motivation

Cancer develops through a process of clonal evolution in which an initially healthy cell gives rise to progeny gradually differentiating through the accumulation of genetic and epigenetic mutations. These mutations can take various forms, including single-nucleotide variants (SNVs), copy number alterations (CNAs) or structural variations (SVs), with each variant type providing complementary insights into tumor evolution as well as offering distinct challenges to phylogenetic inference.

Results

In this work, we develop a tumor phylogeny method, TUSV-ext, which incorporates SNVs, CNAs and SVs into a single inference framework. We demonstrate on simulated data that the method produces accurate tree inferences in the presence of all three variant types. We further dem

SUBMITTER: Fu X 

PROVIDER: S-EPMC9236577 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature