QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction.

ABSTRACT:

Motivation

In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering [reducing dispersion in variant allele frequency estimates (VAFs)] and using all biologically relevant variants.

Results

We present a framework for defining cancer clones using most reliable variants of high depth of coverage and assigning functional mutations to

SUBMITTER: Deveau P 

PROVIDER: S-EPMC5972665 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature