DOI: 10.1101/484402Dec 2, 2018Paper

Ccube: A fast and robust method for estimating cancer cell fractions

BioRxiv : the Preprint Server for Biology
Ke YuanFlorian Markowetz

Abstract

Estimating and clustering cancer cell fractions of genomic alterations are central tasks for studying intratumour heterogeneity. We present Ccube, a probabilistic framework for inferring the cancer cell fraction of somatic point mutations and the subclonal composition from whole-genome sequencing data. We develop a variational inference method for model fitting, which allows us to handle samples with large number of the variants (more than 2 million) while quantifying uncertainty in a Bayesian fashion. Ccube is available at https://github.com/keyuan/ccube.

Related Concepts

Tumor Cells, Malignant
Gene Mutation
Receptor Clustering
Subclone
Whole Genome Sequencing

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