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

Ke Yuan, Geoff Macintyre, Wei Liu, PCAWG-11 working group, Florian Markowetz. 2018. bioRxiv 484402.


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.