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bioRxiv · 10.1101/484402

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

Yuan, K.·Macintyre, G.·Liu, W.·PCAWG Evolution and Heterogeneity Working Group,·Markowetz, F.
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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.

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Yuan, K., Macintyre, G., Liu, W., PCAWG Evolution and Heterogeneity Working Group,, Markowetz, F.. 2018-12-02. Ccube: A fast and robust method for estimating cancer cell fractions. https://doi.org/10.1101/484402

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