A phylogenetic latent feature model for clonal deconvolution

DOI10.1214/16-AOAS986zbMATH Open1454.62360arXiv1604.01715OpenAlexW3103162178WikidataQ56687889 ScholiaQ56687889MaRDI QIDQ512451FDOQ512451

Authors: Francesco Marass, Florent Mouliere, Nitzan Rosenfeld, Ke Yuan, Florian Markowetz 

Publication date: 24 February 2017

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: Tumours develop in an evolutionary process, in which the accumulation of mutations produces subpopulations of cells with distinct mutational profiles, called clones. This process leads to the genetic heterogeneity widely observed in tumour sequencing data, but identifying the genotypes and frequencies of the different clones is still a major challenge. Here, we present Cloe, a phylogenetic latent feature model to deconvolute tumour sequencing data into a set of related genotypes. Our approach extends latent feature models by placing the features as nodes in a latent tree. The resulting model can capture both the acquisition and the loss of mutations, as well as episodes of convergent evolution. We establish the validity of Cloe on synthetic data and assess its performance on controlled biological data, comparing our reconstructions to those of several published state-of-the-art methods. We show that our method provides highly accurate reconstructions and identifies the number of clones, their genotypes and frequencies even at a modest sequencing depth. As a proof of concept we apply our model to clinical data from three cases with chronic lymphocytic leukaemia, and one case with acute myeloid leukaemia.

Full work available at URL: https://arxiv.org/abs/1604.01715

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zbMATH Keywords

admixturephylogenyclonal deconvolutionlatent feature modeltumour heterogeneity

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10)

Cited In (6)

• TreeClone: reconstruction of tumor subclone phylogeny based on mutation pairs using next generation sequencing data
• Phylogeny-based tumor subclone identification using a Bayesian feature allocation model
• A Bayesian nonparametric model for inferring subclonal populations from structured DNA sequencing data
• RNDClone: tumor subclone reconstruction based on integrating DNA and RNA sequence data
• Tumor copy number deconvolution integrating bulk and single-cell sequencing data
• Parsimonious Clone Tree Reconciliation in Cancer.

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