The Annals of Applied Statistics

BayCount: A Bayesian decomposition method for inferring tumor heterogeneity using RNA-Seq counts

Fangzheng Xie, Mingyuan Zhou, and Yanxun Xu

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Abstract

Tumors are heterogeneous. A tumor sample usually consists of a set of subclones with distinct transcriptional profiles and potentially different degrees of aggressiveness and responses to drugs. Understanding tumor heterogeneity is therefore critical for precise cancer prognosis and treatment. In this paper we introduce BayCount—a Bayesian decomposition method to infer tumor heterogeneity with highly over-dispersed RNA sequencing count data. Using negative binomial factor analysis, BayCount takes into account both the between-sample and gene-specific random effects on raw counts of sequencing reads mapped to each gene. For the posterior inference, we develop an efficient compound Poisson-based blocked Gibbs sampler. Simulation studies show that BayCount is able to accurately estimate the subclonal inference, including the number of subclones, the proportions of these subclones in each tumor sample, and the gene expression profiles in each subclone. For real world data examples, we apply BayCount to The Cancer Genome Atlas lung cancer and kidney cancer RNA sequencing count data and obtain biologically interpretable results. Our method represents the first effort in characterizing tumor heterogeneity using RNA sequencing count data that simultaneously removes the need of normalizing the counts, achieves statistical robustness, and obtains biologically/clinically meaningful insights. The R package BayCount implementing our model and algorithm is available for download.

Article information

Source
Ann. Appl. Stat., Volume 12, Number 3 (2018), 1605-1627.

Dates
Received: February 2017
Revised: November 2017
First available in Project Euclid: 11 September 2018

Permanent link to this document
https://projecteuclid.org/euclid.aoas/1536652967

Digital Object Identifier
doi:10.1214/17-AOAS1123

Mathematical Reviews number (MathSciNet)
MR3852690

Keywords
Cancer genomics compound Poisson Markov chain Monte Carlo negative binomial overdispersion

Citation

Xie, Fangzheng; Zhou, Mingyuan; Xu, Yanxun. BayCount: A Bayesian decomposition method for inferring tumor heterogeneity using RNA-Seq counts. Ann. Appl. Stat. 12 (2018), no. 3, 1605--1627. doi:10.1214/17-AOAS1123. https://projecteuclid.org/euclid.aoas/1536652967


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Supplemental materials

  • Supplement to “BayCount: A Bayesian decomposition method for inferring tumor heterogeneity using RNA-Seq counts”. We provide the details for the posterior inference, supplementary figures, comparison with alternative methods for determining number of subclones, additional simulation studies, comparison with the nonnegative matrix factorization on transformed count data and additional convergence diagnostics in the supplementary material.