MAD Bayes for tumor heterogeneity -- feature allocation with exponential family sampling

DOI10.1080/01621459.2014.995794zbMATH Open1373.62556arXiv1402.5090OpenAlexW2064228409WikidataQ28647243 ScholiaQ28647243MaRDI QIDQ5367381FDOQ5367381

Yuan Yuan, Yanxun Xu, Kamalakar Gulukota, P. Müller, Yuan Ji

Publication date: 13 October 2017

Published in: Journal of the American Statistical Association (Search for Journal in Brave)

Abstract: We propose small-variance asymptotic approximations for the inference of tumor heterogeneity (TH) using next-generation sequencing data. Understanding TH is an important and open research problem in biology. The lack of appropriate statistical inference is a critical gap in existing methods that the proposed approach aims to fill. We build on a hierarchical model with an exponential family likelihood and a feature allocation prior. The proposed approach generalizes similar small-variance approximations proposed by Kulis and Jordan (2012) and Broderick et.al (2012) for inference with Dirichlet process mixture and Indian buffet prior models under normal sampling. We show that the new algorithm can successfully recover latent structures of different subclones and is also magnitude faster than available Markov chain Monte Carlo samplers, the latter often practically infeasible for high-dimensional genomics data. The proposed approach is scalable, simple to implement and benefits from the flexibility of Bayesian nonparametric models. More importantly, it provides a useful tool for the biological community for estimating cell subtypes in tumor samples.

Full work available at URL: https://arxiv.org/abs/1402.5090

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Mathematics Subject Classification ID

Bayesian inference (62F15) Nonparametric estimation (62G05) Asymptotic properties of nonparametric inference (62G20) Applications of statistics to biology and medical sciences; meta analysis (62P10)

Cited In (7)

• TreeClone: reconstruction of tumor subclone phylogeny based on mutation pairs using next generation sequencing data
• Tumor heterogeneity estimation for radiomics in cancer
• Consensus Monte Carlo for Random Subsets Using Shared Anchors
• Comparison and Bayesian Estimation of Feature Allocations
• Bayesian inference for latent biologic structure with determinantal point processes (DPP)
• The attraction Indian buffet distribution
• Baycount: a Bayesian decomposition method for inferring tumor heterogeneity using RNA-seq counts

Uses Software

• R

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