A Bayesian nonparametric model for inferring subclonal populations from structured DNA sequencing data

DOI10.1214/20-AOAS1434MaRDI QIDQ2245171zbMATH OpenOpenAlexWikidataFDO

Authors Shai He, Aaron Schein, Vishal Sarsani, Patrick Flaherty

Publication date 15 November 2021

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

Full work available at URL https://doi.org/10.1214/20-aoas1434

zbMATH Keywords

augment-and-marginalizeBayesian nonparametricDirichlet process mixtureDNA sequencingtumor heterogeneity

Mathematics Subject Classification ID

Nonparametric estimation (62G05) Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to biology and medical sciences; meta analysis (62P10) Protein sequences, DNA sequences (92D20)

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Cites work

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• A phylogenetic latent feature model for clonal deconvolution
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• Exact and approximate sum representations for the Dirichlet process
• Hierarchical Dirichlet Processes
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• Inconsistency of Pitman-Yor process mixtures for the number of components
• Markov chain Monte Carlo in approximate Dirichlet and beta two-parameter process hierarchical models
• Modelling heterogeneity with and without the Dirichlet process
• On statistical modeling of sequencing noise in high depth data to assess tumor evolution
• TreeClone: reconstruction of tumor subclone phylogeny based on mutation pairs using next generation sequencing data

Cited in

(9)

• Baycount: a Bayesian decomposition method for inferring tumor heterogeneity using RNA-seq counts
• RNDClone: tumor subclone reconstruction based on integrating DNA and RNA sequence data
• Phylogeny-based tumor subclone identification using a Bayesian feature allocation model
• Clonality: point estimation
• Bayesian feature allocation models for tumor heterogeneity
• Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model
• Joint analysis of single-cell and bulk tissue sequencing data to infer intratumor heterogeneity
• MAD Bayes for tumor heterogeneity -- feature allocation with exponential family sampling
• A Bayesian feature allocation model for tumor heterogeneity

Describes a project that uses

Uses Software

• PurBayes
• PurityEst
• PhyloWGS
• SciClone
• BWA
• PyClone
• TreeClone

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