RNDClone: tumor subclone reconstruction based on integrating DNA and RNA sequence data

DOI10.1214/20-AOAS1368zbMath1498.62279MaRDI QIDQ2078761

Yuan Ji, Subhajit Sengupta, Tianjian Zhou, Peter Mueller

Publication date: 3 March 2022

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

zbMATH Keywords

gene expressionlatent factor modelcopy numbersomatic mutationhigh-throughput sequencingintra-tumor heterogeneity

Mathematics Subject Classification ID

Computational methods for problems pertaining to statistics (62-08) Applications of statistics to biology and medical sciences; meta analysis (62P10) Bayesian inference (62F15) Protein sequences, DNA sequences (92D20)

Uses Software

• R
• BayesDA
• GitHub
• BayCount
• PhyloWGS
• THetA
• PyClone
• TreeClone
• PairClone

Cites Work

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• Reversible jump Markov chain Monte Carlo computation and Bayesian model determination
• A phylogenetic latent feature model for clonal deconvolution
• Baycount: a Bayesian decomposition method for inferring tumor heterogeneity using RNA-seq counts
• Nonparametric Bayesian inference in applications
• Inference from iterative simulation using multiple sequences
• 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
• Sparse Bayesian infinite factor models
• Gibbs Sampling Methods for Stick-Breaking Priors
• High-Dimensional Sparse Factor Modeling: Applications in Gene Expression Genomics