title: A BAYESIAN NONPARAMETRIC MODEL FOR RECONSTRUCTING TUMOR SUBCLONES BASED ON MUTATION PAIRS.
abstract: We present a feature allocation model to reconstruct tumor subclones based on mutation pairs. The key innovation lies in the use of a pair of proximal single nucleotide variants (SNVs) for the subclone reconstruction as opposed to a single SNV. Using the categorical extension of the Indian buffet process (cIBP) we define the subclones as a vector of categorical matrices corresponding to a set of mutation pairs. Through Bayesian inference we report posterior probabilities of the number, genotypes and population frequencies of subclones in one or more tumor sample. We demonstrate the proposed methods using simulated and real-world data. A free software package is available at http://www.compgenome.org/pairclone.
authors.affiliation: Program for Computational Genomics and Medicine, NorthShore University HealthSystem, USA*have equal contributions.
authors.forename: Subhajit
authors.initials: S
authors.lastname: Sengupta
authors.forename: Tianjian
authors.initials: T
authors.lastname: Zhou
authors.forename: Peter
authors.initials: P
authors.lastname: Müeller
authors.forename: Yuan
authors.initials: Y
authors.lastname: Ji
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D003198:Computer Simulation; D006258:Head and Neck Neoplasms / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000706:statistics & numerical data; D006801:Humans; D008390:Markov Chains; D008957:Models, Genetic; D009010:Monte Carlo Method; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012984:Software; D018709:Statistics, Nonparametric