A Bayesian feature allocation model for tumor heterogeneity
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Publication:746649
DOI10.1214/15-AOAS817zbMATH Open1397.62457arXiv1509.04026OpenAlexW1922381576MaRDI QIDQ746649FDOQ746649
Authors: Juhee Lee, Kamalakar Gulukota, Yuan Ji, P. Müller 
Publication date: 28 October 2015
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
Abstract: We develop a feature allocation model for inference on genetic tumor variation using next-generation sequencing data. Specifically, we record single nucleotide variants (SNVs) based on short reads mapped to human reference genome and characterize tumor heterogeneity by latent haplotypes defined as a scaffold of SNVs on the same homologous genome. For multiple samples from a single tumor, assuming that each sample is composed of some sample-specific proportions of these haplotypes, we then fit the observed variant allele fractions of SNVs for each sample and estimate the proportions of haplotypes. Varying proportions of haplotypes across samples is evidence of tumor heterogeneity since it implies varying composition of cell subpopulations. Taking a Bayesian perspective, we proceed with a prior probability model for all relevant unknown quantities, including, in particular, a prior probability model on the binary indicators that characterize the latent haplotypes. Such prior models are known as feature allocation models. Specifically, we define a simplified version of the Indian buffet process, one of the most traditional feature allocation models. The proposed model allows overlapping clustering of SNVs in defining latent haplotypes, which reflects the evolutionary process of subclonal expansion in tumor samples.
Full work available at URL: https://arxiv.org/abs/1509.04026
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Markov chain Monte Carlohaplotypesnext-generation sequencingIndian buffet processfeature allocation modelsrandom binary matricesvariant calling
Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10)
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Cited In (14)
- TreeClone: reconstruction of tumor subclone phylogeny based on mutation pairs using next generation sequencing data
- MAD Bayes for tumor heterogeneity -- feature allocation with exponential family sampling
- Estimating Latent Cell Subpopulations with Bayesian Feature Allocation Models
- Phylogeny-based tumor subclone identification using a Bayesian feature allocation model
- Bayesian feature allocation models for tumor heterogeneity
- Variational Bayes procedure for effective classification of tumor type with microarray gene expression data
- A Bayesian nonparametric model for inferring subclonal populations from structured DNA sequencing data
- Bayesian Edge Regression in Undirected Graphical Models to Characterize Interpatient Heterogeneity in Cancer
- A Bayesian feature allocation model for tumor heterogeneity
- Nonparametric Bayesian inference in applications
- Bayesian Double Feature Allocation for Phenotyping With Electronic Health Records
- Consensus Monte Carlo for Random Subsets Using Shared Anchors
- A Bayesian screening approach for hepatocellular carcinoma using multiple longitudinal biomarkers
- The attraction Indian buffet distribution
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