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Lee, Juhee; Müller, Peter; Gulukota, Kamalakar; Ji, Yuan

A Bayesian feature allocation model for tumor heterogeneity. (English) Zbl 1397.62457

Ann. Appl. Stat. 9, No. 2, 621-639 (2015).
Summary: 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.

Cited in 8 Documents

MSC:

62P10 Applications of statistics to biology and medical sciences; meta analysis
62F15 Bayesian inference

Keywords:

haplotypes; feature allocation models; Indian buffet process; Markov chain Monte Carlo; next-generation sequencing; random binary matrices; variant calling

Software:

BWA; BM-map; Samtools; GATK; PurBayes; PurityEst; KEGG; PyClone
PDF BibTeX XML Cite
\textit{J. Lee} et al., Ann. Appl. Stat. 9, No. 2, 621--639 (2015; Zbl 1397.62457)
Full Text: DOI arXiv Euclid

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