Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History

Intratumoral heterogeneity arises as a result of genetically distinct subclones emerging during tumor progression. These subclones are characterized by various types of somatic genomic aberrations, with single nucleotide variants (SNVs) and copy number aberrations (CNAs) being the most prominent. While single-cell sequencing provides powerful data for studying tumor progression, most existing and newly generated sequencing datasets are obtained through conventional bulk sequencing. Most of the available methods for studying tumor progression from multi-sample bulk sequencing data are either based on the use of SNVs from genomic loci not impacted by CNAs or designed to handle a small number of SNVs via enumerating their possible copy number trees. In this paper, we introduce DETOPT, a combinatorial optimization method for accurate tumor progression tree inference that places SNVs impacted by CNAs on trees of tumor progression with minimal distortion on their variant allele frequencies observed across available samples of a tumor. We show that on simulated data DETOPT provides more accurate tree placement of SNVs impacted by CNAs than the available alternatives. When applied to a set of multi-sample bulk exome-sequenced tumor metastases from a treatment-refractory, triple-positive metastatic breast cancer, DETOPT reports biologically plausible trees of tumor progression, identifying the tree placement of copy number state gains and losses impacting SNVs, including those in clinically significant genes.