Abstract

Copy-number aberrations (CNAs) and whole-genome duplications (WGDs) are frequent somatic mutations in cancer. Accurate quantification of these mutations from DNA sequencing of bulk tumor samples is complicated by varying tumor purity, admixture of multiple tumor clones with distinct mutations, and high aneuploidy. Standard methods for CNA inference analyze tumor samples individually, but recently DNA sequencing of multiple samples from a cancer patient - e.g. from multiple regions of a primary tumor, matched primary/metastases, or multiple time points - has become common. We introduce a new algorithm, Holistic Allele-specific Tumor Copy-number Heterogeneity (HATCHet), that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples. HATCHet provides a fresh perspective on CNA inference and includes several algorithmic innovations that overcome the limitations of existing methods, resulting in a more robust approach even for single-sample analysis. We also develop MASCoTE (Multiple Allele-specific Simulation of Copy-number Tumor Evolution), a framework for generating realistic simulated multi-sample DNA sequencing data with appropriate corrections for the differences in genome lengths between the normal and tumor clone(s) present in mixed samples. HATCHet outperforms current state-of-the-art methods on 256 simulated tumor samples from 64 patients, half with WGD. HATCHet’s analysis of 49 primary tumor and metastasis samples from 10 prostate cancer patients reveals subclonal CNAs in only 29 of these samples, compared to the published reports of extensive subclonal CNAs in all samples. HATCHet’s inferred CNAs are also more consistent with the reports of polyclonal origin and limited heterogeneity of metastasis in a subset of patients. HATCHet’s analysis of 35 primary tumor and metastasis samples from 4 pancreas cancer patients reveals subclonal CNAs in 20 samples, WGDs in 3 patients, and tumor subclones that are shared across primary and metastases samples from the same patient - none of which were described in published analysis of this data. HATCHet substantially improves the analysis of CNAs and WGDs, leading to more reliable studies of tumor evolution in primary tumors and metastases.