Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories

Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories Abstract Tumor evolution is driven by various mutational processes, ranging from single-nucleotide vari- ants (SNVs) to large structural variants (SVs) to dynamic shifts in DNA methylation. Current short-read sequencing methods struggle to accurately capture the full spectrum of these genomic and epigenomic alter- ations due to inherent technical limitations. To overcome that, here we introduce an approach for long-read sequencing of single-cell derived subclones, and use it to profile 23 subclones of a mouse melanoma cell line, characterized with distinct growth phenotypes and treatment responses. We develop a computational frame- work for harmonization and joint analysis of different variant types in the evolutionary context. Uniquely, our framework enables detection of recurrent amplifications of putative driver genes, generated by indepen- dent SVs across different lineages, suggesting parallel evolution. In addition, our approach revealed gradual and lineage-specific methylation changes associated with aggressive clonal phenotypes. We also show our set of phylogeny-constrained variant calls along with openly released sequencing data can be a valuable resource for the development of new computational methods. Competing Interest Statement The authors have declared no competing interest. Funder Information Declared Subject Area - Biochemistry (17715) - Bioengineering (13907) - Bioinformatics (42003) - Biophysics (21470) - Cancer Biology (18624) - Cell Biology (25533) - Clinical Trials (138) - Developmental Biology (13390) - Ecology (19935) - Epidemiology (2067) - Evolutionary Biology (24356) - Genetics (15617) - Genomics (22529) - Immunology (17753) - Microbiology (40432) - Molecular Biology (17200) - Neuroscience (88681) - Paleontology (667) - Pathology (2840) - Pharmacology and Toxicology (4828) - Physiology (7653) - Plant Biology (15171) - Synthetic Biology (4304) - Systems Biology (9826) - Zoology (2271)