Yuelin Liu from the University of Maryland and the National Cancer Institute spoke at the Nanopore Community Meeting in Houston about “Analysis of melanoma evolution using nanopore long-read sequencing data.” Liu spoke about melanoma and skin cancers. While melanoma makes up only about 2% of skin cancers, it is the most aggressive. Liu explained that melanoma is challenging because of intratumor heterogeneity, among other features. Phylogeny reconstruction is a method used that Liu and team leveraged. They also used the M4 Mouse Model-Derived B2905 Mouse Melanoma Cell Line. They generated data by extracting 24 single cells cultured into sublines subjected to long-read sequencing. The goal was to use Nanopore long-read sequencing to infer the phylogeny and include CpG methylation information. Liu’s research question was related to using haplotype-specific CpG methylation for phylogeny reconstruction. Liu shared preliminary results from a subset of cell lines (eight). Collaborators are profiling small variants and structural variants to complement the methylation information from these lines. The team will compare phylogenetic information from these three sources. Liu concluded that they have generated data from twenty-four single-cell sublines from a mouse melanoma model to learn about the evolution of melanoma. I thought this was a really interesting study. I wonder if similar studies can be performed with bacteria from biofilms.
