Project description:Genome profiling of primary tumors and matched metastases from a BALB-NeuT murine breast cancer transplantation model. The first goal of this study was to investigate the differences of primary tumors and metastases with regard to copy number alterations. The second goal was to infer phylogenetic trees reflecting the evolutionary paths of primary tumors and their derived metastases (only mice with at least one metastasis were used for phylogenetic analyses).
2016-09-30 | GSE87469 | GEO
Project description:Phylogenetic analyses of species associated with Protacanthopterygii
| PRJNA1013549 | ENA
Project description:Phylogenetic relationship analyses of complicated class Spirotrichea
Project description:To test if scRNA-seq contains sufficient phylogenetic information to reconstruct a population history of cancer, immunosuppressed NU/J mice were injected with human cancer cells (MDA-MB-231-LM2). The tumors that develop are derived from the same population and thus share a common ancestor, but evolved independently in each mouse and should form separate clades on reconstructed phylogenetic trees when analysed together. We explore and compare results of phylogenetic analyses based on both expression levels and SNVs called from our scRNA-seq data. Both techniques are shown to be useful for reconstructing phylogenetic relationships between cells, refecting the clonal composition of a tumor. Without an explicit error model, standardized expression values appears to be more powerful and informative than the SNV values at a lower computational cost, due to being a by-product of standard expression analysis. Our results suggest that scRNA-seq can be a competitive alternative or useful addition to conventional scDNA-seq phylogenetic reconstruction. Our results open up a new direction of somatic phylogenetics based on scRNA-seq data. Further research is required to refne and improve these approaches to capture the full picture of somatic evolutionary dynamics in cancer.
