Journal: Nature reviews. Genetics

Article Title: The evolution of tumour phylogenetics: principles and practice

doi: 10.1038/nrg.2016.170

Figure Lengend Snippet: Case studies using tumour phylogenetics

Article Snippet: WES-based SNVs and SNP-based CNVs , Broad Institute custom heuristic (parsimony, branch sibling model, and grafting at tips) , 22.

Techniques: Sequencing, Methylation, RNA Expression, Clone Assay

Journal: Nature reviews. Genetics

Article Title: The evolution of tumour phylogenetics: principles and practice

doi: 10.1038/nrg.2016.170

Figure Lengend Snippet: Experimental technologies and data types for tumour phylogenetics

Article Snippet: WES-based SNVs and SNP-based CNVs , Broad Institute custom heuristic (parsimony, branch sibling model, and grafting at tips) , 22.

Techniques: Sequencing, Expressing, Marker, DNA Methylation Assay, Methylation Sequencing, Methylation, Gene Expression

Journal: Nature reviews. Genetics

Article Title: The evolution of tumour phylogenetics: principles and practice

doi: 10.1038/nrg.2016.170

Figure Lengend Snippet: An illustration of a hypothetical scenario described in the main text, in which we seek to infer a phylogenetic history of copy number variant (CNV) events in the progression of a single tumour. Each tree shows the potential evolution of genomic copy number profiles for a set of observed clones (blue lines) and computationally inferred intermediate states (red lines) for a single tumour. a | The hypothetical ‘true’ tree describing the evolution of a set of clones from a diploid root via a series of CNVs: gain or loss of copy number in a localized region, as well as whole-genome duplication, leading to a doubled copy number genome-wide. b | Incorrect inference due to the use of a model designed for single-base changes, leading to a substantially incorrect phylogeny involving various biologically ‘impossible’ evolutionary events, such as partial (non-integer) gain, loss, or whole-genome duplications, leading to fractional copy numbers. c | Improved but still inaccurate inference after correcting to an evolutionary model cognizant of the type of variation occurring with CNVs; this eliminates impossible events and leads to a more accurate tree topology, but still fails to identify the correct tree because the analysis is using an algorithm that identifies biologically plausible but still sub-optimal phylogenies for this kind of evolutionary model. d | Still inaccurate inference after changing to a more sophisticated model and algorithm that are well suited to CNV evolution but make it impractical to use single-cell sequence data; this forces a change to a bulk genomic data type, leading to inadequate sampling of extant clones to capture the rapid mutation process typical of CNV-driven evolution and observed in the true tree.

Article Snippet: WES-based SNVs and SNP-based CNVs , Broad Institute custom heuristic (parsimony, branch sibling model, and grafting at tips) , 22.

Techniques: Variant Assay, Clone Assay, Genome Wide, Sequencing, Sampling, Mutagenesis