The phylogenetic tree tells you the evolutionary history of the cancer by showing the order in which the mutations were acquired and how they co-occur. The algorithm uses DNA information, such as SNVs and CNAs, to determine which cells are more similar to each other, while accounting for errors such as ADO, and variability from sequencing coverage across the DNA panel. The algorithm further uses scoring algorithms that maximize biological plausibility of the resulting phylogenetic tree and clonal architecture. The end result is the clustering together of cells into clones that share the same zygosity for the variants.
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