Fig. 5: Multimodal phylogenetic trees and application on adult cancers.

a NB18 including samples from the primary tumor at diagnosis (B) and after treatment (P4). b Phylogenetic reconstruction using sequencing data alone reveals an APOBEC4 mutation in the stem while c SNP-array identifies a MYCN-amplification and 17q gain. d Combining the data sets gives a refined description of this tumor’s evolution. e NB16 including three biopsies from the tumor before treatment (B1-3). g The tumor is near diploid as seen in the phylogenetic tree comprising the SNP-array data, f while having a larger amount of somatic point mutations. h Also, here combining the data sets gives a more refined phylogenetic description of the tumor. Panel i–l illustrates a phylogenetic analysis of the NSCLC CRUK0038. i A scatterplot illustrating the VAF of the mutations across the biopsies R1 and R2 for the NSCLC CRUK0038. The corresponding phylogenetic trees are based on j MAGOS alone, k DEVOLUTION on the events included in the MAGOS analysis (events present in all samples) as well as l the tree obtained with DEVOLUTION including events present in the individual biopsies. m The number of mutations includable in analysis using DEVOLUTION compared to MAGOS. n The number of phylogenetic branches produced using DEVOLUTION on the full data compared to DEVOLUTION on the events includible in the MAGOS analysis. Dotted lines connect data points from the same tumor. P-values were computed using a two-sided Mann–Whitney U-test. o The number of branches using DEVOLUTION on the events includible in the MAGOS analysis compared to the number of branches obtained in the phylogenetic tree based on nesting of the MAGOS clusters. Dotted lines connect data points from the same tumor. P-values were computed using a two-sided Mann–Whitney U-test. The box plots within the violin plots illustrates the interquartile range and the red dot is the median value. The information used to produce the phylogenies can be found in Supplementary Data 5 and 6.