Fig 1.
Comparison of in-silico clonal phylogenies from single tumour cells with co-isolated DNA and RNA (Han et al., Genome Res 2018).
Dendrograms constructed from clustering of transcript-based inferred single-nucleotide variants (DENDRO) and ground truth DNA-based single-nucleotide variant calls (GATK) and compared by tanglegram. Colours correspond to individual cell lines (yellow: SKBR3, green: HCC827, and light blue: MCF7). Entanglement of the phylograms was 0.097 (an entanglement value of 1 corresponds with full entanglement of two phylograms, whereas an entanglement value of 0 corresponds with no entanglement).
Fig 2.
Comparison of in-silico clonal phylogenies from single tumour cells with co-isolated DNA and RNA (Han et al., Genome Res 2018).
Dendrograms constructed from clustering of transcript-based inferred copy-number variants (inferCNV) and ground truth DNA-based copy number variant calls (WGS-Ginkgo) and compared by tanglegram. Colours correspond to individual cell lines (yellow: SKBR3, green: HCC827, and light blue: MCF7). Entanglement of the phylograms was 0.11 (an entanglement value of 1 corresponds with full entanglement of two phylograms, whereas an entanglement value of 0 corresponds with no entanglement). As adapted from Erickson et al., Nature, 2022, Extended Data Fig 1a.
Fig 3.
Comparison of published DNA-based prostate cancer clonal phylogenies and transcript-based inferred single-nucleotide and copy-number variant derived dendrograms.
a) Phylogeny from patient A21, as published and reproduced from Gundem et al., Nature, 2015. Transcript data were available only for a subset of specimens. b, Phylogeny from patient 498, as published and reproduced from Hong et al., Nat. Comms, 2015. Transcript data available for a subset of specimens. inferCNV-based clonal phylogenies adapted from Erickson et al., Nature, 2022, Extended Data Fig 1b.
Fig 4.
Comparison of published DNA-based (WGS) phylogenetic trees (left) as compared to novel RNA-based (RNA Microarray) phylogenies (right) from Cooper et al., 2015.
A) Phylogenies from patient CRUK0006, B) Phylogenies from patient CRUK0007, C) Phylogenies from patient CRUK0008. RNA phylogenies include blood samples not presented in DNA-based phylogenetic trees.
Fig 5.
Comparison of DNA-based (WGS) phylogenetic trees (left) as compared to transcript-based inferCNV clonal phylogenies (right) from Berglund et al., 2018.
DNA dendrogram constructed using patient-matched blood sample as a reference: such data were not available for inferCNV. Entanglement of the phylograms was 0.35 (an entanglement value of 1 corresponds with full entanglement of two phylograms, whereas an entanglement value of 0 corresponds with no entanglement). A label with the ending of * represents a section containing histologically detected cancer.