Additional file 1 of NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model
Creators: name: Liu, Yushu
name: Edrisi, Mohammadamin
name: Yan, Zhi
name: A Ogilvie, Huw
name: Nakhleh, Luay
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Method S1. Settings used for maximum parsimony and neighbor joining. Method S2. Tree Moves. Fig. S1. Error in estimated copy number profiles. The Hamming distances between the true copy number profile and copy number profile estimated by Ginkgo [45] of each cell are computed and summarized across all simulated data sets. Fig. S2. Copy number profile simulated under different parameters. Fig. S3. The mutation tree inferred by SCICoNE [25] from one of the simulated data set We ran SCICoNE without performing clustering on the cells as a preprocessing step in order to acquire the mutation tree at a single-cell level and make it comparable to the results of NestedBD. However, the result shows that SCICoNE assigns all the CNA events to only one node which suggests all cells in this data set share the same copy number profile. Fig. S4. Inference results using MP on data from colorectal cancer patient CRC01 from [34]. The heat map shows the copy number profiles of the sampled cells and the tree is inferred by MP. At the leaves of the trees, solid rectangles correspond to primary tumor cells, and grey-gradient rectangles correspond to liver metastasis cells. Fig. S5. Inference results using NJ on data from colorectal cancer patient CRC01 from [34]. The heat map shows the copy number profiles of the sampled cells and the tree is inferred by NJ. At the leaves of the trees, solid rectangles correspond to primary tumor cells, and grey-gradient rectangles correspond to liver metastasis cells. Fig.S6. Inference results using MP on data from colorectal cancer patient CRC04 from [34]. The heat map shows the copy number profiles of the sampled cells and the tree is inferred by MP. At the leaves of the trees, solid rectangles correspond to primary tumor cells, and open rectangles correspond to lymph node metastasis cells. Fig. S7. Inference results using NJ on data from colorectal cancer patient CRC04 from [34]. The heat map shows the copy number profiles of the sampled cells and the tree is by NJ. At the leaves of the trees, solid rectangles correspond to primary tumor cells, and open rectangles correspond to lymph node metastasis cells. Fig. S8. Inferred tree using NestedBD from colorectal cancer patient CRC01 from [34], annotated with support value on each clade. (Left) phylogenetic tree inferred by the NestedBD method for the colorectal cancer patient CRC01. Each clade in the tree is annotated with its respective support value, representing the confidence level for the inferred branching patterns. (Right) histogram summarizing the distribution of these support values for all clades within the inferred tree. This figure helps assess the robustness of each branch’s inference and provides an overall confidence distribution for the tree’s topology. Fig. S9. Inferred tree using NestedBD from colorectal cancer patient CRC04 from [34], annotated with support value on each clade. (Left) phylogenetic tree inferred by the NestedBD method for the colorectal cancer patient CRC04. Each clade in the tree is annotated with its respective support value, representing the confidence level for the inferred branching patterns. (Right) histogram summarizing the distribution of these support values for all clades within the inferred tree. This figure helps assess the robustness of each branch’s inference and provides an overall confidence distribution for the tree’s topology.