DOI: 10.5281/zenodo.18429771
title: Processed data for "Leveraging phylogenetic uncertainty using SPICE for robust reconstruction of copy-number tumor evolution"

description: The dataset contains processed data for the manuscript "Leveraging phylogenetic uncertainty using SPICE for robust reconstruction of copy-number tumor evolution".The /benchmarking folder contains details of the benchmarking performed in the manuscript:The /simulations folder contains details of all simulations generated, where for each simulation the following files are generated:



sim_info.tsv - Information about the generated simulation, including the input parameters used and the number of different CNAs included in the simulation.

sim_cn_events.tsv - The CNA estimation info details all the CNAs applied to the simulation, as estimated in the TRACERx dataset.

sim_cn_profiles_bins.tsv.gz - The copy number profiles for all simulated nodes in the phylogeny for every bin.

sim_cn_seg_profiles_GT.tsv.gz - The copy number profiles for all segments (where segments are defined as consecutive bins with the same copy number across all nodes). The Noise column details whether the segment has had simulated noise added, the Noise_effect column details the amplitude of the noise, and the CN_clean column details the original, ground truth copy number without generated noise.

sim_cn_seg_leaf_profiles.tsv.gz - The copy number profiles for all segments (where segments are defined as consecutive bins with the same copy number across all nodes) for only the leaf nodes. This file is the input to SPICE.

sim_medicc_profiles.tsv - This file contains the same information as in sim_cn_seg_leaf_profiles.tsv.gz, but is processed in the format required for input to MEDICC2.


The /evaluation folder contains processed evaluation metrics for each simulated dataset:



evaluation_metrics.tsv - For each simulated instance, the evaluation of tree topology (rfdist), wgd (wgd_branch_dist) and ancestral copy number profiles (hamming, bp_hamming) distance metrics are reported for the phylogenetic trees output by SPICE (both the optimal tree and the top-ranked tree) and MEDICC2.

cn_prob_evaluation.tsv - For each simulated instance, the ancestral copy number profiles (hamming, bp_hamming) distance metric is reported for the SPICE top-ranked tree output when restricting to only genomic segments with a probability greater than 60%, 70%, 80%, and 90%.

all_trees_evaluation.tsv - For each simulation instance with noise = 0, the ancestral copy number profiles (hamming) distance metric is reported for every phylogeny solution output by SPICE.


The /analysis folder contains details of the analysis performed on patient tumour datasets (Gundem et al, 2015) and (Funnell et al, 2022):The /output folder contains the output for SPICE and MEDICC2 run on each dataset (within the /gundem2015 and /funnell2022 folders):



spice/spice_total_edges.tsv.gz - The phylogenetic edges and number of events on each edge for all solutions inferred by SPICE.

spice/spice_total_nodes.tsv.gz - The copy number profiles inferred for all solutions output by SPICE.

spice/spice_solutions_ranked.tsv.gz - The probability and rankings of all solutions output by SPICE.

spice/spice_cn_probabilities.tsv.gz - The probability of each copy number state inferred by SPICE for the top-ranked topology.

medicc2/medicc_total_edges.tsv.gz - The phylogenetic edges and number of events on each edge inferred by MEDICC2.

medicc2/medicc_total_nodes.tsv - The copy number profiles inferred by MEDICC2.


The /processed_data folder contains all the processed data for figures 3-5:figure3_earlylate/[gundem/funnell]whole_genome_probabilities[spice/medicc2].tsv.gz - The probability across the genome of CNAs (Gains, Amplifications, Deletions, and Losses) occurring truncally or subclonally.figure3_earlylate/[gundem/funnell]earlylate_genes[spice/medicc2].tsv.gz - The probability of genes being affected by CNAs (Gains, Amplifications, Deletions, and Losses) occurring truncally or subclonally.



figure4_parallel/[gundem/funnell]parallel_genes[spice/medicc2].tsv.gz - The probability of genes being affected by parallel or recurrent CNAs (Gains, Amplifications, Deletions, and Losses).

figure5_migrations/[patient]/migration_probabilities_[spice/medicc2].tsv - The probability of (proportion of trees supporting) migrations between different tumour sites (where source and target represent the origin and end site of a migration).

figure5_migrations/seeding_table_[spice/medicc2].tsv - Collated output of MACHINA for all trees used to infer migrations.