Driver Phylogenetic Trees of TRACERx project

Question

[Vasei]

There are figures depicting phylogenetic trees for different patients in the two following papers:

1. Tracking the Evolution of Non–Small-Cell Lung Cancer

2. Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

In the supplementary materials of the first study there is a comprehensive detailed list of trees in pdf format. But even this data is not enough to reproduce the tree because data is not complete. For example in the following figure genes mutated in clones 1, 4 and 5 are not listed!

Is the data for these phylogenetic tree structures completely available or I must create this trees from original data? Is there any machine readable source for collecting this data?

[Kevin Blighe]

You will have to assume not available anywhere. Like quite a few project groups, the TRACERx team became expert at never actually sharing their data. The work has now gone into a company in London, called Achilles Therapeutics Limited. Not necessarily a bad thing, as the treatments that they are developing are quite promising. If you email them, you will likely not receive a response, but, by posting this comment here, I may be proved incorrect. I write this having published with them myself while I worked with them: https://www.nature.com/articles/s43018-020-0066-y

[Vasei]

Thank you very much. I saw some publications claiming that they used these phylogenetic trees so I was hoping that maybe this data is available somewhere in appendices where I couldn't find them!!!

Answer 1

[Vasei]

For study 1 which is about lung cancer, in appendix 2, in sheet TableS3, there is a column named PyClonePhyloCluster which shows the number of cluster for each mutation. Binding this data to graphical images in the appendix 1, which is depicted in the question, can result in complete phylogeny trees!

Note: In appendices of study 2 about renal carcinoma, I just found data on wether a mutation is clonal or not. Any guidance on using this data to generate trees in the picture is appreciated!

[itigupta24]

By any chance did you run their latest version of the tool CONIPHER? I am trying to cluster and build trees on my set of samples but unfortunately after their paper came or rather during their revision process they have updated the tool. Now it is giving some weird error at the final clustering stage (Which previously was running fine and generating the tress). Thanks in advance!