About target panel suitability

[HuZhuocheng]

Dear Authors,

Thank you very much for developing your excellent algorithm. I would like to use the algorithm you developed in my project. However, my data is NGS-panel sequencing data. While there are many samples (over 2,000), the panel only covers approximately 250 genes. When reading your article, we noticed that it mentions the applicability of WES, but there is no mention of the suitability for panels throughout the article. We would like to ask: is my data type not suitable for this algorithm, and is gene coverage crucial?

[wlippa]

Hi and apologies for the late reply. I assume you have a multi-sample dataset, i.e. at least two samples for each tumour? If yes, then the question is: can you get good phylogenetic trees with your data? Our method uses the SNV derived tree (obtained with a tool like Conipher) to assign the most likely copy numbers to these clones, so you want to have a tree which identifies SNV subclones well. This might be easier in high TMB tumours, less so in low TMB ones.