Incorporating Amplifications and Deletions into a PyClone Analysis

[Luqman Hodgkinson]

Dear Professor Roth,

Here at Stanford University School of Medicine we are working on an analysis of basal cell carcinoma. Sequencing of the tumors gives us small variant mutations, amplifications, and deletions. It is straightforward to use PyClone with the small variants because we have reference counts and variant counts. How do you recommend, if at all, that amplifications and deletions be incorporated into a PyClone analysis?

Sincerely yours, with appreciation and gratitude to you,

Luqman Mushila Hodgkinson, MS, PhD

[Andrew]

Hi Luqman,

In principle you can use any variants for which ref/alt counts are available. The issue is that there will likely be a strong bias towards reference for indels and structural variants. As a result if you run SNVs and indels together they will likely form separate clusters. I do not have a good solution to solve this problem, thus I would only recommend using PyClone with SNVs.

Best wishes,

Andy