Interpretation of the results

[YanaVassileva]

Dear Prof. Roth,

I have some problems interpreting the results that I obtain from PyClone VI. When I run the analysis on a sample with 6000 mutations, I get 4 clusters, with all of the clusters having a cellular prevalence higher than 0.5. The cellular prevalence is defined as the proportion of malignant cells with the mutation in the sample, such that I would expect that clusters might have the same mutations (shared mutations among the clusters). Especially mutations, assigned to a cluster with a cellular prevalence of 0.99 should be appearing in the other clusters as well. However that is not the case. I have just clusters with non overlapping mutations and also the cellular prevalence of the clusters does not add up to 1 for all the clusters. Can you give me a hint for the correct interpretation. What conclusion can I draw from the PyClone VI output on how heterogeneous my sample is?

Best regards,
Yana Vassileva
Research Group "Biomedical Genomics"

[andreyurch]

Dear developers,

I actually have a similar problem. The sum of cellular_prevalence is higher than 1. It would be great if the authors can clarify this question. I attach my file and the code.

pyclone-vi fit -i test.tsv.txt -o tracerx.h5 -c 15 -d beta-binomial -r 100
pyclone-vi write-results-file -i tracerx.h5 -o test_res.tsv.txt

Best regards,
Andrey Yurchenko

test.tsv.txt

test_res.tsv.txt