Hello everybody,
It is my first time working with cancer genomes and I have some doubts. I found this study in which they provide a lot of different sequencing data for the cell line HCC1395, and I would like to use them to assess a new tool that we are developing for detecting Copy Number Alterations. Problem is, I'm lacking a ground truth. In this study, they provide a golden dataset for SNVs and short INDELS, but they do not provide info about the CNAs. I necessarely need a not simulated normal/cancer sample pairs from the same patient, and this is the only source I found so far whicjh is freely providing a lot of well documented sequencing data.
Since the HCC1395 cell line was already studied before, I found some other studies providing the CNAs they found for it. My question now is: can I use those CNAs found in other studies on the same cell line as a ground truth to compare what I will find with our tool on the data I have?
I don't have much biological knowledge and my doubts arise manly because, If I undersood well, those cells are usually grown independently in a laboratory setting for each study, so I am not sure if they are comparable, or if they could have different mutations occurring between the different studies.
Thanks in advance!
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