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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!
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!