Hello, I am very interested in looking at the fusion data in the latest Genie release. When trying to gather some stats on a few fusions of interest I came to wonder what should I use as a denominator for my total samples queried. In the genie_combined_5.0-public.bed file I can see if the genes of interest have been included in the panel but it doesn't provide any information regarding how this genes are used. In other words, if a gene is part of a panel, can we assume that the gene was queried for fusions? I think it would be of great help having a file with all panels and genes and columns describing if the gene has been used to call copy number, mutations and fusions. Thanks, Julio

Created by Julio Fernandez Banet juferban
Hi Tom, Thanks for the advice. I was processing the data exactly the way you mentioned. I was also using the information in Table 2 of the data guide to know which Cancer Centers provided Fusion/Structural variant information. The problem is what you mentioned at the end of your answer and it is that we don't know how many of the genes in the panel have been used to call fusions. As you, I don't want to assume that all genes in a panel were used but that is what I am doing right now as I couldn't find a way to identify which are the specific genes in the panel that were used for structural variant calling. I will update this post if I find more information on how to do this. Thanks again, J.
Dear Julio, Sorry for the delay in response. This is a really good question. There is a way to match the `SAMPLE_ID` to `SEQ_ASSAY_ID` by taking the samples in the fusion file, and matching them with the clinical sample file. You can then look at the genes in the combined bed file for each `SEQ_ASSAY_ID`. That being said, I'm not sure if there is a definitive file that tells you which genes in the panel were used to call copy number, mutations, and fusions. I don't want to assume that all the genes in a panel were used. Furthermore, I would take a look at the data guide, there could be explanations for the fusion calls. Best, Tom

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