Hi Synapse team! First of all, thank you for the great work you do for the scientific community. I was exploring the clinical panels used in GENIE v16 project. I was specifically interested in the **WAKE panels** (e.g WAKE-CLINICAL-T5A, WAKE-CLINICAL-CF3 and WAKE-CA-01). Therefore, I downloaded the **genomic_information.txt** to look for the regions targeted by these panels, but I saw that the **regions covered were just of 1bp size**. However, when looking at the AACR Project GENIE 16.0-public Data Guide file, I saw that these WAKE panels cover** coding exon regions and not hotspots**. Hence, I expected to have regions much bigger than 1bp for each of the genes targeted in these panels (like it is the case for NKI or VHIO panels that also cover coding exons). Am I correct in assuming that the regions in these panels should be of bigger sizes? If so, is there a way I can get this information (ideally in a bed-like format)? Furthermore, for some of these WAKE panels I see that in the ID column from the **genomic_information.txt** file there are more genes compared to the number of genes reported in the **assay_information.txt** file. For example, looking at WAKE-CLINICAL-CF3, in the assay_information.txt file there are just 11 genes targeted in the number_of_genes column, but when looking at the ID column from the genomic_information.txt I find 39 unique genes. Could you help me understand this discrepancy, please? Thank you very much in advance. Best, Diego.

Created by Diego García López diegogl
Hi @chelsea.nayan! Thank you very much for your response. It has been really useful. Please keep me updated about the solution to the potential issue of the regions of the WAKE panels. Thank you very much in advance. Diego.
Hi @diegogl, Thank you for your patience! "Am I correct in assuming that the regions in these panels should be of bigger sizes? If so, is there a way I can get this information (ideally in a bed-like format)?" We’ve contacted the site and discussed the potential issue; they are actively working on a resolution. Unfortunately, there is no update at this time. "Furthermore, for some of these WAKE panels I see that in the ID column from the genomic_information.txt file there are more genes compared to the number of genes reported in the assay_information.txt file." This discrepancy should have been resolved in the 17.0-public releases and on. This was a known issue related to processing the bed files. Best, Chelsea
Dear @chelsea.nayan, I hope you are doing well. I just wanted to kindly follow up and check if there are any updates regarding this topic, and to confirm I have not missed anything. Looking forward to hearing from you. Thank you very much in advance. Best, Diego.
Dear @diegogl, Thank you for your patience. We are actively working with the site on how to resolve this discrepancy. We will provide an update by end of next week. Best, Chelsea
Hi guys! Sorry to insist on this topic. Is there any news about these WAKE panel data? Thank you very much in advance! Best. Diego.
Hi Chelsea and Jumi, It would be awesome to have the updated data for the WAKE panels (I am specifically interested in the WAKE-CLINICAL-T5A, WAKE-CLINICAL-CF3 and WAKE-CA-01). I am really looking forward to it! Thank you very much for your help. Best, Diego.
Dear Diego, Thank you for your interest in GENIE data and apologies for our delay in responding. We have reached out to WAKE directly to clarify some of the issues you have come across. Unfortunately we are unable to provide bed files for our data, but will get back to you as soon as we get additional information about the data. The WAKE-CLINICAL-CF3 assay does contain only 11 genes and we are in touch with the center to rectify this in the genomic information submitted to GENIE. Thanks again for your patience and best wishes Jumi
Dear @diegogl, Thank you for you interest in the GENIE data. We will get back to you as soon as we can! Best, Chelsea
Hi Synapse team! I hope this message finds you well. Did you have a chance to review this post? Thank you very much in advance. Diego.

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