This article addresses the method validation process of a novel CGP panel across seven centers, comparing the results of the new OncoDEEP CGP assay on 250 samples. Four of the centers are located in Belgium and three in The Netherlands. The concordance of the results was assessed by comparison with the TSO500 assay.
In total, 674 SNVs and indels, 33 amplifications with a fold change (FC) ≥6, 172 fusions, and 20 splice variants were identified. Additionally, MSI and HRD status were evaluated in a few samples.
The OncoDEEP panel is a hybrid-capture based panel with a total size of 1.8 Mb. It covers 638 cancer-related genes, enabling the detection of SNVs, indels, CNVs, and LOH at the DNA level. Information on key genomic biomarkers such as TMB, MSI, and HRD is also routinely provided. Clinically significant rearrangements at the RNA level can be detected in 11 genes (13 in the current panel), and splice variants in 9 genes.
The comparison with TSO500 is very pertinent and stress the easiness to perform the librairie preparation. This article deserves to be published if the comments are solved

Comments :
1) Quality criteria : we need to have a discussion around the coverage of the main genes, essentially the one with a actionability recognized by ESMO guidelines. It is important as most of the missed variants are related to low coverage.
2) CNV detection is good for amplification - what about large rearrangement intragenic as deletion in BRCA1 ?
3) Among the seven discordant fusion genes, the reciprocal fusion was detected in three cases (e.g., ALK::TIMP3 versus TIMP3::ALK). In one case, OncoDEEP reported MYO18A::ROS1, while TSO500 identified MYO18A fused to the ROS1-flanking gene GOPC. For the remaining three fusions not detected by OncoDEEP (with ALK, BRAF, and NTRK3 drivers), no clear explanation are provided for their absence. Notably, aberrations involving the same drivers were detected in several other samples, including the reference RNA sample.
4) The assessment for MSI / HR are too limited to conclude for its clinical applications.
5) The OncoDEEP kit has not yet been reported in the literature for its diagnostic value. In the comment, the author should position their solution with the requirement on the IVDR as clinical results.
The author conclude in the reimbursement issue. It will be interesting to have a global economic comparison. An affordable CGP will be also important to diffuse this approach.

Thanks for the authors answers which help to better understand their results.