The authors have carried out a comparative study between the OncoDNA OncoDeep kit and the TSO500 across multiple centres. I commend the authors (and the company who presuambly provided support) on the honest appraisal they have carried out of the technology and their clear reporting. I have a number of clarifications that are needed before the paper is suitable for publication:

1) Sample selection (2.2) - "exon and fusion skipping on most of the samples" - how many exactly, and why were all not done
2) Chelex extracted DNA does not work in the OncoDeep assay - why not, please expand?
3) Content of Oncodeep panel should be provided in the appendix, either as a table but ideally as a BED file
4) Results - why does Oncodeep need RNA speedvac - explain the rationale - is it to concentrate down the RNA?
5) "For six TSO500 variants with VAF between 9.5% and 56%, no evidence whatsoever was available for those variants in the Bam file of the OncoDEEP analysis." - does this mean when the authors examined the aligned BAM files there was no evidence in the OncoDEEP BAMS but there was in the TSO500? If so, what was the nature of the variants e.g. C>T typical of FFPE? It may be that in fact there was no variant and there was a sequencing error because of FFPE in the TSO500 or vice versa
6) What is the rationale for picking a CN>6 as being pathogenic - can this be justified?
7)For the final 3 fusion genes which were not detected was there a manual examination of the BAM file to see if there were any supporting reads to clarify whether this was an algorithm failure or chemistry failure
8) Immunohistochemistry was performed and showed an MSI High result - what IHC was this? Was it MMR? i.e. MLH1
9) There needs to be a 2x2 table for all comparisons and reporting of Sensitivity and Specificity based on TSO500 as the gold standard
10) There appears to be no cost comparison for TSO500 vs. OncoDeep. Clearly the sequencing is cheaper because of greater pooling, but what about the kit?

Generally the reviewers have made the changes I asked for and improved the manuscript generally. I am happy for this to be published.