Clinical Value of NGS Genomic Studies for Clinical Management of Pediatric and Young Adult Bone Sarcomas

Round 1

Reviewer 1 Report

This manuscript of Gutierrez-Jimeno et al. describes the NGS analysis for bone sarcomas of pediatric and young adult patients. They analyzed 55 clinical samples diagnosed as malignant bone tumors. DNA and RNA samples were extracted from FFPE or frozen tissues and were subjected to NGS. They identified genetic alterations in 44 patients including CNVs, fusions, missense and truncating mutations. EWSR1-FLI1, TP53, RB1, MYC, KIT, and PTEN were affected as frequent mutation targets. The identifications of these mutations were useful to correct the diagnosis and to obtain actionable targets for molecular targeted therapies. Overall, the results presented in this study are solid and reasonable, however, the mutations have been well known in bone sarcomas and no novel information is provided. Moreover, due to lack of important histopathological data, I cannot evaluate the value of NGS results to correct the initial diagnosis. These corrections can be caused by the poor performance in the routine pathological diagnosis.

 

Specific comments:

1. The authors describe that amplification of KIT and PDGFRA was mutually exclusive (lines 192-193). Although this conclusion is quite reasonable, the cases with PDGFRA amplification are completely overlapping with those with KIT amplification in Figure 1 and 4.
2. Copy number alterations are indicated as gene names in Figure 2. Did the authors check the expression of these genes by RNA-seq? Discrepancies between gene expression and copy number alterations are frequently observed.
3. The authors describe correction of the diagnosis for Ewing’s sarcoma as angiomatoid fibrous histiocytoma by detecting EWSR1-CREB1 (case #50). These two neoplasms show distinctive histological findings from each other. The detection of the split signal of EWSR1 by FISH is not strong evidence for Ewing’s sarcoma, given that EWSR1 fusions are shown in more than 10 different tumor types.
4. In case #40, they changed the diagnosis from synovial sarcoma to pleomorphic undifferentiated sarcoma, because SS18 rearrangement was not detected. The initial diagnosis was made based on the positive SS18 staining (lines 265-268). The diagnostic immunostaining of synovial sarcoma requires the anti-SS18-SSX antibody, not anti-SS18 antibody.
5. The last paragraph of the result section (lines 312-314) sound like a memorandum and is confusing. This part should be removed.

Author Response

We very much acknowledge the comments and suggested modifications raised by the reviewers, that we think that have significantly increased the quality of our work. Please find enclosed a point-by-point response to all the issues raised by the reviewer´s. Thank you for giving us the opportunity to re-submit and publish our work in Cancers. 

Author Response File: Author Response.pdf

Reviewer 2 Report

This is a very nicely written clinical report that details the utility of NGS based molecular testing in the clinical management of children and adolescents with sarcomas. The authors clearly demonstrate the clinical utility of these approaches at their institutions. While the presented information regarding the clinical utility of NGS testing in sarcomas has already been published, this report confirms previous findings and presents the experience of NGS testing to two centers in Spain over a period of 8 years. There are a couple of of issues that need to be addressed to improve the clinical impact of this manuscript.

1. In section 3.3, the authors should add more details about the 11 cases where NGS testing changed the initial diagnosis.
2. The authors mention that there were 9 cases where NGS testing changed therapy decisions. However, the authors detail only 7 cases in section 3.3. The authors should either describe the other two cases or revise the summary to say that therapy was changed in only 7 cases.
3. The authors show that 18 patients had actionable mutations. However, only one patient had a therapy change in this cohort. This experience is common in many health systems performing routine NGS testing. The authors can consider expanding the reasons why more patients did not have the opportunity for therapy change. It will helpful to add some discussion on what changes need to be made to increase the proportion of patients with actionable mutations for whom therapy is actually altered.  

Author Response

We very much acknowledge the comments and suggested modifications raised by the reviewers, that we think that have significantly increased the quality of our work. Please find enclosed a point-by-point response to all the issues raised by the reviewer´s. Thank you for giving us the opportunity to re-submit and publish our work in Cancers. 

Author Response File: Author Response.pdf

Reviewer 3 Report

The authors present their results concerning NGS evaluation in a series of pediatric and young adult bone sarcomas. This topic is interesting: it is the basis for increasing knowledge of sarcoma pathogenesis and may have therapeutic relevance. 

Comments:

1. Title: 

Utility--> better advantages or value

2. Clarity and English editing should be improved in simple summary and abstract

3. In the introduction, the relevance of personalized medicine should be emphasized. Cite appropriate references such as:   

-Cancers. 2021 May 13;13(10):2359.  doi: 10.3390/cancers13102359  

-Ther Adv Med Oncol. 2021 Jul 25;13:17588359211029125. doi: 10.1177/17588359211029125.

-Curr Opin Oncol. 2021 Jul 1;33(4):315-322. doi: 10.1097/CCO.0000000000000741

4. Only in two cases is available analysis on primary and metastatic samples: are there any difference? Please comment.

5. Discussion should be better organized.

I suggest a reorganization: first comment on your results (lines 322-328) and thereafter the remaining text. Part of the discussion (333-358) may be anticipated in the introduction. 

Author Response

We very much acknowledge the comments and suggested modifications raised by the reviewers, that we think that have significantly increased the quality of our work. Please find enclosed a point-by-point response to all the issues raised by the reviewer´s. Thank you for giving us the opportunity to re-submit and publish our work in Cancers. 

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Although the authors addressed a part of my concerns in the revised manuscript, the revisions have not improve the overall scientific significance of the manuscript.  I do not find the novelty sufficient to merit readers' interest. Therefore, I would not recommend the manuscript to be accepted for publication in Cancers.