Comparative Study of NGS Platform Ion Torrent Personal Genome Machine and Therascreen Rotor-Gene Q for the Detection of Somatic Variants in Cancer
, Floriana Morgillo 1, Virginia Tirino 2, Gabriella Misso 1, Erika Martinelli 1, Teresa Troiani 1, Vincenzo Desiderio 2, Gianpaolo Papaccio 2, Francesco Iovino 3, Giuseppe Argenziano 4, Elvira Moscarella 4, Pasquale Sperlongano 5, Gennaro Galizia 5, Raffaele Addeo 6, Alois Necas 7, Andrea Necasova 7, Fortunato Ciardiello 1, Andrea Ronchi 8, Michele Caraglia 1,9 and add
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Round 1
Reviewer 1 Report
Dear authors, please see attached word file for my review report.
Comments for author File: 
Comments.pdf
Author Response
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Author Response File: 
Author Response.docx
Reviewer 2 Report
Comments to the Autor:
The authors performed a comparative analysis of two platforms: Ion Torrent Personal Genome Machine and Therascreen Rotor Gene Q for detecting mutations in target genes in cancer samples. Furthermore, they suggested using a more sensitive analysis method to study avoid the presence of a small neoplastic clone. However, based on my opinion, the current manuscript with data presented are insufficient to make the conclusions and significant enough to publish in this journal.
Some suggestions and questions are listed:
Overall:
Writing need to be better polished, especially the Redundant sentences present in both introduction and discussion. Need to introduce two platforms in the introduction section. Result section needs to be better organized. It is hard to read through it with clear points and logic. Gene names should be italic. What coverage (distribution) of each sequenced gene need to be presented clearly.Details:
Page 1, line 38 to line 40: those are not two sequencing methods. Page 2, line 60: the sentence “The most common type of lung cancer is adenocarcinoma” needs to be rewritten to better connected to the previous sentence.3 Page 3, line 110 to line 113 needs to be rewritten.
Page 3, line 114: Therascreen Rotor Gene Q is not a sequencing method, and you should state the main conclusion of your comparative analysis in this sentence. Page 5, line 137 to line 138 needs to be rewritten. Page 6, line 159: delete “been”. Page 7, line 231 to line 233 needs to be rewritten. Page 7, line 238: should avoid using “In the second case” too many times in the manuscript.9 Page 7, line 248: “it is recommended BRAF mutation testing” change to “BRAF mutation test is recommended”.
Page 8, line 253 to line 255: add citations for the “several studies”. Page 8, line 258 to 259: reconstruct the sentence. Page 8, line 262 to 263: delete “for two samples……” which is useless. Page 10, Figure 1 is not clear which needed to be plotted.
Author Response
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Author Response File: Author Response.docx
Round 2
Reviewer 1 Report
Although the manuscript is much improved, I am not convinced that the English language and style are of a sufficient standard for this work to be published. I recommend that you keep working on this manuscript and consider enlisting the help of professional English language editing services.
Author Response
"Please see the attachment."
Author Response File: Author Response.docx
Reviewer 2 Report
The authors have done thorough developments to address most of my comments well. I am glad that my suggestions are helpful. Although I still feel that the result section was not well presented. In the first paragraph of the result section, the author mentioned three directions of analysis, although I can't get in the manuscript. On the other hand, the result section focuses on the inconsistent results between the two methods, although it is suggested to state clearly the overall comparison results ahead to give the readers a full picture.
Minor comments:
1. In the abstract, the sentence of "Our analysis demonstrated that the two techniques did not show the same and overlapping results" should be more specific with the percentage of consistency.
2. Many mistakes should be corrected throughout the manuscript. For example: the # 8 address in the updated author list is missing; two "in in" in line 121; "analysed" should be corrected to "analyzed"; remove "Next-generation genetic sequencing" and move the "Next generation sequencing" out from the parentheses in line 136.
Author Response
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Author Response File: Author Response.docx
Round 3
Reviewer 1 Report
The authors have clearly extensively improved the manuscript since the first version and made all of the changes requested. However, the language still requires substantial editing. In the current form, the article is very difficult to read and this impacts on the ability of the reader to interpret the science. I recommend accepting this article but extensive text editing is still required.
