Title: A novel immune checkpoint score system for prognostic evaluation in pancreatic
adenocarcinoma
Version: 3 Date: 16 Feb 2023
Reviewer's report:
"PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses one or several
testable research questions? (Brief or other article types: is there a clear objective?)
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
Yes - the approach is appropriate
EXECUTION - Are the experiments and analyses performed with sufficient technical rigor to
allow confidence in the results?
Yes - experiments and analyses were performed appropriately
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
Yes - the author's interpretation is reasonable
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your concerns sufficiently
for you to now recommend the work as a technically sound contribution? If not, can further
revisions be made to make the work technically sound?
Probably - with minor revisions
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: A potentially interesting retrospective in-silico gene expression
model for checkpoint inhibitor response in pancreatic carcinomas. Brief and concise (maybe too
concise in places) but well considered and relatively well written. The statistics and analysis
seem appropriate and the model potentially useful within this context. Please note: the figures
were not included in this review pack, so only the figure legends have been included in this
review.
ADDITIONAL REQUESTS/SUGGESTIONS:
The established acronym for pancreatic ductal carcinomas is PDAC; in the TCGA dataset PAAD
refers to a heterogenous group of tumours; if possible, please give breakdown of the subtypes
included in this analysis (expand Table 1 if necessary). If not, please flag this heterogeneity in
the text as a study limitation.
Human gene names should follow the HUGO/HGVS convention: bold and italicised.
Key results should be given in brief in the results section e.g. mean, range, p-value, cell subtypes
detected, etc; just a reference to the related figure is not sufficient.
Was mutation effect prediction taken into account in mutation analysis? If so, how; if not, why?"
Title: A novel immune checkpoint score system for prognostic evaluation in pancreatic
adenocarcinoma
Version: 3 Date: 16 Feb 2023
Reviewer's report:
"PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses one or several
testable research questions? (Brief or other article types: is there a clear objective?)
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
Yes - the approach is appropriate
EXECUTION - Are the experiments and analyses performed with sufficient technical rigor to
allow confidence in the results?
Yes - experiments and analyses were performed appropriately
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
Yes - the author's interpretation is reasonable
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your concerns sufficiently
for you to now recommend the work as a technically sound contribution? If not, can further
revisions be made to make the work technically sound?
Probably - with minor revisions
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: A potentially interesting retrospective in-silico gene expression
model for checkpoint inhibitor response in pancreatic carcinomas. Brief and concise (maybe too
concise in places) but well considered and relatively well written. The statistics and analysis
seem appropriate and the model potentially useful within this context. Please note: the figures
were not included in this review pack, so only the figure legends have been included in this
review.
ADDITIONAL REQUESTS/SUGGESTIONS:
The established acronym for pancreatic ductal carcinomas is PDAC; in the TCGA dataset PAAD
refers to a heterogenous group of tumours; if possible, please give breakdown of the subtypes
included in this analysis (expand Table 1 if necessary). If not, please flag this heterogeneity in
the text as a study limitation.
Human gene names should follow the HUGO/HGVS convention: bold and italicised.
Key results should be given in brief in the results section e.g. mean, range, p-value, cell subtypes
detected, etc; just a reference to the related figure is not sufficient.
Was mutation effect prediction taken into account in mutation analysis? If so, how; if not, why?"
Please review this paper.
user
Title: A novel immune checkpoint score system for prognostic evaluation in pancreatic
adenocarcinoma
Version: 3 Date: 16 Feb 2023
Reviewer's report:
"PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses one or several
testable research questions? (Brief or other article types: is there a clear objective?)
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
Yes - the approach is appropriate
EXECUTION - Are the experiments and analyses performed with sufficient technical rigor to
allow confidence in the results?
Yes - experiments and analyses were performed appropriately
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
Yes - the author's interpretation is reasonable
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your concerns sufficiently
for you to now recommend the work as a technically sound contribution? If not, can further
revisions be made to make the work technically sound?
Probably - with minor revisions
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: A potentially interesting retrospective in-silico gene expression
model for checkpoint inhibitor response in pancreatic carcinomas. Brief and concise (maybe too
concise in places) but well considered and relatively well written. The statistics and analysis
seem appropriate and the model potentially useful within this context. Please note: the figures
were not included in this review pack, so only the figure legends have been included in this
review.
ADDITIONAL REQUESTS/SUGGESTIONS:
The established acronym for pancreatic ductal carcinomas is PDAC; in the TCGA dataset PAAD
refers to a heterogenous group of tumours; if possible, please give breakdown of the subtypes
included in this analysis (expand Table 1 if necessary). If not, please flag this heterogeneity in
the text as a study limitation.
Human gene names should follow the HUGO/HGVS convention: bold and italicised.
Key results should be given in brief in the results section e.g. mean, range, p-value, cell subtypes
detected, etc; just a reference to the related figure is not sufficient.
Was mutation effect prediction taken into account in mutation analysis? If so, how; if not, why?"
assistant