Reviewer ’s report  
 
Title: Variables affecting penetrance of gastric and duodenal phenotype in familial adenomatous 
polyposis patients  
 
Version: 0 Date: 05 Apr 2018  
 
Reviewer: Ben Woolbright  
 
Reviewer's report:  
 
The follow ing is a review of the manuscript from Sample et al. The purpose of this manuscript 
was to identify superior methods for identifying penetrance of APC based colon tumors, focusing 
on the upper GI. The authors performed a secondary analysis of a chemopreven tion trial to look 
at these data. The authors did a good job addressing potential biases and limitations.  
The discussion of this paper is somewhat limited. There are no references to other manuscripts in 
the first paragraph of the discussion and I counted  one in the second.  It would be nice to see the 
authors' data placed in the context of the literature. This would certainly improve the manuscript.  
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary cont rols?  
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
Are you able to assess any statistic s in the manuscript or would you recommend an  
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require further  
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Qual ity of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years re ceived reimbursements, fees, funding, or salary from an  
organisation that may in any way gain or lose financially from the publication of this  
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in any w ay gain or lose  
financially from the publication of this manuscript, either now or in the future?  
 
3. Do you hold or are you currently applying for any patents relating to the content of the  
manuscript?  
 
4. Have you received reimbursements, fees, funding, or salary from an organization that 
holds  or has applied for patents relating to the content of the manuscript?  
 
5. Do you have any other financial competing interests?  
 
6. Do you have any non -financial com peting interests in relation to this paper?  
 
If you can answer no to all of the above, write 'I declare that I have no competing interests' 
below.  If your reply is yes to any, please give details below.  
 
I declare that I have no competing interests  
 
I agree t o the open peer review policy of the journal. I understand that my name will be included  
on my report to the authors and, if the manuscript is accepted for publication, my named report  
including any attachments I upload will be posted on the website along with the authors'  
responses.  I agree for my report to be made available under an Open Access Creative Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do  not wish to be included in my named report can be included as confidential comments 
to the  editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
Reviewer ’s report  
 
Title: Variables affecting penetrance of gastric and duodenal phenotype in familial adenomatous 
polyposis patients  
 
Version: 0 Date: 05 Apr 2018  
 
Reviewer: Ben Woolbright  
 
Reviewer's report:  
 
The follow ing is a review of the manuscript from Sample et al. The purpose of this manuscript 
was to identify superior methods for identifying penetrance of APC based colon tumors, focusing 
on the upper GI. The authors performed a secondary analysis of a chemopreven tion trial to look 
at these data. The authors did a good job addressing potential biases and limitations.  
The discussion of this paper is somewhat limited. There are no references to other manuscripts in 
the first paragraph of the discussion and I counted  one in the second.  It would be nice to see the 
authors' data placed in the context of the literature. This would certainly improve the manuscript.  
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary cont rols?  
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
Are you able to assess any statistic s in the manuscript or would you recommend an  
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require further  
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Qual ity of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years re ceived reimbursements, fees, funding, or salary from an  
organisation that may in any way gain or lose financially from the publication of this  
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in any w ay gain or lose  
financially from the publication of this manuscript, either now or in the future?  
 
3. Do you hold or are you currently applying for any patents relating to the content of the  
manuscript?  
 
4. Have you received reimbursements, fees, funding, or salary from an organization that 
holds  or has applied for patents relating to the content of the manuscript?  
 
5. Do you have any other financial competing interests?  
 
6. Do you have any non -financial com peting interests in relation to this paper?  
 
If you can answer no to all of the above, write 'I declare that I have no competing interests' 
below.  If your reply is yes to any, please give details below.  
 
I declare that I have no competing interests  
 
I agree t o the open peer review policy of the journal. I understand that my name will be included  
on my report to the authors and, if the manuscript is accepted for publication, my named report  
including any attachments I upload will be posted on the website along with the authors'  
responses.  I agree for my report to be made available under an Open Access Creative Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do  not wish to be included in my named report can be included as confidential comments 
to the  editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
Please review this paper.
user
Reviewer ’s report  
 
Title: Variables affecting penetrance of gastric and duodenal phenotype in familial adenomatous 
polyposis patients  
 
Version: 0 Date: 05 Apr 2018  
 
Reviewer: Ben Woolbright  
 
Reviewer's report:  
 
The follow ing is a review of the manuscript from Sample et al. The purpose of this manuscript 
was to identify superior methods for identifying penetrance of APC based colon tumors, focusing 
on the upper GI. The authors performed a secondary analysis of a chemopreven tion trial to look 
at these data. The authors did a good job addressing potential biases and limitations.  
The discussion of this paper is somewhat limited. There are no references to other manuscripts in 
the first paragraph of the discussion and I counted  one in the second.  It would be nice to see the 
authors' data placed in the context of the literature. This would certainly improve the manuscript.  
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary cont rols?  
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
Are you able to assess any statistic s in the manuscript or would you recommend an  
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require further  
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Qual ity of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years re ceived reimbursements, fees, funding, or salary from an  
organisation that may in any way gain or lose financially from the publication of this  
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in any w ay gain or lose  
financially from the publication of this manuscript, either now or in the future?  
 
3. Do you hold or are you currently applying for any patents relating to the content of the  
manuscript?  
 
4. Have you received reimbursements, fees, funding, or salary from an organization that 
holds  or has applied for patents relating to the content of the manuscript?  
 
5. Do you have any other financial competing interests?  
 
6. Do you have any non -financial com peting interests in relation to this paper?  
 
If you can answer no to all of the above, write 'I declare that I have no competing interests' 
below.  If your reply is yes to any, please give details below.  
 
I declare that I have no competing interests  
 
I agree t o the open peer review policy of the journal. I understand that my name will be included  
on my report to the authors and, if the manuscript is accepted for publication, my named report  
including any attachments I upload will be posted on the website along with the authors'  
responses.  I agree for my report to be made available under an Open Access Creative Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do  not wish to be included in my named report can be included as confidential comments 
to the  editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
assistant