Reviewer ’s report  
 
Title: The association of genetic polymorphisms and nonalc oholic fatty liver disease in a 
longitudinal study  
 
Version: 0 Date: 25 Mar 2020  
 
Reviewer: Pirola Jose Carlos  
 
Reviewer's report:  
 
The MS entitled "The association of genetic  polymorphisms and nonalcoholic fatty liver disease  
in a longitudinal study," by Chung GE et al. about a GWAS on NAFLD incidence and regression 
in a population -based sample from South Korea is timely, well -written, but major caveats arise.  
The strength of the study is the follow -up period of around three years in a moderate -sized 
population -based sample for NAFLD development. Ultrasound as a diagnostic criterium in place 
of gold standard diagnostic techniques is a problem already discussed b y the authors, and it is 
acceptable in this setting.  
Although in the opinion of this reviewer, the division of the sample in a discovery and 
replication stage is not totally justified, because it rests statistical, it is unclear how subjects are 
distribut ed in terms of NAFLD development and regression in the discovery and validation 
stage. The classification should be clearly indicated in a Table (and Figure 1) in place of showing 
data of the entire cohort. How were the ~800 and ~340 subjects, who develope d NAFLD and 
regressed from NAFLD, respectively, distributed in the two stages?. Estimation of statistical 
power should be provided. In the validation stage, it seems that all SNPs were analyzed. Then it 
is not a formal validation or replication. Again, thi s reviewer found no reason for the sample 
division.  
The association of NAFLD development and regression with the worsening and improving of 
metabolic traits, respectively, is essential for its own and should be deeper analysed and more 
emphasized.  
Regardin g the genetic associations, as accepted by the authors, the statistical power (worsen 
because of the two stages design) is probably deficient. This reviewer allows its inclusion as an 
exploratory study, but conclusions should be moderated (i.e. page 10, li nes 11 -14). This study in 
the present form does not support the lack of genetic influences for NAFLD development or 
regression.  
As already reported by the own research group on the same population and discussed in the 
paper, variants of the PNPLA3, TM6SF2,  HSD17B13, and though controversial, MBOAT7 
(others can be added with still good power in this sample size) are associated with NAFLD in 
case-control studies. This reviewer strongly suggests the inclusion of the data for these variants 
in the MS with stron g evidence support. As these are a posteriori hypothesis, a less stringent 
criterium for p -value cut -off is recommended, in this case, a p -value &lt;0.001 is sufficient. In 
this scenario, the contribution of the MS will be the study of the development of N AFLD (or its 
regression) according to major genetic determinants of the disease. To mitigate the lack of a gold 
standard diagnostic technique is paramount to add the profile of changes in liver enzymes as, 
although imperfect, biomarkers of disease developm ent or regression. Changes in liver enzymes 
are significant between baseline and follow -up in both situations.  
Accepting the lack of plasma insulin (and HOMA)  values, besides age, sex, and BMI, the 
adjusted analysis should include type 2 diabetes as a con founder.  
The discussion will need to be re -written, adding new references. Please cite the original 
contributions for both NAFLD and its severity, including controversial findings on a specific 
topic.  
 
Are t he methods appropriate and well described?  
If not, please specify wha t is required in your comments to the authors.  
 
No 
 
Does the work include the necessary controls?  
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.  
 
No 
 
Are you able to assess any statistics in the manus cript or would you recommend an 
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require fu rther 
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Quality 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 received reimbursements, f ees, funding, or salary 
from an organisation that may in any way gain or lose financially from the 
publi cation of this manuscript, either now or in the future?  
 
2.  Do you hold any stocks or shares in an organisation t hat may in any way gain or 
lose financially from the publication of this manuscript, either now or in the 
future?  
 
3.  Do you hold or are you curr ently 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 competing 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 to the open peer review policy of the journal. I understan d that my name will be i ncluded 
on my report to the authors and, if the manuscript is accepted for publication, my named repo rt 
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 understan d that any comments 
which I do not wish to be included in my named report can be in cluded 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: The association of genetic polymorphisms and nonalc oholic fatty liver disease in a 
longitudinal study  
 
Version: 0 Date: 25 Mar 2020  
 
Reviewer: Pirola Jose Carlos  
 
Reviewer's report:  
 
The MS entitled "The association of genetic  polymorphisms and nonalcoholic fatty liver disease  
in a longitudinal study," by Chung GE et al. about a GWAS on NAFLD incidence and regression 
in a population -based sample from South Korea is timely, well -written, but major caveats arise.  
The strength of the study is the follow -up period of around three years in a moderate -sized 
population -based sample for NAFLD development. Ultrasound as a diagnostic criterium in place 
of gold standard diagnostic techniques is a problem already discussed b y the authors, and it is 
acceptable in this setting.  
Although in the opinion of this reviewer, the division of the sample in a discovery and 
replication stage is not totally justified, because it rests statistical, it is unclear how subjects are 
distribut ed in terms of NAFLD development and regression in the discovery and validation 
stage. The classification should be clearly indicated in a Table (and Figure 1) in place of showing 
data of the entire cohort. How were the ~800 and ~340 subjects, who develope d NAFLD and 
regressed from NAFLD, respectively, distributed in the two stages?. Estimation of statistical 
power should be provided. In the validation stage, it seems that all SNPs were analyzed. Then it 
is not a formal validation or replication. Again, thi s reviewer found no reason for the sample 
division.  
The association of NAFLD development and regression with the worsening and improving of 
metabolic traits, respectively, is essential for its own and should be deeper analysed and more 
emphasized.  
Regardin g the genetic associations, as accepted by the authors, the statistical power (worsen 
because of the two stages design) is probably deficient. This reviewer allows its inclusion as an 
exploratory study, but conclusions should be moderated (i.e. page 10, li nes 11 -14). This study in 
the present form does not support the lack of genetic influences for NAFLD development or 
regression.  
As already reported by the own research group on the same population and discussed in the 
paper, variants of the PNPLA3, TM6SF2,  HSD17B13, and though controversial, MBOAT7 
(others can be added with still good power in this sample size) are associated with NAFLD in 
case-control studies. This reviewer strongly suggests the inclusion of the data for these variants 
in the MS with stron g evidence support. As these are a posteriori hypothesis, a less stringent 
criterium for p -value cut -off is recommended, in this case, a p -value &lt;0.001 is sufficient. In 
this scenario, the contribution of the MS will be the study of the development of N AFLD (or its 
regression) according to major genetic determinants of the disease. To mitigate the lack of a gold 
standard diagnostic technique is paramount to add the profile of changes in liver enzymes as, 
although imperfect, biomarkers of disease developm ent or regression. Changes in liver enzymes 
are significant between baseline and follow -up in both situations.  
Accepting the lack of plasma insulin (and HOMA)  values, besides age, sex, and BMI, the 
adjusted analysis should include type 2 diabetes as a con founder.  
The discussion will need to be re -written, adding new references. Please cite the original 
contributions for both NAFLD and its severity, including controversial findings on a specific 
topic.  
 
Are t he methods appropriate and well described?  
If not, please specify wha t is required in your comments to the authors.  
 
No 
 
Does the work include the necessary controls?  
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.  
 
No 
 
Are you able to assess any statistics in the manus cript or would you recommend an 
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require fu rther 
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Quality 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 received reimbursements, f ees, funding, or salary 
from an organisation that may in any way gain or lose financially from the 
publi cation of this manuscript, either now or in the future?  
 
2.  Do you hold any stocks or shares in an organisation t hat may in any way gain or 
lose financially from the publication of this manuscript, either now or in the 
future?  
 
3.  Do you hold or are you curr ently 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 competing 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 to the open peer review policy of the journal. I understan d that my name will be i ncluded 
on my report to the authors and, if the manuscript is accepted for publication, my named repo rt 
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 understan d that any comments 
which I do not wish to be included in my named report can be in cluded 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: The association of genetic polymorphisms and nonalc oholic fatty liver disease in a 
longitudinal study  
 
Version: 0 Date: 25 Mar 2020  
 
Reviewer: Pirola Jose Carlos  
 
Reviewer's report:  
 
The MS entitled "The association of genetic  polymorphisms and nonalcoholic fatty liver disease  
in a longitudinal study," by Chung GE et al. about a GWAS on NAFLD incidence and regression 
in a population -based sample from South Korea is timely, well -written, but major caveats arise.  
The strength of the study is the follow -up period of around three years in a moderate -sized 
population -based sample for NAFLD development. Ultrasound as a diagnostic criterium in place 
of gold standard diagnostic techniques is a problem already discussed b y the authors, and it is 
acceptable in this setting.  
Although in the opinion of this reviewer, the division of the sample in a discovery and 
replication stage is not totally justified, because it rests statistical, it is unclear how subjects are 
distribut ed in terms of NAFLD development and regression in the discovery and validation 
stage. The classification should be clearly indicated in a Table (and Figure 1) in place of showing 
data of the entire cohort. How were the ~800 and ~340 subjects, who develope d NAFLD and 
regressed from NAFLD, respectively, distributed in the two stages?. Estimation of statistical 
power should be provided. In the validation stage, it seems that all SNPs were analyzed. Then it 
is not a formal validation or replication. Again, thi s reviewer found no reason for the sample 
division.  
The association of NAFLD development and regression with the worsening and improving of 
metabolic traits, respectively, is essential for its own and should be deeper analysed and more 
emphasized.  
Regardin g the genetic associations, as accepted by the authors, the statistical power (worsen 
because of the two stages design) is probably deficient. This reviewer allows its inclusion as an 
exploratory study, but conclusions should be moderated (i.e. page 10, li nes 11 -14). This study in 
the present form does not support the lack of genetic influences for NAFLD development or 
regression.  
As already reported by the own research group on the same population and discussed in the 
paper, variants of the PNPLA3, TM6SF2,  HSD17B13, and though controversial, MBOAT7 
(others can be added with still good power in this sample size) are associated with NAFLD in 
case-control studies. This reviewer strongly suggests the inclusion of the data for these variants 
in the MS with stron g evidence support. As these are a posteriori hypothesis, a less stringent 
criterium for p -value cut -off is recommended, in this case, a p -value &lt;0.001 is sufficient. In 
this scenario, the contribution of the MS will be the study of the development of N AFLD (or its 
regression) according to major genetic determinants of the disease. To mitigate the lack of a gold 
standard diagnostic technique is paramount to add the profile of changes in liver enzymes as, 
although imperfect, biomarkers of disease developm ent or regression. Changes in liver enzymes 
are significant between baseline and follow -up in both situations.  
Accepting the lack of plasma insulin (and HOMA)  values, besides age, sex, and BMI, the 
adjusted analysis should include type 2 diabetes as a con founder.  
The discussion will need to be re -written, adding new references. Please cite the original 
contributions for both NAFLD and its severity, including controversial findings on a specific 
topic.  
 
Are t he methods appropriate and well described?  
If not, please specify wha t is required in your comments to the authors.  
 
No 
 
Does the work include the necessary controls?  
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.  
 
No 
 
Are you able to assess any statistics in the manus cript or would you recommend an 
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require fu rther 
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Quality 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 received reimbursements, f ees, funding, or salary 
from an organisation that may in any way gain or lose financially from the 
publi cation of this manuscript, either now or in the future?  
 
2.  Do you hold any stocks or shares in an organisation t hat may in any way gain or 
lose financially from the publication of this manuscript, either now or in the 
future?  
 
3.  Do you hold or are you curr ently 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 competing 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 to the open peer review policy of the journal. I understan d that my name will be i ncluded 
on my report to the authors and, if the manuscript is accepted for publication, my named repo rt 
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 understan d that any comments 
which I do not wish to be included in my named report can be in cluded as confidential comments 
to the editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
assistant