Title: The role of PNPLA3 and TM6SF2 polymorphisms on liver fibrosis and metabolic
abnormalities in Brazilian patients with chronic hepatitis C
Version: 1 Date: 03 Dec 2020
Reviewer's report:
-The background needs more development. In fact, why this study is important for the Brazilian
people? I mean what this study is for?? The author needs to talk about chronic hepatitis in brazil
in addition to worldwide. Moreover, as I know these genes are involved in non-alcoholic fatty
liver disease NAFLD. Hence it is worthy to talk about this type in your population.
-The author said “in a recent year” which is not correct according to references 4 and 5. The
author needs to be accurate or change the references to be in recent year which mean (2019
minimum)
-The references cited (from 4 to 6) concern the non-alcoholic fatty liver disease specifically thus
the author must mention that. Second, it is not like “several “studies. The author needs to correct
the expression
-Same idea in the first line on page 5 and the first line in the second paragraph on the same page.
The author needs to be coherent in his redaction and once for all present the problem followed
by his aim (which is logically the solution for the problem or the initiation of this resolution).
Thus, the introduction needs more development, talking about chronic liver disease in brazil,
then the physiology (clinical part) combined with the effect of the two genes (without so much
citing the details of which allele) and finally the problem followed by the aim.
-“Most studies”, “various studies”, “numerous studies”, when we use such vocabularies we need
to cite more than two studies, and the references are commonly a meta-analysis or review. The
author needs to revise the introduction and redaction part seriously.
-The author introduces the word “metabolic syndrome (MetS)” at the end of his introduction.
Such words should be explained in the introduction. The author needs to be coherent and explain
his words from the beginning.
-Statistically, I believe that the number of healthy controls which is 1/3 of patients is not
sufficient. Would like to ask the authors to add in the methods calculation of study power (in
the section of statistical) and add the results in the result section. Moreover, please cite the low
number of healthy control as a limitation of the study at the end of the main document.
-Why the authors use only the test of Mann-Whitney and Kruskal-Wallis only?  Both of the
tests are non-parametric?? The author needs to explain why he is using such an alternative.
Otherwise, the manuscript needs to be revised by a statistical expert and the statistical section
needs to be revised and consequently, the results may be.  Additionally, please cite the way used
for calculating the power of the study as requested previously.
-In the result please separate the section into two paragraphs. In the first one, you should describe
the clinical and demographic results and in the second you put the genetic results. This would
make it easier for the reader to follow the manuscript.
- Having 55.1% of women in your cohort cannot be described as “most of the patients”. It is
approximately half but absolutely not the most. Please correct the statement in the first paragraph
of the result section.
-As a result, you have a problem with the age of your healthy controls as you mentioned that
they are younger. Normally in the perfect condition, no differences in age and gender need to be
mentioned between controls and patients. Hence, the fact that they are younger (your controls)
mean they are biased. Consequently, I wonder if the p-value used in this manuscript was adjusted
according to gender differences?? If yes, you need to mention that in the statistical part and in
the tables of your results.
- Hardy-Weinberg equilibrium is important among the healthy controls as we want to be sure
that controls are selected correctly and deemed to be “a control group” reference. However,
I believe that the Hardy-Weinberg equilibrium among patients is not that necessary because
we don’t select patients we only genotype randomly the patients who answer to the required
condition of your study.
-For p=0.0471 I really see it as 0.05 and I believe that this p is biased and a statistic revision
needs to be done
- What do you mean by multivariate regression and univariate regression??  How you select
your variables for multivariate regression. As I mentioned earlier the statistics section needs to
be revised
- Why the author repeats another study for the same SNPs in the same population ?? Manchiero
C, Nunes AKDS, Magri MC, et al. The rs738409 polymorphism of the PNPLA3 gene is
associated with hepatic steatosis and fibrosis in Brazilian patients with chronic hepatitis C. BMC
Infect Dis 2017;17:780. The author needs to explain
-The discussion needs to be revised
-The English needs to be revised
Title: The role of PNPLA3 and TM6SF2 polymorphisms on liver fibrosis and metabolic
abnormalities in Brazilian patients with chronic hepatitis C
Version: 1 Date: 03 Dec 2020
Reviewer's report:
-The background needs more development. In fact, why this study is important for the Brazilian
people? I mean what this study is for?? The author needs to talk about chronic hepatitis in brazil
in addition to worldwide. Moreover, as I know these genes are involved in non-alcoholic fatty
liver disease NAFLD. Hence it is worthy to talk about this type in your population.
-The author said “in a recent year” which is not correct according to references 4 and 5. The
author needs to be accurate or change the references to be in recent year which mean (2019
minimum)
-The references cited (from 4 to 6) concern the non-alcoholic fatty liver disease specifically thus
the author must mention that. Second, it is not like “several “studies. The author needs to correct
the expression
-Same idea in the first line on page 5 and the first line in the second paragraph on the same page.
The author needs to be coherent in his redaction and once for all present the problem followed
by his aim (which is logically the solution for the problem or the initiation of this resolution).
Thus, the introduction needs more development, talking about chronic liver disease in brazil,
then the physiology (clinical part) combined with the effect of the two genes (without so much
citing the details of which allele) and finally the problem followed by the aim.
-“Most studies”, “various studies”, “numerous studies”, when we use such vocabularies we need
to cite more than two studies, and the references are commonly a meta-analysis or review. The
author needs to revise the introduction and redaction part seriously.
-The author introduces the word “metabolic syndrome (MetS)” at the end of his introduction.
Such words should be explained in the introduction. The author needs to be coherent and explain
his words from the beginning.
-Statistically, I believe that the number of healthy controls which is 1/3 of patients is not
sufficient. Would like to ask the authors to add in the methods calculation of study power (in
the section of statistical) and add the results in the result section. Moreover, please cite the low
number of healthy control as a limitation of the study at the end of the main document.
-Why the authors use only the test of Mann-Whitney and Kruskal-Wallis only?  Both of the
tests are non-parametric?? The author needs to explain why he is using such an alternative.
Otherwise, the manuscript needs to be revised by a statistical expert and the statistical section
needs to be revised and consequently, the results may be.  Additionally, please cite the way used
for calculating the power of the study as requested previously.
-In the result please separate the section into two paragraphs. In the first one, you should describe
the clinical and demographic results and in the second you put the genetic results. This would
make it easier for the reader to follow the manuscript.
- Having 55.1% of women in your cohort cannot be described as “most of the patients”. It is
approximately half but absolutely not the most. Please correct the statement in the first paragraph
of the result section.
-As a result, you have a problem with the age of your healthy controls as you mentioned that
they are younger. Normally in the perfect condition, no differences in age and gender need to be
mentioned between controls and patients. Hence, the fact that they are younger (your controls)
mean they are biased. Consequently, I wonder if the p-value used in this manuscript was adjusted
according to gender differences?? If yes, you need to mention that in the statistical part and in
the tables of your results.
- Hardy-Weinberg equilibrium is important among the healthy controls as we want to be sure
that controls are selected correctly and deemed to be “a control group” reference. However,
I believe that the Hardy-Weinberg equilibrium among patients is not that necessary because
we don’t select patients we only genotype randomly the patients who answer to the required
condition of your study.
-For p=0.0471 I really see it as 0.05 and I believe that this p is biased and a statistic revision
needs to be done
- What do you mean by multivariate regression and univariate regression??  How you select
your variables for multivariate regression. As I mentioned earlier the statistics section needs to
be revised
- Why the author repeats another study for the same SNPs in the same population ?? Manchiero
C, Nunes AKDS, Magri MC, et al. The rs738409 polymorphism of the PNPLA3 gene is
associated with hepatic steatosis and fibrosis in Brazilian patients with chronic hepatitis C. BMC
Infect Dis 2017;17:780. The author needs to explain
-The discussion needs to be revised
-The English needs to be revised
Please review this paper.
user
Title: The role of PNPLA3 and TM6SF2 polymorphisms on liver fibrosis and metabolic
abnormalities in Brazilian patients with chronic hepatitis C
Version: 1 Date: 03 Dec 2020
Reviewer's report:
-The background needs more development. In fact, why this study is important for the Brazilian
people? I mean what this study is for?? The author needs to talk about chronic hepatitis in brazil
in addition to worldwide. Moreover, as I know these genes are involved in non-alcoholic fatty
liver disease NAFLD. Hence it is worthy to talk about this type in your population.
-The author said “in a recent year” which is not correct according to references 4 and 5. The
author needs to be accurate or change the references to be in recent year which mean (2019
minimum)
-The references cited (from 4 to 6) concern the non-alcoholic fatty liver disease specifically thus
the author must mention that. Second, it is not like “several “studies. The author needs to correct
the expression
-Same idea in the first line on page 5 and the first line in the second paragraph on the same page.
The author needs to be coherent in his redaction and once for all present the problem followed
by his aim (which is logically the solution for the problem or the initiation of this resolution).
Thus, the introduction needs more development, talking about chronic liver disease in brazil,
then the physiology (clinical part) combined with the effect of the two genes (without so much
citing the details of which allele) and finally the problem followed by the aim.
-“Most studies”, “various studies”, “numerous studies”, when we use such vocabularies we need
to cite more than two studies, and the references are commonly a meta-analysis or review. The
author needs to revise the introduction and redaction part seriously.
-The author introduces the word “metabolic syndrome (MetS)” at the end of his introduction.
Such words should be explained in the introduction. The author needs to be coherent and explain
his words from the beginning.
-Statistically, I believe that the number of healthy controls which is 1/3 of patients is not
sufficient. Would like to ask the authors to add in the methods calculation of study power (in
the section of statistical) and add the results in the result section. Moreover, please cite the low
number of healthy control as a limitation of the study at the end of the main document.
-Why the authors use only the test of Mann-Whitney and Kruskal-Wallis only?  Both of the
tests are non-parametric?? The author needs to explain why he is using such an alternative.
Otherwise, the manuscript needs to be revised by a statistical expert and the statistical section
needs to be revised and consequently, the results may be.  Additionally, please cite the way used
for calculating the power of the study as requested previously.
-In the result please separate the section into two paragraphs. In the first one, you should describe
the clinical and demographic results and in the second you put the genetic results. This would
make it easier for the reader to follow the manuscript.
- Having 55.1% of women in your cohort cannot be described as “most of the patients”. It is
approximately half but absolutely not the most. Please correct the statement in the first paragraph
of the result section.
-As a result, you have a problem with the age of your healthy controls as you mentioned that
they are younger. Normally in the perfect condition, no differences in age and gender need to be
mentioned between controls and patients. Hence, the fact that they are younger (your controls)
mean they are biased. Consequently, I wonder if the p-value used in this manuscript was adjusted
according to gender differences?? If yes, you need to mention that in the statistical part and in
the tables of your results.
- Hardy-Weinberg equilibrium is important among the healthy controls as we want to be sure
that controls are selected correctly and deemed to be “a control group” reference. However,
I believe that the Hardy-Weinberg equilibrium among patients is not that necessary because
we don’t select patients we only genotype randomly the patients who answer to the required
condition of your study.
-For p=0.0471 I really see it as 0.05 and I believe that this p is biased and a statistic revision
needs to be done
- What do you mean by multivariate regression and univariate regression??  How you select
your variables for multivariate regression. As I mentioned earlier the statistics section needs to
be revised
- Why the author repeats another study for the same SNPs in the same population ?? Manchiero
C, Nunes AKDS, Magri MC, et al. The rs738409 polymorphism of the PNPLA3 gene is
associated with hepatic steatosis and fibrosis in Brazilian patients with chronic hepatitis C. BMC
Infect Dis 2017;17:780. The author needs to explain
-The discussion needs to be revised
-The English needs to be revised
assistant