Title: PNPLA3 and TM6SF2 genetic variants and hepatic fibrosis and cirrhosis in Pakistani
chronic hepatitis C patients: a genetic association study
Version: 0 Date: 07 Jun 2022
Reviewer's report:
This study by Rauff et al. “PNPLA3 and TM6SF2 genetic variants and hepatic fibrosis and
cirrhosis in Pakistani chronic hepatitis C patients: a genetic association study” investigates the
association of two major genetic risk variants with fibrosis and cirrhosis in Pakistani chronic
hepatitis C patients. The role of both variants for fibrosis/cirrhosis risk in patient with chronic
hepatitis C is debated. The current study is well written and provides important and detailed
information on this issue. The tested PNPLA3 and TM6SF2 polymorphisms were not identified
as major determinants of liver fibrosis/cirrhosis in Pakistani patients with CHC. One limitation
of this study is the limited power to detect true associations with modest effect sizes (OR ~1.3)
for cirrhosis.  However, this limitation is already stated by the authors.
Association results for rs738409 and rs58542926 allelic, recessive and genotypic unadjusted
analysis are clearly presented.
Multivariate regression analysis
1. Association results for rs738409 and rs58542926 from the multivariate regression analysis
are not provided.
Provide odds ratios and p values for rs738409 and rs58542926 from  multivariate regression
analysis for advanced hepatic fibrosis and hepatic cirrhosis to Table 5. Statistical models should
include the SNP (rs738409 or rs58542926) age, sex, body mass index and HCV viral load.
Models should not include liver enzymes. Variants PNPLA3 rs738409 and TM6SF2 rs58542926
are associated with increased ALT and AST (PMID: 34315874). Both enzymes are known
surrogate measures of liver fibrosis. Including liver enzymes in the model weakens the effect
for PNPLA3 and TM6SF2.
Correct the statement accordingly: “The same trend of no association with hepatic fibrosis or
cirrhosis persisted in the multivariate logistic regression models adjusting for age, gender, body
mass index, HCV viral load and liver enzymes (p = >0.05).
2. Diabetes mellitus is a significant risk factor for the development of liver cirrhosis in chronic
hepatitis C patients (PMID: 28831144). This is also acknowledged in the manuscript. “Indeed,
presence of hepatic steatosis and features of metabolic syndrome (including obesity and diabetes
mellitus) have been shown to exacerbate progression of hepatic fibrosis and cirrhosis in CHC
settings”.
But information on type 2 diabetes status is not provided.  Regression models were not adjusted
for diabetes status. If available, provide diabetes information in Table 1 and include diabetes in
the multivariate regression models. If not available, indicate absence of diabetes status in the
limitation sections of your manuscript.
Title: PNPLA3 and TM6SF2 genetic variants and hepatic fibrosis and cirrhosis in Pakistani
chronic hepatitis C patients: a genetic association study
Version: 0 Date: 07 Jun 2022
Reviewer's report:
This study by Rauff et al. “PNPLA3 and TM6SF2 genetic variants and hepatic fibrosis and
cirrhosis in Pakistani chronic hepatitis C patients: a genetic association study” investigates the
association of two major genetic risk variants with fibrosis and cirrhosis in Pakistani chronic
hepatitis C patients. The role of both variants for fibrosis/cirrhosis risk in patient with chronic
hepatitis C is debated. The current study is well written and provides important and detailed
information on this issue. The tested PNPLA3 and TM6SF2 polymorphisms were not identified
as major determinants of liver fibrosis/cirrhosis in Pakistani patients with CHC. One limitation
of this study is the limited power to detect true associations with modest effect sizes (OR ~1.3)
for cirrhosis.  However, this limitation is already stated by the authors.
Association results for rs738409 and rs58542926 allelic, recessive and genotypic unadjusted
analysis are clearly presented.
Multivariate regression analysis
1. Association results for rs738409 and rs58542926 from the multivariate regression analysis
are not provided.
Provide odds ratios and p values for rs738409 and rs58542926 from  multivariate regression
analysis for advanced hepatic fibrosis and hepatic cirrhosis to Table 5. Statistical models should
include the SNP (rs738409 or rs58542926) age, sex, body mass index and HCV viral load.
Models should not include liver enzymes. Variants PNPLA3 rs738409 and TM6SF2 rs58542926
are associated with increased ALT and AST (PMID: 34315874). Both enzymes are known
surrogate measures of liver fibrosis. Including liver enzymes in the model weakens the effect
for PNPLA3 and TM6SF2.
Correct the statement accordingly: “The same trend of no association with hepatic fibrosis or
cirrhosis persisted in the multivariate logistic regression models adjusting for age, gender, body
mass index, HCV viral load and liver enzymes (p = >0.05).
2. Diabetes mellitus is a significant risk factor for the development of liver cirrhosis in chronic
hepatitis C patients (PMID: 28831144). This is also acknowledged in the manuscript. “Indeed,
presence of hepatic steatosis and features of metabolic syndrome (including obesity and diabetes
mellitus) have been shown to exacerbate progression of hepatic fibrosis and cirrhosis in CHC
settings”.
But information on type 2 diabetes status is not provided.  Regression models were not adjusted
for diabetes status. If available, provide diabetes information in Table 1 and include diabetes in
the multivariate regression models. If not available, indicate absence of diabetes status in the
limitation sections of your manuscript.
Please review this paper.
user
Title: PNPLA3 and TM6SF2 genetic variants and hepatic fibrosis and cirrhosis in Pakistani
chronic hepatitis C patients: a genetic association study
Version: 0 Date: 07 Jun 2022
Reviewer's report:
This study by Rauff et al. “PNPLA3 and TM6SF2 genetic variants and hepatic fibrosis and
cirrhosis in Pakistani chronic hepatitis C patients: a genetic association study” investigates the
association of two major genetic risk variants with fibrosis and cirrhosis in Pakistani chronic
hepatitis C patients. The role of both variants for fibrosis/cirrhosis risk in patient with chronic
hepatitis C is debated. The current study is well written and provides important and detailed
information on this issue. The tested PNPLA3 and TM6SF2 polymorphisms were not identified
as major determinants of liver fibrosis/cirrhosis in Pakistani patients with CHC. One limitation
of this study is the limited power to detect true associations with modest effect sizes (OR ~1.3)
for cirrhosis.  However, this limitation is already stated by the authors.
Association results for rs738409 and rs58542926 allelic, recessive and genotypic unadjusted
analysis are clearly presented.
Multivariate regression analysis
1. Association results for rs738409 and rs58542926 from the multivariate regression analysis
are not provided.
Provide odds ratios and p values for rs738409 and rs58542926 from  multivariate regression
analysis for advanced hepatic fibrosis and hepatic cirrhosis to Table 5. Statistical models should
include the SNP (rs738409 or rs58542926) age, sex, body mass index and HCV viral load.
Models should not include liver enzymes. Variants PNPLA3 rs738409 and TM6SF2 rs58542926
are associated with increased ALT and AST (PMID: 34315874). Both enzymes are known
surrogate measures of liver fibrosis. Including liver enzymes in the model weakens the effect
for PNPLA3 and TM6SF2.
Correct the statement accordingly: “The same trend of no association with hepatic fibrosis or
cirrhosis persisted in the multivariate logistic regression models adjusting for age, gender, body
mass index, HCV viral load and liver enzymes (p = >0.05).
2. Diabetes mellitus is a significant risk factor for the development of liver cirrhosis in chronic
hepatitis C patients (PMID: 28831144). This is also acknowledged in the manuscript. “Indeed,
presence of hepatic steatosis and features of metabolic syndrome (including obesity and diabetes
mellitus) have been shown to exacerbate progression of hepatic fibrosis and cirrhosis in CHC
settings”.
But information on type 2 diabetes status is not provided.  Regression models were not adjusted
for diabetes status. If available, provide diabetes information in Table 1 and include diabetes in
the multivariate regression models. If not available, indicate absence of diabetes status in the
limitation sections of your manuscript.
assistant