Review for 10.1186/s12876-021-02041-8 (2021)

Title: Variations in TM6SF2, PCSK9 and PCSK7 genes and risk of hepatic steatosis after liver
transplantation: a cross-sectional study
Version: 1 Date: 21 Mar 2021
Reviewer's report:
Title: Variations in TM6SF2, PCSK9 and PCSK7 genes and risk of hepatic steatosis after liver
transplantation
In this manuscript authors describe how distinct genetic variations can affect the risk for liver
steatosis following liver transplantation on a study cohort of 107 liver transplant recipients.
Although the topic of the manuscript is interesting enough, some major concerns are raised.
Authors should thoroughly revise the paper before considering it for publication in BMC
Gastroenterology.
Comments:
1) Title and abstract: Authors should indicate their study design using a commonly used term
(eg. “cohort”, “cross-sectional”).
2) Methods: However the authors slightly describe the inclusion criteria of their study, it would
be more precise to report those criteria in a row using a lower letter at the beginning of each
one (eg. a), b) etc.).
3) Methods: Authors describe that “Patients with acute rejection episodes and those with serum
aminotransferase levels higher than 5 times upper limit of normal range were excluded from the
study”. Please explain which aminotransferase’s cut-offs were used (AST, ALT or both?).
4) Methods: Authors declared the cut-offs for the grade of liver steatosis based on CAP
measurements as following “The cutoff scores for CAP estimation of hepatic steatosis were as
follows: # 238 dB/m for S1 (corresponding to 11–32% liver fat), # 259 dB/m for S2 (33–65%
liver fat), and # 292 dB/m for S3 (#66% liver fat)”.
Though, it would be clearer for the readers to reformat them as:
“The cutoff scores for CAP estimation of hepatic steatosis were as follows: # 238 dB/m and
<259dB/m for S1 (corresponding to 11–32% liver fat), # 259 dB/m and < 292 dB/m for S2 (33–
65% liver fat) and # 292 dB/m for S3 (#66% liver fat)”.
5) Methods: Statistical analysis. Authors described that “Data were presented using means ±
standard deviation for numeric variables, and percents and counts for categorical variables”.
It would be more precise if categorical variables were presented by counts and (percentages)
demonstrating how they illustrated the variables.
Moreover, authors should perform the appropriate statistical tests for comparisons between
quantitative variables depending on each variable distribution rather than performing Student’s
t-test for every single one.
6) Results: The authors declared that “The presence of TT genotype of TM6SF2 rs58542926 was
associated with hepatic stetosis measured by CAP after liver transplantation (OR: 1.057; 95 %
CI: 0.978-1.146; P-value = 0.045)” demonstrating a significant association. However, since 95%
Confidence interval of the OR includes 1, it should not be statistically significant and p-value
should be >0.05 rather than “0.045”. Please carefully revise the statistical analysis in this topic.
7) Table 2: Authors should provide units of measurement for each variable of the Table 2. (eg.
AST, ALT etc.)
8) Results demonstrated in Tables 3 and 4: Authors provided two tables including results from
both univariate and multivariate logistic regression analyses.
Though, the context of these tables is not clear especially for univariate analyses.
Authors should either perform and subsequently demonstrate univariate logistic regression
models for each covariate (eg. sex, BMI, AST) using the development of liver steatosis as
dependent variable or perform appropriate statistical tests (Student’s t-test/Mann-Whitney or
Chi-squared test) and demonstrate these results in order to show the difference of each variable
among the “Steatosis (+)” and “Steatosis (-)” groups and among “High Grade Steatosis” and
“Low Grade Steatosis groups” for Table 3 and Table 4 respectively.
Also, the headings across the tables should be unified demonstrating the same data (OR, 95%
CI, p-value).
Furthermore, authors should carefully clarify which of the variables were included in the
multivariable analyses.
9) Discussion: Authors should discuss the strength and limitations of their study considering
sources of potential bias or imprecision. Discuss both direction and magnitude of any potential
bias.
10) Grammatical errors: Authors should carefully revise the manuscript for grammatical errors.
Some examples of grammatical errors are outlined below.
a) Page 2. line 15: “hepatic stetosis”. Kindly rephrase.
b) Page 5. Line 5. “we aimed to investigate association between genetic variations” Kindly
rephrase.
c) Page 5. Line 19. “: weight (kg) divided by height (m2) squared. Patients with BMI < 25 Kg/
m2”. Kindly correct it with 2 superscripted (m2).
d) Page 6. Line 5. “All CAP measurements was done”. Kindly rephrase.
e) Page 6. Line 13. “all pahses of DNA extraction was done”. Kindly rephrase.
f) Page 8. Line 19. “hepatic stetosis”. Kindly rephrase.
g) Page 9. Line 18. “In multivariate regression model, AG+GG genotypes of PCSK9 rs505151
was associated”. Kindly rephrase.
h) Page 10. Line 8. Abbreviation is needed for “NASH”.
i) Page 11. Line 18. “fed with hiugh fructose diet”. Kindly rephrase.
10)  Figures: In Figure 2A, there is no reference line above the two graph bars in contrast to
the other schemas.