Title: Investigating the shared genetic information between serum concentration levels of liver
enzymes and cholelithiasis
Version: 2 Date: 23 May 2025
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
Dear Authors, please address the following points below
-Insufficient detail on phenotyping and diagnosis:
The manuscript lacks a clear definition of how liver enzyme levels and cholelithiasis cases were
measured or diagnosed. For example, were the liver enzymes measured at a single time point
or averaged over multiple visits? How was cholelithiasis defined—ICD codes, imaging reports,
or self-reporting?
-Population characteristics underreported:
Although the use of the UK Biobank is mentioned, there is no detailed information about
population characteristics such as age range, sex distribution, or adjustment for potential
confounders (e.g., BMI, alcohol consumption, metabolic status), which could influence both
liver enzymes and gallstone risk.
-Lack of clarity on statistical thresholds:
The LDSC, MR, and MTAG methods are described at a high level, but the manuscript does
not specify key parameters such as the threshold for declaring significant genetic correlation
(e.g., Bonferroni correction?), or how multiple testing was controlled across different traits and
methods.
-No justification for MR assumptions:
While MR was used to assess causal relationships, the authors do not elaborate on how the three
core MR assumptions (relevance, independence, and exclusion restriction) were evaluated or
justified. For example, were F-statistics reported to demonstrate instrument strength?
-Pleiotropy and heterogeneity checks are mentioned but not elaborated:
MR-Egger intercept and Cochran’s Q test are referenced, but results or thresholds for
interpreting pleiotropy and heterogeneity are not described. Readers may question how the
authors concluded that causal estimates were robust.
-Functional annotation pipeline needs more detail:
While FUMA, MAGMA, and DEPICT are mentioned, the manuscript does not explain how
input data were processed for each tool, what gene sets or tissues were included, or how
enrichment significance was determined. This limits reproducibility.
-Colocalization lacks resolution detail:
The COLOC analysis is briefly mentioned without specifying the resolution of loci (e.g., 1 Mb
windows), choice of prior probabilities, or how posterior probabilities (PP4) were interpreted.
The absence of this information undermines confidence in shared causal variant claims.
-No replication strategy:
The study appears to rely solely on the UK Biobank for both exposure and outcome GWAS.
There is no mention of replication in an independent cohort, which limits the generalizability of
findings and raises concerns about overfitting.
-Ethical considerations not mentioned:
There is no explicit mention of ethical approval, participant consent, or data use agreements,
even though the UK Biobank has strict usage guidelines. This should be clearly stated.
Title: Investigating the shared genetic information between serum concentration levels of liver
enzymes and cholelithiasis
Version: 2 Date: 23 May 2025
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
Dear Authors, please address the following points below
-Insufficient detail on phenotyping and diagnosis:
The manuscript lacks a clear definition of how liver enzyme levels and cholelithiasis cases were
measured or diagnosed. For example, were the liver enzymes measured at a single time point
or averaged over multiple visits? How was cholelithiasis defined—ICD codes, imaging reports,
or self-reporting?
-Population characteristics underreported:
Although the use of the UK Biobank is mentioned, there is no detailed information about
population characteristics such as age range, sex distribution, or adjustment for potential
confounders (e.g., BMI, alcohol consumption, metabolic status), which could influence both
liver enzymes and gallstone risk.
-Lack of clarity on statistical thresholds:
The LDSC, MR, and MTAG methods are described at a high level, but the manuscript does
not specify key parameters such as the threshold for declaring significant genetic correlation
(e.g., Bonferroni correction?), or how multiple testing was controlled across different traits and
methods.
-No justification for MR assumptions:
While MR was used to assess causal relationships, the authors do not elaborate on how the three
core MR assumptions (relevance, independence, and exclusion restriction) were evaluated or
justified. For example, were F-statistics reported to demonstrate instrument strength?
-Pleiotropy and heterogeneity checks are mentioned but not elaborated:
MR-Egger intercept and Cochran’s Q test are referenced, but results or thresholds for
interpreting pleiotropy and heterogeneity are not described. Readers may question how the
authors concluded that causal estimates were robust.
-Functional annotation pipeline needs more detail:
While FUMA, MAGMA, and DEPICT are mentioned, the manuscript does not explain how
input data were processed for each tool, what gene sets or tissues were included, or how
enrichment significance was determined. This limits reproducibility.
-Colocalization lacks resolution detail:
The COLOC analysis is briefly mentioned without specifying the resolution of loci (e.g., 1 Mb
windows), choice of prior probabilities, or how posterior probabilities (PP4) were interpreted.
The absence of this information undermines confidence in shared causal variant claims.
-No replication strategy:
The study appears to rely solely on the UK Biobank for both exposure and outcome GWAS.
There is no mention of replication in an independent cohort, which limits the generalizability of
findings and raises concerns about overfitting.
-Ethical considerations not mentioned:
There is no explicit mention of ethical approval, participant consent, or data use agreements,
even though the UK Biobank has strict usage guidelines. This should be clearly stated.
Please review this paper.
user
Title: Investigating the shared genetic information between serum concentration levels of liver
enzymes and cholelithiasis
Version: 2 Date: 23 May 2025
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
Dear Authors, please address the following points below
-Insufficient detail on phenotyping and diagnosis:
The manuscript lacks a clear definition of how liver enzyme levels and cholelithiasis cases were
measured or diagnosed. For example, were the liver enzymes measured at a single time point
or averaged over multiple visits? How was cholelithiasis defined—ICD codes, imaging reports,
or self-reporting?
-Population characteristics underreported:
Although the use of the UK Biobank is mentioned, there is no detailed information about
population characteristics such as age range, sex distribution, or adjustment for potential
confounders (e.g., BMI, alcohol consumption, metabolic status), which could influence both
liver enzymes and gallstone risk.
-Lack of clarity on statistical thresholds:
The LDSC, MR, and MTAG methods are described at a high level, but the manuscript does
not specify key parameters such as the threshold for declaring significant genetic correlation
(e.g., Bonferroni correction?), or how multiple testing was controlled across different traits and
methods.
-No justification for MR assumptions:
While MR was used to assess causal relationships, the authors do not elaborate on how the three
core MR assumptions (relevance, independence, and exclusion restriction) were evaluated or
justified. For example, were F-statistics reported to demonstrate instrument strength?
-Pleiotropy and heterogeneity checks are mentioned but not elaborated:
MR-Egger intercept and Cochran’s Q test are referenced, but results or thresholds for
interpreting pleiotropy and heterogeneity are not described. Readers may question how the
authors concluded that causal estimates were robust.
-Functional annotation pipeline needs more detail:
While FUMA, MAGMA, and DEPICT are mentioned, the manuscript does not explain how
input data were processed for each tool, what gene sets or tissues were included, or how
enrichment significance was determined. This limits reproducibility.
-Colocalization lacks resolution detail:
The COLOC analysis is briefly mentioned without specifying the resolution of loci (e.g., 1 Mb
windows), choice of prior probabilities, or how posterior probabilities (PP4) were interpreted.
The absence of this information undermines confidence in shared causal variant claims.
-No replication strategy:
The study appears to rely solely on the UK Biobank for both exposure and outcome GWAS.
There is no mention of replication in an independent cohort, which limits the generalizability of
findings and raises concerns about overfitting.
-Ethical considerations not mentioned:
There is no explicit mention of ethical approval, participant consent, or data use agreements,
even though the UK Biobank has strict usage guidelines. This should be clearly stated.
assistant