Reviewer's report
Title:The VEGF -634G>C promoter polymorphism is associated with risk of
gastric cancer
Version: 1Date:11 June 2009
Reviewer: Stefania Boccia
Reviewer's report:
The paper of Guan et al. reports the results of an hospital-based case- control
study conducted in US aimed to investigate the association between selected
SNP in TGFB1 and VEGF genes and risk of gastric cancer. Results suggest that
subjects heterozygous for the -634 CG genotype of VEGF gene have an
increased risk for gastric cancer. Haplotype analysis and stratified analyses did
not show significant associations.
Even though the study is methodologically well conducted, authors acknowledge
the fact that the genotype data of VEGF-634 among controls do nor respect the
Hardy-Weinberg equilibrium. This observation strongly affects their results, as
the p-value for the chi-square test (not reported in the results) is 5 x10 -13, which
is particularly high. Selection bias of the control is not likely to explain such a
large deviation of HWE, as authors claim. The most common reason for the
violation of the equilibrium is a genotyping error, and even though authors
acknowledge that for 10% of samples the assay was repeated with 100%
concordance, this cannot exclude that a genotyping error might affect the validity
of the results of the entire study. Additionally, if they exclude that a laboratory
error happened, they should have stratify the VEGF -634 CG results according to
ethnicity (e.g., by excluding non-white), as the second most probable reason for
violation of the HWE is population stratification.
As such, I find hard to accept the results of the manuscript in view of the
aforementioned observations.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I have no competing interests.
Reviewer's report
Title:The VEGF -634G>C promoter polymorphism is associated with risk of
gastric cancer
Version: 1Date:11 June 2009
Reviewer: Stefania Boccia
Reviewer's report:
The paper of Guan et al. reports the results of an hospital-based case- control
study conducted in US aimed to investigate the association between selected
SNP in TGFB1 and VEGF genes and risk of gastric cancer. Results suggest that
subjects heterozygous for the -634 CG genotype of VEGF gene have an
increased risk for gastric cancer. Haplotype analysis and stratified analyses did
not show significant associations.
Even though the study is methodologically well conducted, authors acknowledge
the fact that the genotype data of VEGF-634 among controls do nor respect the
Hardy-Weinberg equilibrium. This observation strongly affects their results, as
the p-value for the chi-square test (not reported in the results) is 5 x10 -13, which
is particularly high. Selection bias of the control is not likely to explain such a
large deviation of HWE, as authors claim. The most common reason for the
violation of the equilibrium is a genotyping error, and even though authors
acknowledge that for 10% of samples the assay was repeated with 100%
concordance, this cannot exclude that a genotyping error might affect the validity
of the results of the entire study. Additionally, if they exclude that a laboratory
error happened, they should have stratify the VEGF -634 CG results according to
ethnicity (e.g., by excluding non-white), as the second most probable reason for
violation of the HWE is population stratification.
As such, I find hard to accept the results of the manuscript in view of the
aforementioned observations.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I have no competing interests.
Please review this paper.
user
Reviewer's report
Title:The VEGF -634G>C promoter polymorphism is associated with risk of
gastric cancer
Version: 1Date:11 June 2009
Reviewer: Stefania Boccia
Reviewer's report:
The paper of Guan et al. reports the results of an hospital-based case- control
study conducted in US aimed to investigate the association between selected
SNP in TGFB1 and VEGF genes and risk of gastric cancer. Results suggest that
subjects heterozygous for the -634 CG genotype of VEGF gene have an
increased risk for gastric cancer. Haplotype analysis and stratified analyses did
not show significant associations.
Even though the study is methodologically well conducted, authors acknowledge
the fact that the genotype data of VEGF-634 among controls do nor respect the
Hardy-Weinberg equilibrium. This observation strongly affects their results, as
the p-value for the chi-square test (not reported in the results) is 5 x10 -13, which
is particularly high. Selection bias of the control is not likely to explain such a
large deviation of HWE, as authors claim. The most common reason for the
violation of the equilibrium is a genotyping error, and even though authors
acknowledge that for 10% of samples the assay was repeated with 100%
concordance, this cannot exclude that a genotyping error might affect the validity
of the results of the entire study. Additionally, if they exclude that a laboratory
error happened, they should have stratify the VEGF -634 CG results according to
ethnicity (e.g., by excluding non-white), as the second most probable reason for
violation of the HWE is population stratification.
As such, I find hard to accept the results of the manuscript in view of the
aforementioned observations.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I have no competing interests.
assistant