Reviewer's report
Title:The Helicobacter pylori duodenal ulcer promoting gene, dupA in China
Version: 3Date:4 July 2008
Reviewer: Dulciene M Queiroz
Reviewer's report:
The results of the study are not innovative and there are several conceptual
errors along the manuscript, but the work has some value in the way that it adds
information about the prevalence of dupA in China. My suggestion is that the
study should be rewritten as a short communication and the authors should be
prepared to undertake a revision taking into account the comments listed below.
Major Compulsory Revisions
Introduction:
The authors did not mention that there are regional differences for dupA
prevalence and its association with H. pylori outcomes which would be the main
justification for the publication of their results that, although not innovative, add
information of dupA prevalence in China.
The authors did not justify/explain why they included in the work the detection of
IL-1# gene polymorphisms which seemed to be dispensable information.
Methods:
In the “Biopsy protocol”, it is not clear how the authors manage to culture H.
pylori and to evaluate the histology in the cases of gastric cancer since they had
only one biopsy fragment to work with.
The information of what was considered dupA-positive or negative and what was
used as positive and negative controls have to be mentioned in the Methods, not
in the results.
Results:
The authors made a huge mistake. They considered as control of the presence
of dupA the strain J99 that is dupA-negative. Although the strain has both
jhp0917 and jhp0918 sequences, it does not have the insertion of C or T after the
position 1385 in the jhp0917 3’ region that characterizes the dupA gene. Since
the authors did not sequence the PCR products containing the region, what the
authors consider dupA-positive was the presence of both genes. Although the
presence of both genes correlates well with the presence of the insertion, it is not
the same thing and this is not clearly stated.
The results regarding associations should be accompanied by not only the p
value but also the confidence intervals.
The authors state that “the result showed that the presence of jhp0917 and
jhp0918 genes was strongly linked” but they did not present the results. In how
many cases they found only one sequence? It is not clear either what were
considered to be dupA-negative: the absence of one or both genes?
The first sentence in the topic “Association of dupA with histological findings” was
already explained in Methods and is not necessary. Caution also has to be made
when using words such as “effect” since the study is only evaluating an
association between the presence of dupA and histological alterations, not the
effect of dupA on gastric histology.
It is not clear in the text (neither in the table 3) what groups were included in
histological analysis.
The topic “Association with other putative virulence factors” only repeats what is
shown on table 4 and there are no results about the association of dupA and the
virulence factors. The table 4 does not add any information and lacks statistical
analysis.
The result in the topic “Association of dupA with IL-1# gene polymorphism” is out
of context and it does not add any relevant information.
Minor Essential Revisions
Abstract:
Revise the conclusion.
Methods:
The written informed consent and ethics committee approval should be put in the
“Patients” topic.
In “DNA extraction and PCR amplification" topic, the sequences of the primers
are repeated (in the text and also in the table)
Results:
“The mean age of the patients with DU was lower (not younger) than those with
GU gastric cancer or gastritis”. The p values are missing.
When the P is significant, specific values must be put (not only p<0.05).
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
Reviewer's report
Title:The Helicobacter pylori duodenal ulcer promoting gene, dupA in China
Version: 3Date:4 July 2008
Reviewer: Dulciene M Queiroz
Reviewer's report:
The results of the study are not innovative and there are several conceptual
errors along the manuscript, but the work has some value in the way that it adds
information about the prevalence of dupA in China. My suggestion is that the
study should be rewritten as a short communication and the authors should be
prepared to undertake a revision taking into account the comments listed below.
Major Compulsory Revisions
Introduction:
The authors did not mention that there are regional differences for dupA
prevalence and its association with H. pylori outcomes which would be the main
justification for the publication of their results that, although not innovative, add
information of dupA prevalence in China.
The authors did not justify/explain why they included in the work the detection of
IL-1# gene polymorphisms which seemed to be dispensable information.
Methods:
In the “Biopsy protocol”, it is not clear how the authors manage to culture H.
pylori and to evaluate the histology in the cases of gastric cancer since they had
only one biopsy fragment to work with.
The information of what was considered dupA-positive or negative and what was
used as positive and negative controls have to be mentioned in the Methods, not
in the results.
Results:
The authors made a huge mistake. They considered as control of the presence
of dupA the strain J99 that is dupA-negative. Although the strain has both
jhp0917 and jhp0918 sequences, it does not have the insertion of C or T after the
position 1385 in the jhp0917 3’ region that characterizes the dupA gene. Since
the authors did not sequence the PCR products containing the region, what the
authors consider dupA-positive was the presence of both genes. Although the
presence of both genes correlates well with the presence of the insertion, it is not
the same thing and this is not clearly stated.
The results regarding associations should be accompanied by not only the p
value but also the confidence intervals.
The authors state that “the result showed that the presence of jhp0917 and
jhp0918 genes was strongly linked” but they did not present the results. In how
many cases they found only one sequence? It is not clear either what were
considered to be dupA-negative: the absence of one or both genes?
The first sentence in the topic “Association of dupA with histological findings” was
already explained in Methods and is not necessary. Caution also has to be made
when using words such as “effect” since the study is only evaluating an
association between the presence of dupA and histological alterations, not the
effect of dupA on gastric histology.
It is not clear in the text (neither in the table 3) what groups were included in
histological analysis.
The topic “Association with other putative virulence factors” only repeats what is
shown on table 4 and there are no results about the association of dupA and the
virulence factors. The table 4 does not add any information and lacks statistical
analysis.
The result in the topic “Association of dupA with IL-1# gene polymorphism” is out
of context and it does not add any relevant information.
Minor Essential Revisions
Abstract:
Revise the conclusion.
Methods:
The written informed consent and ethics committee approval should be put in the
“Patients” topic.
In “DNA extraction and PCR amplification" topic, the sequences of the primers
are repeated (in the text and also in the table)
Results:
“The mean age of the patients with DU was lower (not younger) than those with
GU gastric cancer or gastritis”. The p values are missing.
When the P is significant, specific values must be put (not only p<0.05).
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
Please review this paper.
user
Reviewer's report
Title:The Helicobacter pylori duodenal ulcer promoting gene, dupA in China
Version: 3Date:4 July 2008
Reviewer: Dulciene M Queiroz
Reviewer's report:
The results of the study are not innovative and there are several conceptual
errors along the manuscript, but the work has some value in the way that it adds
information about the prevalence of dupA in China. My suggestion is that the
study should be rewritten as a short communication and the authors should be
prepared to undertake a revision taking into account the comments listed below.
Major Compulsory Revisions
Introduction:
The authors did not mention that there are regional differences for dupA
prevalence and its association with H. pylori outcomes which would be the main
justification for the publication of their results that, although not innovative, add
information of dupA prevalence in China.
The authors did not justify/explain why they included in the work the detection of
IL-1# gene polymorphisms which seemed to be dispensable information.
Methods:
In the “Biopsy protocol”, it is not clear how the authors manage to culture H.
pylori and to evaluate the histology in the cases of gastric cancer since they had
only one biopsy fragment to work with.
The information of what was considered dupA-positive or negative and what was
used as positive and negative controls have to be mentioned in the Methods, not
in the results.
Results:
The authors made a huge mistake. They considered as control of the presence
of dupA the strain J99 that is dupA-negative. Although the strain has both
jhp0917 and jhp0918 sequences, it does not have the insertion of C or T after the
position 1385 in the jhp0917 3’ region that characterizes the dupA gene. Since
the authors did not sequence the PCR products containing the region, what the
authors consider dupA-positive was the presence of both genes. Although the
presence of both genes correlates well with the presence of the insertion, it is not
the same thing and this is not clearly stated.
The results regarding associations should be accompanied by not only the p
value but also the confidence intervals.
The authors state that “the result showed that the presence of jhp0917 and
jhp0918 genes was strongly linked” but they did not present the results. In how
many cases they found only one sequence? It is not clear either what were
considered to be dupA-negative: the absence of one or both genes?
The first sentence in the topic “Association of dupA with histological findings” was
already explained in Methods and is not necessary. Caution also has to be made
when using words such as “effect” since the study is only evaluating an
association between the presence of dupA and histological alterations, not the
effect of dupA on gastric histology.
It is not clear in the text (neither in the table 3) what groups were included in
histological analysis.
The topic “Association with other putative virulence factors” only repeats what is
shown on table 4 and there are no results about the association of dupA and the
virulence factors. The table 4 does not add any information and lacks statistical
analysis.
The result in the topic “Association of dupA with IL-1# gene polymorphism” is out
of context and it does not add any relevant information.
Minor Essential Revisions
Abstract:
Revise the conclusion.
Methods:
The written informed consent and ethics committee approval should be put in the
“Patients” topic.
In “DNA extraction and PCR amplification" topic, the sequences of the primers
are repeated (in the text and also in the table)
Results:
“The mean age of the patients with DU was lower (not younger) than those with
GU gastric cancer or gastritis”. The p values are missing.
When the P is significant, specific values must be put (not only p<0.05).
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
assistant