Reviewer's report
Title:Association between PPARGC1A polymorphisms and the occurrence of
nonalcoholic fatty liver disease (NAFLD)
Version: 1Date:2 February 2008
Reviewer: Anna Baranova
Reviewer's report:
This is the review of the paper â##Association between PPARGC1A
polymorphisms and the occurentce of non-alcoholic fatty liver disease
(NAFLD)â## by Yoneda at co-authors
Authors of this manuscript undertook relatively small case-control study of
polymorphisms located in PPARG1C gene in attempt to reveal their possible
associations with NAFLD or NASH. 115 NAFLD and 441 controls were
genotyped. Significant association of one of the polymorphisms, rs2290602, and
NAFLD was revealed (P <0.0143) after Bonferroni correction. Despite
significance of these findings, I do not think that this paper should be published in
BMC Gastroenterology as it is submitted now. My explanations are given below:
1. Is the question posed by the authors well defined?
Yes
2. Are the methods appropriate and well described?
Methods are appropriate, but they could be described better. E.g. In â##DNA
preparation and SNP genotypingâ## part first paragraph reads â##genomics
DNA was prepared from each blood sample according to standard protocolsâ##.
First, this phrase implies more than one protocol applied. Second, it need
clarification, e.g. what kit has been used?
3. Are the data sound?
Data are not sufficient. Larger population of cases needs to be tested, especially
in case when NASH alone was tested against controls. Rule of thumb for these
kinds of studies is at least 400 cases. If it is not feasible, functional
(experimental) study of the effect of the rs2290602 on splicing needs to be
performed and reported.
4. Does the manuscript adhere to the relevant standards for reporting and data
deposition?
Yes
5. Are the discussion and conclusions well balanced and adequately supported
by the data?
No. Authors should at least discuss SNP that they found to be associated with
NAFLD, give its sequence and location (which is, by the way, interesting â## it
might influence gene splicing).
6. Are limitations of the work clearly stated?
Not.
7. Do the authors clearly acknowledge any work upon which they are building,
both published and unpublished?
Yes
8. Do the title and abstract accurately convey what has been found?
yes
9. Is the writing acceptable?
yes
Major Revision is recommended. Either sample size needs to be increased,
either functional (experimental) study of the effect of the rs2290602 on splicing
needs to be performed and reported.
Unable to decide on acceptance or rejection until the authors have responded to
the major compulsory revisions
Level of interest
-----------------
- An article whose findings are important to those with closely related research
interests
Quality of written English
--------------------------
- Acceptable
Statistical review
------------------
Is it essential that this manuscript be seen by an expert statistician?
- Yes, and I have assessed the statistics in my report. It is fine.
Declaration of competing interests
----------------------------------
- Have you in the past five years received reimbursements, fees, funding, or
salary from an organisation that may in any way gain or lose financially from the
publication of this paper, either now or in the future?
No
- Do you hold any stocks or shares in an organisation that may in any way gain
or lose financially from the publication of this paper, either now or in the future?
No
- Do you hold or are you currently applying for any patents relating to the content
of the manuscript? Have you received reimbursements, fees, funding, or salary
from an organization that holds or has applied for patents relating to the content
of the manuscript?
No
- Do you have any other financial competing interests?
No
Do you have any non-financial competing interests in relation to this paper?
No
I declare that I have no competing interests
Dr. Ancha Baranova
Associate Professor,
Molecular Biology and Microbiology,
David King Hall, MSN 3E1
George Mason University,
Fairfax, VA, 22030
tel 703-993-42-93
e-mail: abaranov@gmu.edu
What next?: Unable to decide on acceptance or rejection until the authors have
responded to the major compulsory revisions
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 declare that I have no competing interests
Reviewer's report
Title:Association between PPARGC1A polymorphisms and the occurrence of
nonalcoholic fatty liver disease (NAFLD)
Version: 1Date:2 February 2008
Reviewer: Anna Baranova
Reviewer's report:
This is the review of the paper â##Association between PPARGC1A
polymorphisms and the occurentce of non-alcoholic fatty liver disease
(NAFLD)â## by Yoneda at co-authors
Authors of this manuscript undertook relatively small case-control study of
polymorphisms located in PPARG1C gene in attempt to reveal their possible
associations with NAFLD or NASH. 115 NAFLD and 441 controls were
genotyped. Significant association of one of the polymorphisms, rs2290602, and
NAFLD was revealed (P <0.0143) after Bonferroni correction. Despite
significance of these findings, I do not think that this paper should be published in
BMC Gastroenterology as it is submitted now. My explanations are given below:
1. Is the question posed by the authors well defined?
Yes
2. Are the methods appropriate and well described?
Methods are appropriate, but they could be described better. E.g. In â##DNA
preparation and SNP genotypingâ## part first paragraph reads â##genomics
DNA was prepared from each blood sample according to standard protocolsâ##.
First, this phrase implies more than one protocol applied. Second, it need
clarification, e.g. what kit has been used?
3. Are the data sound?
Data are not sufficient. Larger population of cases needs to be tested, especially
in case when NASH alone was tested against controls. Rule of thumb for these
kinds of studies is at least 400 cases. If it is not feasible, functional
(experimental) study of the effect of the rs2290602 on splicing needs to be
performed and reported.
4. Does the manuscript adhere to the relevant standards for reporting and data
deposition?
Yes
5. Are the discussion and conclusions well balanced and adequately supported
by the data?
No. Authors should at least discuss SNP that they found to be associated with
NAFLD, give its sequence and location (which is, by the way, interesting â## it
might influence gene splicing).
6. Are limitations of the work clearly stated?
Not.
7. Do the authors clearly acknowledge any work upon which they are building,
both published and unpublished?
Yes
8. Do the title and abstract accurately convey what has been found?
yes
9. Is the writing acceptable?
yes
Major Revision is recommended. Either sample size needs to be increased,
either functional (experimental) study of the effect of the rs2290602 on splicing
needs to be performed and reported.
Unable to decide on acceptance or rejection until the authors have responded to
the major compulsory revisions
Level of interest
-----------------
- An article whose findings are important to those with closely related research
interests
Quality of written English
--------------------------
- Acceptable
Statistical review
------------------
Is it essential that this manuscript be seen by an expert statistician?
- Yes, and I have assessed the statistics in my report. It is fine.
Declaration of competing interests
----------------------------------
- Have you in the past five years received reimbursements, fees, funding, or
salary from an organisation that may in any way gain or lose financially from the
publication of this paper, either now or in the future?
No
- Do you hold any stocks or shares in an organisation that may in any way gain
or lose financially from the publication of this paper, either now or in the future?
No
- Do you hold or are you currently applying for any patents relating to the content
of the manuscript? Have you received reimbursements, fees, funding, or salary
from an organization that holds or has applied for patents relating to the content
of the manuscript?
No
- Do you have any other financial competing interests?
No
Do you have any non-financial competing interests in relation to this paper?
No
I declare that I have no competing interests
Dr. Ancha Baranova
Associate Professor,
Molecular Biology and Microbiology,
David King Hall, MSN 3E1
George Mason University,
Fairfax, VA, 22030
tel 703-993-42-93
e-mail: abaranov@gmu.edu
What next?: Unable to decide on acceptance or rejection until the authors have
responded to the major compulsory revisions
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 declare that I have no competing interests
Please review this paper.
user
Reviewer's report
Title:Association between PPARGC1A polymorphisms and the occurrence of
nonalcoholic fatty liver disease (NAFLD)
Version: 1Date:2 February 2008
Reviewer: Anna Baranova
Reviewer's report:
This is the review of the paper â##Association between PPARGC1A
polymorphisms and the occurentce of non-alcoholic fatty liver disease
(NAFLD)â## by Yoneda at co-authors
Authors of this manuscript undertook relatively small case-control study of
polymorphisms located in PPARG1C gene in attempt to reveal their possible
associations with NAFLD or NASH. 115 NAFLD and 441 controls were
genotyped. Significant association of one of the polymorphisms, rs2290602, and
NAFLD was revealed (P <0.0143) after Bonferroni correction. Despite
significance of these findings, I do not think that this paper should be published in
BMC Gastroenterology as it is submitted now. My explanations are given below:
1. Is the question posed by the authors well defined?
Yes
2. Are the methods appropriate and well described?
Methods are appropriate, but they could be described better. E.g. In â##DNA
preparation and SNP genotypingâ## part first paragraph reads â##genomics
DNA was prepared from each blood sample according to standard protocolsâ##.
First, this phrase implies more than one protocol applied. Second, it need
clarification, e.g. what kit has been used?
3. Are the data sound?
Data are not sufficient. Larger population of cases needs to be tested, especially
in case when NASH alone was tested against controls. Rule of thumb for these
kinds of studies is at least 400 cases. If it is not feasible, functional
(experimental) study of the effect of the rs2290602 on splicing needs to be
performed and reported.
4. Does the manuscript adhere to the relevant standards for reporting and data
deposition?
Yes
5. Are the discussion and conclusions well balanced and adequately supported
by the data?
No. Authors should at least discuss SNP that they found to be associated with
NAFLD, give its sequence and location (which is, by the way, interesting â## it
might influence gene splicing).
6. Are limitations of the work clearly stated?
Not.
7. Do the authors clearly acknowledge any work upon which they are building,
both published and unpublished?
Yes
8. Do the title and abstract accurately convey what has been found?
yes
9. Is the writing acceptable?
yes
Major Revision is recommended. Either sample size needs to be increased,
either functional (experimental) study of the effect of the rs2290602 on splicing
needs to be performed and reported.
Unable to decide on acceptance or rejection until the authors have responded to
the major compulsory revisions
Level of interest
-----------------
- An article whose findings are important to those with closely related research
interests
Quality of written English
--------------------------
- Acceptable
Statistical review
------------------
Is it essential that this manuscript be seen by an expert statistician?
- Yes, and I have assessed the statistics in my report. It is fine.
Declaration of competing interests
----------------------------------
- Have you in the past five years received reimbursements, fees, funding, or
salary from an organisation that may in any way gain or lose financially from the
publication of this paper, either now or in the future?
No
- Do you hold any stocks or shares in an organisation that may in any way gain
or lose financially from the publication of this paper, either now or in the future?
No
- Do you hold or are you currently applying for any patents relating to the content
of the manuscript? Have you received reimbursements, fees, funding, or salary
from an organization that holds or has applied for patents relating to the content
of the manuscript?
No
- Do you have any other financial competing interests?
No
Do you have any non-financial competing interests in relation to this paper?
No
I declare that I have no competing interests
Dr. Ancha Baranova
Associate Professor,
Molecular Biology and Microbiology,
David King Hall, MSN 3E1
George Mason University,
Fairfax, VA, 22030
tel 703-993-42-93
e-mail: abaranov@gmu.edu
What next?: Unable to decide on acceptance or rejection until the authors have
responded to the major compulsory revisions
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 declare that I have no competing interests
assistant