Submited on: 27 Jan 2012 02:06:08 PM GMT
Published on: 31 Jul 2012 06:28:17 PM GMT
 

  • What are the main claims of the paper and how important are they?

    The method showed is useful and can be replicated elsewere.


  • Are these claims novel? If not, please specify papers that weaken the claims to the originality of this one.

    This is an alternative method, but reader also may refer to others one.


  • Are the claims properly placed in the context of the previous literature?

    Yes, but authors should go further discussing advantages in using their method diplayed.


  • Do the results support the claims? If not, what other evidence is required?

    Authors say “there is no other known polymorphism at the restriction site” but do not provide gene-sequencing data or reference that support this assumption. This is particularly relevant for applying the test in different ethnic populations.


  • If a protocol is provided, for example for a randomized controlled trial, are there any important deviations from it? If so, have the authors explained adequately why the deviations occurred?

    Its is fine


  • Is the methodology valid? Does the paper offer enough details of its methodology that its experiments or its analyses could be reproduced?

    Yes, but it can be improved.


  • Would any other experiments or additional information improve the paper? How much better would the paper be if this extra work was done, and how difficult would such work be to do, or to provide?

    Should the authors show if it is really necessary stopping enzyme reaction at 0 C? This is particularly interesting for saving genotyping time. For many enzymes, this step is pointless if the only purpose is to run a gel.

    Besides electrophoresis is a critical step for RFLP analysis, authors do not show the their best electrophoresis conditions. They should at least show the voltage/cm and time.

    Authors should state the ladder kb size as well as add number to the lines in the figure 1.


  • Is this paper outstanding in its discipline? (For example, would you like to see this work presented in a seminar at your hospital or university? Do you feel these results need to be incorporated in your next general lecture on the subject?) If yes, what makes it outstanding? If not, why not?

    Not.


  • Other Comments:

    1. Authors should italicize “Homo sapiens” and the gene name throughout the article.
    2. Authors state the study’s objective in the methods section. As a method article, I think they should go further and entering information regarding the advantages of introduction a RFLP method for genotyping this SNP in the introduction.
    3. Here it goes something critical.Someone needs to correct the PDF version since there are question marks replacing the symbols of concentration. There are other errors as well, for example, PCR conditions show temperature at 940 C. If methods are not show correctly, this article would be completely useless.

  • Competing interests:
    None
  • Invited by the author to review this article? :
    No
  • Have you previously published on this or a similar topic?:
    Yes
  • References:

    http://www.ncbi.nlm.nih.gov/pubmed/19258736 http://www.ncbi.nlm.nih.gov/pubmed/22788240 http://www.ncbi.nlm.nih.gov/pubmed/20923563

  • Experience and credentials in the specific area of science:
    None
  • How to cite:  Magno L V.Review On: A New PCR-RFLP Method for Diagnosing PNPLA3 rs738409 Polymorphism [Review of the article 'A New PCR-RFLP Method for Diagnosing PNPLA3 rs738409 Polymorphism ' by Dutta A].WebmedCentral 2013;4(1):WMCRW002458
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A New PCR-RFLP Method for Diagnosing PNPLA3
Posted by Anonymous Reviewer on 06 Aug 2012 12:08:51 AM GMT

  • What are the main claims of the paper and how important are they?

    The manuscript claims an elegant assay for PNPLA3 rs738409 by PCR-RFLP, which is developed by the author. Since PNPLA3 rs738409 polymorphism is associated with nonalcoholic fatty liver disease, fibrosis, alcoholic cirrhosis, the PCR-RFLP method is important for determining the PNPLA3 rs738409 polymorphism. 


  • Are these claims novel? If not, please specify papers that weaken the claims to the originality of this one.

    As claimed by the author, these is a novel method for analysis of PNPLA3 rs738409 polymorphism.


  • Are the claims properly placed in the context of the previous literature?

    Author elaborated in details about the geentic location, distribution and polymorphism of PNPLA3 in the Introduction section, which was supported with relevent literatures. 


  • Do the results support the claims? If not, what other evidence is required?

    The Figure supports the claim.


  • If a protocol is provided, for example for a randomized controlled trial, are there any important deviations from it? If so, have the authors explained adequately why the deviations occurred?

    Author provided the sequence of primer, PCR components and reaction in the Material and Methods sections. These informations are adequate enough for following the protocol.


  • Is the methodology valid? Does the paper offer enough details of its methodology that its experiments or its analyses could be reproduced?

    Yes.


  • Would any other experiments or additional information improve the paper? How much better would the paper be if this extra work was done, and how difficult would such work be to do, or to provide?

    Other experiments are not required.


  • Is this paper outstanding in its discipline? (For example, would you like to see this work presented in a seminar at your hospital or university? Do you feel these results need to be incorporated in your next general lecture on the subject?) If yes, what makes it outstanding? If not, why not?

    This paper is outstanding because diagnosing PNPLA3 rs738409 polymorphism is necessary for nonalcoholic fatty liver disease, fibrosis, alcoholic cirrhosis and elevation of serumalanine transaminase in humans.


  • Other Comments:

    This is a nice study describing a novel methodoloy with nice Introduction, Methodology and discussion with interesting result.

  • Competing interests:
    No
  • Invited by the author to review this article? :
    No
  • Have you previously published on this or a similar topic?:
    No
  • References:
  • Experience and credentials in the specific area of science:

    The PCR, RFLP and genetic polymorphism is under my area of expertise.

  • How to cite:  Anonymous.A New PCR-RFLP Method for Diagnosing PNPLA3[Review of the article 'A New PCR-RFLP Method for Diagnosing PNPLA3 rs738409 Polymorphism ' by Dutta A].WebmedCentral 2013;3(8):WMCRW002163
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A new PCR-RFLP Method for Diagnosing PNPLA3....
Posted by Dr. Mary C Maj on 02 Aug 2012 04:03:50 AM GMT

  • What are the main claims of the paper and how important are they?

    Simple diagnostic test to detect a polymorphism linked to a disease process


  • Are these claims novel? If not, please specify papers that weaken the claims to the originality of this one.

    Not novel but appropriate for a laboratory which does not employ real-time PCR or microarray


  • Are the claims properly placed in the context of the previous literature?

    Yes


  • Do the results support the claims? If not, what other evidence is required?

    The test appears robust and reproducible


  • If a protocol is provided, for example for a randomized controlled trial, are there any important deviations from it? If so, have the authors explained adequately why the deviations occurred?

    The protocol is sound


  • Is the methodology valid? Does the paper offer enough details of its methodology that its experiments or its analyses could be reproduced?

    The authors have reported adequate methodology


  • Would any other experiments or additional information improve the paper? How much better would the paper be if this extra work was done, and how difficult would such work be to do, or to provide?

    No


  • Is this paper outstanding in its discipline? (For example, would you like to see this work presented in a seminar at your hospital or university? Do you feel these results need to be incorporated in your next general lecture on the subject?) If yes, what makes it outstanding? If not, why not?

    This work is not outstanding but would allow a diagnostic lab to detect this polymorphism for relatively low cost and does not require expensive equipment


  • Other Comments:

    A simple methodology paper which may be important to detect this polymorphism that is efficient and does not require expensive equipment and can be performed at low cost

  • Competing interests:
    No
  • Invited by the author to review this article? :
    No
  • Have you previously published on this or a similar topic?:
    Yes
  • References:

    Mol Genet Metab. 2007 Jan;90(1):15-23 Identification of a canine model of pyruvate dehydrogenase phosphatase 1 deficiency. Cameron JM, Maj MC, Levandovskiy V, MacKay N, Shelton GD, Robinson BH.

  • Experience and credentials in the specific area of science:
    None
  • How to cite:  Maj M C.A new PCR-RFLP Method for Diagnosing PNPLA3....[Review of the article 'A New PCR-RFLP Method for Diagnosing PNPLA3 rs738409 Polymorphism ' by Dutta A].WebmedCentral 2013;3(8):WMCRW002156
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1 Is the subject of the article within the scope of the subject category? Yes
2 Are the interpretations / conclusions sound and justified by the data? Yes
3 Is this a new and original contribution? Yes
4 Does this paper exemplify an awareness of other research on the topic? No
5 Are structure and length satisfactory? No
6 Can you suggest brief additions or amendments or an introductory statement that will increase the value of this paper for an international audience? Yes
7 Can you suggest any reductions in the paper, or deletions of parts? No
8 Is the quality of the diction satisfactory? Yes
9 Are the illustrations and tables necessary and acceptable? No
10 Are the references adequate and are they all necessary? Yes
11 Are the keywords and abstract or summary informative? Yes
  • Other Comments:

    The manuscript in its current form displays considerable limitations in content, and would basically require restructuring to make it a valuable contribution.

    For instance, the result and discussion sections appear particularly weak. A more stringent description of the data will help to streamline this article: (The Figure 1 is not included???).

  • Competing interests:
    none
  • Invited by the author to review this article? :
    No
  • Have you previously published on this or a similar topic?:
    No
  • References:
    None
  • Experience and credentials in the specific area of science:

    Genetic and molecular diagnosis of fragile X syndrome

     

  • How to cite:  Hmadcha K .A New PCR-RFLP Method for Diagnosing PNPLA3 rs738409 Polymorphism [Review of the article 'A New PCR-RFLP Method for Diagnosing PNPLA3 rs738409 Polymorphism ' by Dutta A].WebmedCentral 2013;2(11):WMCRW001095
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1 Is the subject of the article within the scope of the subject category? Yes
2 Are the interpretations / conclusions sound and justified by the data? Yes
3 Is this a new and original contribution? Yes
4 Does this paper exemplify an awareness of other research on the topic? No
5 Are structure and length satisfactory? No
6 Can you suggest brief additions or amendments or an introductory statement that will increase the value of this paper for an international audience? Yes
7 Can you suggest any reductions in the paper, or deletions of parts? No
8 Is the quality of the diction satisfactory? Yes
9 Are the illustrations and tables necessary and acceptable? No
10 Are the references adequate and are they all necessary? Yes
11 Are the keywords and abstract or summary informative? No
  • Other Comments:

    the results and discussion are too short, I guess that they might be separated and widely discussed.

  • Competing interests:
    no
  • Invited by the author to review this article? :
    No
  • Have you previously published on this or a similar topic?:
    No
  • References:
    None
  • Experience and credentials in the specific area of science:

    genetics lead faculty

  • How to cite:  Lo Vasco V .A New PCR-RFLP Method for Diagnosing PNPLA3 rs738409 Polymorphism [Review of the article 'A New PCR-RFLP Method for Diagnosing PNPLA3 rs738409 Polymorphism ' by Dutta A].WebmedCentral 2013;2(11):WMCRW001090
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