PONE-D-22-13603The impact of SNP rs5743836 of TLR9 on the risk and prognosis of Hodgkin’s Lymphoma: a case-control study PLOS ONE

Dear Dr. Al Khatib,

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Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: In this manuscript Al-Khatib et al. evaluated the frequency of TLR9 SNP rs5743836 in Hodgkin Lymphoma patients. Although scientifically sounds, the manuscript has several points that should be addressed:

The title of the manuscript is misleading since no association of the evaluated SNP was observed concerning HL prognosis.

Although authors claim that “particular single nucleotide polymorphism (SNP) on Toll-Like Receptor 9 (TLR9) has been the center of multiple studies that analyzed its relation to lymphoma formation; this SNP is rs5743836 (TLR9-1237T>C). In the aforementioned studies, results have demonstrated that this SNP significantly increased the risk of developing HL and NHL.” they forgot to mention references that find no association if this specific SNP and HL (see, for example, Martin et al. Leuk Lymphoma. 2017 Feb;58(2):438-444. doi: 10.1080/10428194.2016.1190972.)

What should be the connection between rs5743836 and HL? Why to evaluate this and not other TLR9 variants (or any other gene variants)? The question is: What is the biological reason for choosing this gene variant? All these points were only superficially approached in the Discussion, but should be deeply presented in Introduction.

I was quite puzzled by the nomenclature used. Why authors refer to SNP TLR9-1237T>C but A/G genotypes? Please, standardize the manuscript nomenclature. It is quite difficult to follow the results comparing allele versus genotype (in fact, there is some confusion between alleles and genotypes all along the manuscript, please revise this point).

Please, revise the manuscript concerning the way results are described. For example, instead of saying “...a statistically significant higher distribution of the rs5743836”, I would suggest to say “how a statistically significant higher frequency of rs5743836 allele A among patients”.

In fact, a qui-square testing with Yate’s correction resulted in a p = 0.031. Please, review calculations.

Considering the acknowledged relation of EBV infection and HL development, I would expect data concerning EBV positivity in this cohort.

As highlighted by the authors, sample size is extremely low. As comparison, the reported study from Carvalho et al, back in the 2012’s included three distinct cohorts encompassing respectively 797 Portuguese, 494 Italian and 868 US patients. In this context, besides significance, I wonder about the originality/novelty of the present study.

Reviewer #2: Dear Author,

Please mention the possible relationship between genotypes and clinical parameters. And also you should give information about how this base change affects the TLR-9 gene function.

Best Regards

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Reviewer #1: No

Reviewer #2: No

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Association of TLR9-1237T>C; rs5743836 polymorphism with increased risk of Hodgkin’s Lymphoma: a case-control study

PONE-D-22-13603R1

Dear Dr. Al Khatib,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Alvaro Galli

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

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Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: All comments previously made by this reviewer were adequately approached in this new version. Specifically, the manuscript title was changed; a mention to studies who did not found association between the evaluated gene polymorphism and HD was added; the choice for this specific polymorphism was justified at Introduction with data from the literature; some misleading nomenclature were corrected; and some statistical data were also revised. Concerning the absence of data about EBV positivity in this cohort, I understand that authors are not able to come back to the original patients to include this point, and I also agree with authors concerning comparisons with the study from Carvalho et al.

Minor points that I would suggest, would be the inclusion of data from Table 1 at the text (under the section Material and Methods), and a review of the English-language usage and grammar, although these two points should not hinder the publication, since all methodological and scientific aspects are adequate.

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Reviewer #1: No

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