Peer Review History
| Original SubmissionOctober 9, 2024 |
|---|
|
PONE-D-24-45194Association of the TTN, PDK4, and RNF207 mutations with dilated cardiomyopathy in Dobermanns from the United KingdomPLOS ONE Dear Dr. Dutton, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Dec 21 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols . We look forward to receiving your revised manuscript. Kind regards, Nejat Mahdieh Academic Editor PLOS ONE Journal Requirements: 1. When submitting your revision, we need you to address these additional requirements. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 2. We note that your Data Availability Statement is currently as follows: [All relevant data are within the manuscript and its Supporting Information files.] Please confirm at this time whether or not your submission contains all raw data required to replicate the results of your study. Authors must share the “minimal data set” for their submission. PLOS defines the minimal data set to consist of the data required to replicate all study findings reported in the article, as well as related metadata and methods (https://journals.plos.org/plosone/s/data-availability#loc-minimal-data-set-definition ). For example, authors should submit the following data: - The values behind the means, standard deviations and other measures reported; - The values used to build graphs; - The points extracted from images for analysis. Authors do not need to submit their entire data set if only a portion of the data was used in the reported study. If your submission does not contain these data, please either upload them as Supporting Information files or deposit them to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of recommended repositories, please see https://journals.plos.org/plosone/s/recommended-repositories . If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. If data are owned by a third party, please indicate how others may request data access. 3. Please upload a copy of Figure 2B to which you refer in your text on page 11. If the figure is no longer to be included as part of the submission please remove all reference to it within the text. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. 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 Reviewer #2: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ********** 3. 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 Reviewer #2: Yes ********** 4. 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 Reviewer #2: Yes ********** 5. 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: Abstract The abstract presents a study investigating the association of specific genetic mutations with dilated cardiomyopathy (DCM) in Dobermanns, focusing on three genes: TTN, PDK4, and RNF207. The authors hypothesized that the TTN and PDK4 mutations would not be associated with DCM in a UK cohort, while expecting an association for the RNF207 mutation. The study involved 74 dogs, including both controls and DCM-affected animals. Undoubtedly, the hypothesis is clearly stated, providing a solid foundation for the study and the methods are appropriate for the research question. In addition, the results are presented in a concise manner, highlighting the key findings regarding allele frequencies and statistical significance and finally in conclusion you emphasize the relevance of the findings for screening and breeding practices, which is important for practical applications in veterinary genetics. However, there are some areas for improvement that should be noticed. First of all, while the abstract mentions previous findings from US and European cohorts, it could benefit from a brief explanation of why these specific mutations were chosen and their relevance to DCM. Secondly, the sample size of 74 dogs may be considered small for genetic studies. A statement addressing the potential limitations of this sample size and its impact on the generalizability of the results would strengthen the abstract. Beyond that, while p-values are provided, additional context regarding the methodology for calculating odds ratios (OR) and confidence intervals (CI) would enhance transparency and reproducibility. Eventually, it might be helpful to specify whether the mutations are novel or previously identified, as this could inform readers about the novelty of the findings. Overall, the abstract effectively summarizes the research conducted and presents meaningful findings regarding the association of RNF207 with DCM in Dobermanns in the UK. Addressing the areas for improvement could enhance clarity and provide a more comprehensive understanding of the study's significance and limitations. Introduction The introduction provides a thorough overview of dilated cardiomyopathy (DCM) in dogs, particularly focusing on Dobermanns. It outlines the disease's prevalence, genetic implications, and previous research findings related to specific gene mutations. The authors set the stage for their hypothesis regarding the association of TTN, PDK4, and RNF207 with DCM in a UK cohort. The introduction effectively establishes the significance of DCM in Dobermanns, including its prevalence and impact on health, which helps readers understand the importance of the study. The authors provide a well-rounded review of existing literature, discussing both US and European studies that have explored genetic associations with DCM. This contextualizes their research within the broader scientific conversation. However, here are some specific comments and suggestions to enhance the introduction further: Several studies, including the RNF207 gene's potential role in DCM, are mentioned but lack detailed explanations. The transition between previous findings and the hypothesis could be smoother. It is suggested to include specific research objectives or questions to guide the study beyond gene sequencing for a clearer narrative flow. Materials and Methods Here are some comments and suggestions regarding the "Materials and Methods" section of your study: The multicenter, retrospective case-control design is clearly stated, which helps readers understand the framework of the study. Mentioning the ethical review committee and approval number adds credibility and shows adherence to ethical standards. The detailed diagnostic criteria for DCM, including specific measurements and thresholds, is well-articulated and demonstrates rigor in identifying cases. The DNA extraction process is adequately described, including the use of specific kits and methods for quality assessment. There is no mention of statistical methods used for analysis. This is crucial for understanding how results will be interpreted. Results With regard to positive aspects: the study provides a detailed description of the study population, including the selection criteria and demographic information (e.g., age, sex distribution). This enhances transparency and reproducibility. The results present specific echocardiographic measurements that highlight significant differences between DCM and control groups. This is crucial for understanding the physiological implications of DCM in Dobermanns. The inclusion of allele frequencies for the TTN, PDK4, and RNF207 variants adds valuable genetic context to the study, which is important for understanding potential genetic predispositions to DCM. When it comes to negative points: the study's sample size (74 Dobermanns) may limit the generalizability of the findings. Small sample sizes can lead to type II errors, where true associations are missed. Lack of Longitudinal Data: The cross-sectional nature of the study does not allow for insights into disease progression or the effects of potential interventions over time. Limited Genetic Analysis: While allele frequencies are reported, the association analyses do not seem to demonstrate a significant link between genetic variants and DCM, which may warrant further investigation or different analytical approaches. Practical Comments: Consider Increasing Sample Size: Future studies could benefit from a larger sample size to enhance the power of statistical analyses and improve the reliability of findings regarding genetic associations with DCM. Longitudinal Studies: Conducting longitudinal studies could provide insights into how DCM progresses over time in Dobermanns and how genetic factors might influence this progression. Broaden Genetic Analysis: Expanding the analysis to include additional genetic variants or employing whole-genome sequencing could uncover more significant associations with DCM. Discussion The study commences with a well-defined objective, which effectively sets the stage for the ensuing findings and provides a solid context for the results. The authors make pertinent comparisons between human and canine dilated cardiomyopathy (DCM), underscoring the differences in genetic links and their implications for understanding the disease across both species. This enriches the discussion and highlights the importance of canine models in human research. The authors successfully place their findings within the wider framework of genetic research on DCM, referencing prior studies and established genetic mutations related to the disease in both dogs and humans. However, there are some points that should be addressed. Although the association with RNF207 is acknowledged, there is insufficient exploration of its biological significance or the possible mechanisms through which it may impact DCM in Dobermanns. A more in-depth discussion regarding how this variant could influence cardiac function would enhance this section. In addition, the discussion fails to provide explicit recommendations for future research or how the findings could guide breeding practices, genetic screening, or clinical interventions. This omission may leave readers seeking more definitive next steps. Reviewer #2: This well-written article makes a valuable contribution to animal cardiogenetics, offering insights relevant to both dogs and humans with dilated cardiomyopathy. Below are a few points that may enhance the manuscript's clarity and impact. 1. Have the authors considered whether regional breeding practices might influence the prevalence of certain DCM-associated mutations within the UK cohort compared to other European or U.S. populations? This could be expanded by discussing the possibility of founder effects, especially given the historically limited genetic diversity within the Dobermann breed. 2. Could the authors clarify if there were any specific subgroups or characteristics within the DCM cohort that influenced the strength of the RNF207 association? Were there phenotype variations based on the homozygous presence of the RNF207 variant? 3. Did the authors perform a power analysis to determine if this sample size was adequate to detect statistically significant differences, especially given the allele frequencies presented? It would strengthen the study to discuss the potential limitations related to sample size, especially for low-frequency variants. 4. Are chi-square tests appropriate given the sample size, particularly for rare genotype combinations? Did the authors consider alternative statistical methods (e.g., Fisher’s exact test) for smaller samples? 5. While the abstract suggests some genetic differences across populations, it would be valuable if limitations regarding population sampling, genetic heterogeneity, and broader applicability were noted. Could the authors acknowledge any potential biases in their cohort selection or limitations regarding sample representativeness? 6. Could the authors draw further parallels between the mechanisms of action of these mutations in humans and dogs, especially concerning how TTN and RNF207 may differentially influence DCM phenotypes? ********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean? ). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy . Reviewer #1: No Reviewer #2: Yes: Saeideh Kavousi ********** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org . Please note that Supporting Information files do not need this step. |
| Revision 1 |
|
Association of the TTN, PDK4, and RNF207 mutations with dilated cardiomyopathy in Dobermanns from the United Kingdom PONE-D-24-45194R1 Dear Dr. Dutton, 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. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Nejat Mahdieh Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions 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 #3: All comments have been addressed ********** 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 #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #3: 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 #3: Yes ********** 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 #3: 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 #3: Thank you for submitting your manuscript for review. I appreciate the effort and time you dedicated to this work. I have carefully evaluated the paper and noted that you have made a commendable effort to address all the comments provided. It is evident that you have taken the feedback into account, and I acknowledge the revisions made to improve the clarity and quality of the manuscript. Should you have any further questions or require additional feedback, please feel free to reach out. ********** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean? ). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy . Reviewer #3: No ********** |
| Formally Accepted |
|
PONE-D-24-45194R1 PLOS ONE Dear Dr. Dutton, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Nejat Mahdieh Academic Editor PLOS ONE |
Open letter on the publication of peer review reports
PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.
We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.
Learn more at ASAPbio .