Toward a methodology for evaluating DNA variants in nuclear families

Dustin B. Miller; Reid Robison; Stephen R. Piccolo

doi:10.1371/journal.pone.0258375

Peer Review History

Original SubmissionJune 29, 2021
23 Aug 2021 Decision Letter - Alvaro Galli, Editor PONE-D-21-21297 Toward a methodology for evaluating DNA variants in nuclear families PLOS ONE Dear Dr. Piccolo, 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 Oct 07 2021 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. 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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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Thank you for stating the following in the Acknowledgments Section of your manuscript: “Brigham Young University provided startup funds to SRP and a graduate assistantship to DBM.” We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. 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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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: The manuscript entitled "Toward a methodology for evaluating DNA variants in nuclear families" is a rather interesting approach to evaluate pedriatic cancer risk of children carrying rare variants. Data are exhaustive and the manuscript deserves publication after minor revision just to increase clarity for a non expert reader. Manuscript is well written and methods well explained; however, I recommend some change in the figure legends. Figure 1 needs a more detailed legends. Question marks mean that children have cancer or not? or not sure? Figure two is fine. From figure 3, I understand that sample ID 29 (from family 1) carries 16 SNPs, 2 indels and 2 SV; totally, 20 potentially damaging variants, right? In table 1, family 1, 1 child carries 12 damaging variants: are these the same data as reported in figure 3? Please explain. Supplementry tables are exhastive, discussion is fine; however, the authors should point out more convincingly, the importance of the study. ****** 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 [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. https://doi.org/10.1371/journal.pone.0258375.r001
Revision 1
22 Sep 2021 Author Response We have prefixed our responses with ">>". When submitting your revision, we need you to address these additional requirements. 1. 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf >> We have updated our manuscript to address these requirements. Please let us know if anything else needs to be changed with the formatting. 2. Thank you for stating the following in the Acknowledgments Section of your manuscript: “Brigham Young University provided startup funds to SRP and a graduate assistantship to DBM.” We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: “The author(s) received no specific funding for this work” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. >> Thank you for letting us know. We have removed our previous statement from the manuscript. Please change our Funding Statement to: "The College of Life Sciences at Brigham Young University provided faculty startup funds to SRP. The Department of Biology at Brigham Young University provided a graduate assistantship to DBM." 3. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. >> We are unaware of any references that have been retracted. We went through and checked these in PubMed and did not find any that had been retracted. Please let us know if you are aware of any that we missed. Reviewer #1: The manuscript entitled "Toward a methodology for evaluating DNA variants in nuclear families" is a rather interesting approach to evaluate pediatric cancer risk of children carrying rare variants. Data are exhaustive and the manuscript deserves publication after minor revision just to increase clarity for a non expert reader. Manuscript is well written and methods well explained; however, I recommend some change in the figure legends. >> We thank the reviewer for taking time to review the manuscript and for these encouraging comments. Figure 1 needs more detailed legends. Question marks mean that children have cancer or not? or not sure? Figure two is fine. >> We have added clarifying details to the legend for Figure 1, as shown below: >> "Each diagram in this figure represents one family from our study. In each diagram, shapes at the top represent parents; shapes at the bottom represent children. Numbers below children are sample identifiers. These identifiers do not necessarily correspond to birth order or any other factor. One child in each family had been diagnosed with pediatric cancer, but the disease status of all children was unknown to the primary author until after disease-history predictions were made. This unknown status is represented using question marks." From figure 3, I understand that sample ID 29 (from family 1) carries 16 SNPs, 2 indels and 2 SV; totally, 20 potentially damaging variants, right? >> That is correct. We have added more details to the figure legend to help clarify, as shown below: >> "This figure shows the number of potentially damaging variants for each variant type (simple heterozygous, homozygous alternate, and compound heterozygous) and category (SNP, indel, and SV) in each sample. Potentially damaging variants met specific MAF, CADD and impact severity thresholds (see Methods)." In table 1, family 1, 1 child carries 12 damaging variants: are these the same data as reported in figure 3? Please explain. >> We apologize for the confusion. Although Table 1 and Figure 3 are complementary, they provide different types of information. Figure 3 illustrates variants that were present in each individual in each family, whereas Table 1 summarizes the overlap in variants among siblings in a given family. Both types of information are important to communicate. We have rewritten the legend for Table 1 to clarify what is shown in that table: >> "Table 1. An overview of variants in common among children within each nuclear family. We excluded variants that were present in more than two children in a given nuclear family. This table shows the number of variants in common among a specified number of siblings. For example, in Family 1, 12 variants (in 10 genes) were unique to a single child; 5 variants (in 5 genes) were shared between two children. These numbers reflect the number of "potentially damaging" variants—including simple-heterozygous, compound-heterozygous, and homozygous-alternate variants—that met specific MAF, CADD and impact-severity thresholds (see Methods)." Supplementary tables are exhaustive, discussion is fine; however, the authors should point out more convincingly, the importance of the study. >> We thank the reviewer for this recommendation. We have added a paragraph at the beginning of the Discussion section that describes additional ways that our study is unique and important: >> "This study contributes a novel methodology for estimating the translational importance of DNA variants in a given family. Unlike other designs that use trios or quads or that focus primarily on affected family members, we collect data mostly from unaffected individuals, including parents and siblings. Despite the inherent small sample size of comparing individuals within a nuclear family, family members are often exposed to environmental conditions, cultural practices, and dietary habits that are more similar to each other than to the general population, thus potentially reducing confounding factors that could bias an analysis. Although we were not able to demonstrate that our predictions were more accurate than expected by random chance, we have introduced a methodology for identifying candidate variants that can be expanded or refined. Furthermore, we have shared a unique dataset with the community; we are unaware of other WGS datasets from nuclear families with as many as seven children." >> Later in the Discussion section, we highlight additional factors that make this study unique and important. For example, we explain how our study differs from population-based studies, how we combined quantitative and qualitative methods, the ability to include a wide range of variants (including compound-heterozygous and de novo variants that are not profiled in most genetic studies), our methodology for combining multiple lines of evidence from diverse sources, and insights we gained about potential biases. Finally, even if this manuscript reports some negative results, we are confident that it meets all of the PLOS Publishing Criteria. >> Thanks again! Attachments Attachment Submitted filename: PedFam_response_to_reviewers_PLOS.pdf https://doi.org/10.1371/journal.pone.0258375.r002
27 Sep 2021 Decision Letter - Alvaro Galli, Editor Toward a methodology for evaluating DNA variants in nuclear families PONE-D-21-21297R1 Dear Dr. Piccolo, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, 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, Alvaro Galli 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 #1: 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 #1: Yes ****** 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 ****** 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: (No Response) ****** 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 #1: No https://doi.org/10.1371/journal.pone.0258375.r003
Formally Accepted
30 Sep 2021 Acceptance Letter - Alvaro Galli, Editor PONE-D-21-21297R1 Toward a methodology for evaluating DNA variants in nuclear families Dear Dr. Piccolo: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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 plosone@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. Alvaro Galli Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0258375.r004

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