Peer Review History
Original SubmissionNovember 10, 2020 |
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PONE-D-20-35246 R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting PLOS ONE Dear Dr. Kawakami, 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. (As an AE, I would like to apologize for the delay in evaluating your submission - it was very difficult to find reviewers over the holiday period. ) Reviewer 1 raises several valid criticisms and pertinent comments that need to be addressed during the revision of your manuscript. Reviewer 1 would also like to see more follow-up experiments, incl. functional validation, of the variant. While I agree that it would be of great value to see such a validation and more information on the biological underpinnings of this variant and its phenotypic effects, I will not consider such experiments as a requirement for a successful manuscript revision. Your main result that the USH2A variant is strongly associated with the roaning phenotype is in itself a stand-alone and robust result (cf. PLOS ONE’s publication criteria). In addition, I suggest you follow the advice of reviewer 1 by (a) reworking (reducing) the discussion of the effects on flecking, as not much can be said at this stage and (b) evaluate more specifically biological hypotheses on how the USH2A variant may exert its effects. Importantly, please check that all data used for/generated in this study can be accessed. Please submit your revised manuscript by Mar 13 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. Please include the following items when submitting your revised manuscript:
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Thank you for providing the following Funding Statement: 'This study was funded by Embark Veterinary, Inc. and the participants that provided DNA and phenotypic information via Embark’s web-based platform.' a. We note that one or more of the authors is affiliated with the funding organization, indicating the funder may have had some role in the design, data collection, analysis or preparation of your manuscript for publication; in other words, the funder played an indirect role through the participation of the co-authors. 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The specific roles of these authors are articulated in the ‘author contributions’ section.” If the funding organization did have an additional role, please state and explain that role within your Funding Statement. b. We note that one or more of the authors are employed by commercial companies: Mascoma LLC Lallemand Corporation and Amazon Web Services, Inc. Please ensure that you declare these commercial affiliations in the amended Funding Statement , as well as a statement regarding the Role of Funders in your study. c. 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Please know it is PLOS ONE policy for corresponding authors to declare, on behalf of all authors, all potential competing interests for the purposes of transparency. PLOS defines a competing interest as anything that interferes with, or could reasonably be perceived as interfering with, the full and objective presentation, peer review, editorial decision-making, or publication of research or non-research articles submitted to one of the journals. Competing interests can be financial or non-financial, professional, or personal. Competing interests can arise in relationship to an organization or another person. Please follow this link to our website for more details on competing interests: http://journals.plos.org/plosone/s/competing-interests Please know it is PLOS ONE policy for corresponding authors to declare, on behalf of all authors, all potential competing interests for the purposes of transparency. PLOS defines a competing interest as anything that interferes with, or could reasonably be perceived as interfering with, the full and objective presentation, peer review, editorial decision-making, or publication of research or non-research articles submitted to one of the journals. Competing interests can be financial or non-financial, professional, or personal. Competing interests can arise in relationship to an organization or another person. Please follow this link to our website for more details on competing interests: http://journals.plos.org/plosone/s/competing-interests [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: Partly 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: No 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: Kawakami et al. utilized dog samples and photographs that were submitted to Embark for commercial genetic profiling. The authors used the data to investigate the genetic basis of several canine coat color phenotypes, roaning, ticking, and flecking. The authors performed GWAS and identified an association signal for roaning on chromosome 38. Further analyses revealed an intronic 11 kb duplication in the USH2A gene encoding usherin, which is very strongly associated with the roaning phenotype. Somewhat surprisingly, the authors did not detect any association signal for ticking. The analysis on flecking is very indirect and circumstantial. It is based on the hypothesis that flecking in Dalmatians is linked to the hyperuricosuria locus, which was published in 1976 (Schaible et al.), before the availability of genetic markers. I was not able to access the full text of this 1976 publication. Given that the authors also show that the previous assumption on an interaction between ticking and flecking in Dalmatian spotting is apparently not true, I consider the work on flecking as too superficial and premature to be published at this time. The main result of the study is the identification of a plausible candidate cuasative variant for roaning. Demonstrating a causal role of USH2A for this phenotype would be an important finding of broad scientific interest. Unfortunately, the authors only report in (too) great detail about the identification of the variant, but provide no functional follow-up or at least a plausible mechanistic hypothesis how the duplication in USH2A might exert its effect. Major comments: (1) Some functional confirmation experiments are essential. Is there a qualitative (splicing) or quantitative effect on USH2A splicing? This should not be too difficult to assess in heterozygous animals where the transcripts from the wildtype and mutant allele can be directly compared to each other (e.g. by RNA-seq). (2) At least a hypothesis should be presented how a dominant USH2A allele (gain of function?) might lead to increased pigmentation in the "white" patches of white spotted dogs. (3) The manuscript gives a huge amount of details on various imputation procedures, haplotype phasing, and other means to extract maximum information from the existing SNP chip genotypes. While this is admittedly very important for a diagnostic lab, it yields little insight into the biology of the trait. I wonder whether the manuscript could be restructured in a way that the manuscript also becomes informative and interesting to readers with a more focussed interest in pigmentation biology. Could some of the technical/diagnostic details be moved to supplementary data (perhaps as a supplemenatry methods text)? (4) Lines 380-382: "Since Variant Effect Predictor (VEP) [25] suggested that none of these variants had a large impact on the function of USH2A...". This statement is not true. VEP predicted several missense and frameshift variants. These were only excluded due to their genotype distribution, not due to the VEP prediction. The presentation of the manuscript makes it very difficult to follow the argumentation of the authors. The chapter "functional annotation" should be placed here (~line 380), before the search for structural variants. (5) The work on flecking is too premature and inconclusive. The authors either need to present more complete data including a plausible mechanistic hypothesis how the flecking allele could work together with the roaning allele to produce the large solid spots in Dalmations or the entire sections should be reduced to a very short statement that the data on flecking are inconclusive (similar to the situation with ticking). (6) File S1: PLoS journals require deposition of the complete raw data. The file with the marker names (bim-file) is insufficient. The authors should make bed-, bim-, and fam-files available or alternatively a ped and map file. Minor comments: (7) Line 81: Roan in horses is linked to the KIT locus, not the KITLG locus. (8) Line 207: Insert an "and" between roaned and 567. (9) Line 541: 120 roaned and 154 control dogs (10) Line 618: It does not make sense to give amino acid exchanges for chromosomal (genomic) positions. The authors should give the amino acid variants with respect to specific proteins. HGVS nomenclature rules should be followed (https://varnomen.hgvs.org/). (11) Figure S8: It should be explicitly stated what the marker in the magenta circle is. Is this the 11 kb duplication? (12) Table S7: This table either needs much more detailed explanation or it can be deleted entirely. How do the authors determine K^B vs K^y when it is unknwon whether any K^br alleles are present? This will be difficult with an illumina array. To the best of my knowledge there are at least 3 different published e-alleles and 5 different b-alleles. The causal variant underlying the various agouti alleles ahve not been published (or under dispute). If this table shall remain in the manuscript, it must be explicitly stated which markers were genotyped to predict the coat color genotypes. (13) File S9: This is a relatively small table. This should be given as a Supplementary table (Excel-file), rather than as a compressed zip-file. Reviewer #2: The authors use citizen science provided by dog owners in the form of photos of their dogs to find molecular explanation for coat color patterning in dogs. This is a lengthy study and authors mostly do a great job in describing this study in detail. The manuscript is technically sound, and data support the conclusions. The authors have made data underlining the data adequately available. The manuscript is written in standard English. Minor comments: 1) The authors have had various breeds in the non-roan control group that should be mentioned and instead not include at all the breed Labrador Retriever that would be phenotypically always non-roan despite of the roaning genotype it might have due to this breed not presenting any color patches of white were the roan could be observed. 2) Chromosome-wide association analysis (CWAS) is incorrectly abbreviated. ********** 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: 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. |
Revision 1 |
R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting PONE-D-20-35246R1 Dear Dr. Kawakami, 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, Christian Braendle Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
Formally Accepted |
PONE-D-20-35246R1 R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting Dear Dr. Kawakami: 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. Christian Braendle Academic Editor PLOS ONE |
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