Dear Marsh,

Thank you very much for submitting your manuscript "The properties of human disease mutations at protein interfaces" for consideration at PLOS Computational Biology.

As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. In light of the reviews (below this email), we would like to invite the resubmission of a significantly-revised version that takes into account the reviewers' comments.

We cannot make any decision about publication until we have seen the revised manuscript and your response to the reviewers' comments. Your revised manuscript is also likely to be sent to reviewers for further evaluation.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to the review comments and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Please prepare and submit your revised manuscript within 60 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. Please note that revised manuscripts received after the 60-day due date may require evaluation and peer review similar to newly submitted manuscripts.

Thank you again for your submission. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Petras J Kundrotas

Guest Editor

PLOS Computational Biology

Arne Elofsson

Deputy Editor

PLOS Computational Biology

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Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: Review upload as attachment

Reviewer #2: This paper studies the enrichment of pathogenic variants according to their protein locations or interfaces. The differences in terms of protein interfaces may influence the potential pathogenicity and can be included as a factor in variant effect prediction. The study in general would be useful for exploring the effect of protein interfaces on the pathogenicity of variants. The paper is well written and easy to understand. I list my comments below.

1. There might be some kind of circular logic in the analysis, which is related to the difficulty of defining pathogenic variants. The paper uses ClinVar data to define pathogenicity, which are likely influenced/predicted by variant effect prediction tools, and many tools might have used features correlated with the protein interface to train their classifiers. Therefore, the protein interfaces might have already been considered as a factor explicitly/implicitly to define pathogenicity. We need to keep this potential circular logic in mind when interpreting the analysis results. The authors might discuss this in the discussion or conclusion section.

2. The analysis pools all genes/proteins together and do the enrichment analysis using Fisher’s exact test. We need to be cautious about potential confounding factors or heterogeneity ignored when pooling all genes together. To be more convincing, it would be helpful to stratify the genes/proteins into different groups and do the analysis within each group to make sure the patterns observed can still hold. Here are some suggested stratifications: 1) stratify genes into bins of different gene length; 2) stratify genes into bins of different number of variants; 3) stratify genes by whether they are transcription factors or not.

3. Figure 6 and related explanation in the manuscript is not easy to understand, not intuitive to show the differences between different location types. We don’t know how statistically significant of these differences as described in the main text. For example, a “narrow” distribution is hard to define.

4. In the section: Performance of variant effect predictors on interface mutations, the ROC statistics is used. For data sets with very unbalanced positive & negative samples, the precision-recall curve might be more informative. Can the authors add the comparisons using the precision-recall AUC?

5. Figure 5 shows high enrichment for mutations away from cysteine and mutations to proline. Strictly speaking, a mutation is defined by both the “from” and “to”. Can the author also show the enrichment results of all mutations from cysteine? Similarly, the enrichment results of all mutations to the damaging proline? Is there a specific dominating mutation pattern or there is an almost even enrichment for all patterns?

6. When collecting variants from gnomAD, is there an allele frequency threshold? Or matching the variant allele frequency in ClinVar?

7. Figure 5 legend: It should be odds ration instead of log odds ratio

8. The following is not correctly referenced: Vitkup et al, 2003

Reviewer #3: Title; The properties of human disease mutations at protein interfaces.

Comments;

I would like to suggest authors to include most deleterious mutations (Experimentally proved) and the least deleterious mutations in the current data set.

Any insight on the mutation(s) altering interface (protein-RNA, protein-protein, Protein-DNA and protein-ligand ect) simultaneously.

An explanation required on location (near, far ,very far from the interface) of the mutation site and its disease association.

Does the author point out any particular mutation /type affecting various interactions or the frequent type of mutation?

It will be good a information if authors incorporate frequency of mutation and the disease association. Second information on the nature of amino acid mutation and the disease association.

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #1: No

Reviewer #2: Yes: Wenan Chen

Reviewer #3: No

Figure 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. 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 us at figures@plos.org.

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Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example in PLOS Biology see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

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To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

Attachments

Attachment

Submitted filename: PLOS_One _review.docx

Dear Marsh,

Thank you very much for submitting your manuscript "The properties of human disease mutations at protein interfaces" for consideration at PLOS Computational Biology. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations.

Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to all review comments, and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Petras J Kundrotas

Guest Editor

PLOS Computational Biology

Arne Elofsson

Deputy Editor

PLOS Computational Biology

***********************

A link appears below if there are any accompanying review attachments. If you believe any reviews to be missing, please contact ploscompbiol@plos.org immediately:

[LINK]

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: The authors have addressed all comments and the revised manuscript can be accepted for publication

Reviewer #2: The authors addressed my questions well except the following one:

It is not the precision score metric I suggested but the area under the curve (AUC) of the precision-recall curve. The ROC curve uses the sensitivity and specificity as x and y axis, the precision-recall curve uses the precision and the sensitivity as the x and y axis. We can calculate the AUC of either the precision-recall curve or the ROC curve, as long as positive and negative samples are available and a score is defined for each sample. The should both work for the purpose of comparing the performance stratified by the protein locations and interface types. Usually the AUC of the precision-recall curve gives us another view of the performance especially when the positive-negative ratio is far away from 1. The authors can check the REVEL paper where both AUC of ROC curve and precision-recall curve were calculated: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5065685/

Reviewer #3: ./

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

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: Wenan Chen

Reviewer #3: Yes: Dr. Rituraj Purohit

Figure 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. 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 us at figures@plos.org.

Data Requirements:

Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example in PLOS Biology see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

References:

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.

Dear Marsh,

We are pleased to inform you that your manuscript 'The properties of human disease mutations at protein interfaces' has been provisionally accepted for publication in PLOS Computational Biology.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology. 

Best regards,

Petras J Kundrotas

Guest Editor

PLOS Computational Biology

Arne Elofsson

Deputy Editor

PLOS Computational Biology

***********************************************************

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #2: Good, no further questions. Thanks.

**********

Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #2: Yes

**********

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 #2: Yes: Wenan Chen