PONE-D-20-28113

Frameshift variant in MITF gene in a large family with Waardenburg Syndrome type II and a Co-segregation of a C2orf74 variant

PLOS ONE

Dear Dr. Basit,

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 provide the detailed explanation of the data analysis and also make the data available somewhere in the database archives.

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We look forward to receiving your revised manuscript.

Kind regards,

Obul Reddy Bandapalli, MSc, PhD

Academic Editor

PLOS ONE

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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: Partly

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

Reviewer #1: Yes

Reviewer #2: Yes

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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: No

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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

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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: I have no major concern. I only have 2 minor issues-

1) In the whole exome sequencing studies, please outline the filtering steps undertaken to reach at 67 coding variants.

2) please make all data publicly available and not by request to author. Please upload mutation data to dbSNP.

Reviewer #2: In this manuscript, the authors found that the mutations in the MITF gene and C2orf74 are potentially the causal factor for a family with multiple individuals affected by Waardenburg syndrome type II. The potential mutants were first identified in two affected individuals with whole-exome sequencing (WES) and then verified in other members with Sanger sequencing. Based on the genotypes of family members, MITF and C2orf74 are highly likely the genes leading to this disease in this family.

My first concern is that not enough details were provided in the genetic analysis. More details need to be provided instead of simply saying “Various filters were applied and coding variants were reduced to 67”. Otherwise, the chosen mutation can be an artifact that happens to segregate well. Additionally, the WES data or genotype data is not available for validation by other researchers. Finally, there are quite many grammar errors that need to be fixed (see below for some examples).

Page 9: change “Further subtypes do exists” to “Further subtypes do exist”.

Page 9: change “an individual patients” to “an individual patient”.

Page 9: change “mutations in PAX3 gene is” to “mutation of PAX3 gene is”.

Page 9: change “Majority of” to “The majority of”.

Page 10: change “20-30% patients” to “20-30% of patients”.

Page 11: change “The read length of the paired end” to “The length of the paired end read”.

Page 11: “Reads were aligned to the human reference genome (GRCh38/hg38) and variants were annotated”. How variants were called?

Page 11: change “variant specific” to “variant-specific”.

Page 11: change “Detailed examination rule out presence” to “Detailed examination ruled out the presence”

Page 12: change “hypothesis free” to “hypothesis-free”.

Page 12: change “the variants in MITF and C2orf74 segregates” to “the variants in MITF and C2orf74 segregate”.

Page 12: change “Sanger sequencing validate” to “Sanger sequencing validates”.

Page 13: change “It is highly heterogeneous syndrome” to “It is a highly heterogeneous syndrome”

Page 14: references were needed for “Mutations in melanocyte inducing transcription factor (MITF), coding for a basic helix-loop-helix (BHLH) leucine zipper protein, are known to cause the WS2 phenotype”.

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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.]

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PONE-D-20-28113R1

Frameshift variant in MITF gene in a large family with Waardenburg Syndrome type II and a Co-segregation of a C2orf74 variant

PLOS ONE

Dear Dr. Basit,

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 Feb 25 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:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled '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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Obul Reddy Bandapalli, MSc, PhD

Academic Editor

PLOS ONE

[Note: HTML markup is below. Please do not edit.]

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

Reviewer #2: 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

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: 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

Reviewer #2: 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

Reviewer #2: 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)

Reviewer #2: The authors have addressed my concerns. Just some suggestions: add software version for GATK and others. For gnomAD and other databases, the version is also necessary. Also, it will be recommended to include a table to summarize the 67 variants (or just some more likely variants), including their location in genome, allele frequency in gnomAD, gene, protein change, mutation affect prediction, number of individuals with the variant, and other important information that showing that they are risk mutations.

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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

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.

Frameshift variant in MITF gene in a large family with Waardenburg Syndrome type II and a Co-segregation of a C2orf74 variant

PONE-D-20-28113R2

Dear Dr. Basit,

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.

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Kind regards,

Obul Reddy Bandapalli, MSc, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: