PONE-D-20-31424

DACH1 mutation frequency in endometrial cancer is associated with high tumor mutation burden

PLOS ONE

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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: Partly

Reviewer #2: Yes

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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: Yes

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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: The title of this paper is DACH1 mutation frequency in endometrial cancer is associated with high tumor mutation burden. Based on that title a couple required elements are missing and pieces are out of place. Endometrial cancer, immediately thinking subsets (see major point 4). These subsets are somewhat addressed in table 6 (and are a confounder of table 3) but need to be flushed out in more detail and much earlier in the manuscript. The TCGA has MSI information in the unrestricted access clinical tables so this comparison is doable. It's possible DACH1 doesn't fit into neatly into those subsets and that could justify all the pathway analysis but right now I wonder why the pathway analysis is there. I'd like to see a much deeper dive into analyses that support the title of the paper (e.g. the mutations in DACH1 or TMB by DACH1 status and also analyzed within subgroups). What's reported is technically correct but it lacks a greater context.

Major points:

1) Data availability, the authors should state what data is available in addition to the current statements about what data is not available.

2) The bioinformatics method section only describes in very general terms the RNAseq methodology. Is Figure 1 copied from a brochure? Ideally would describe with references and version numbers. False discovery rate method for Figure 3 should be described here as well. Considering most of the figures are bioinformatics analyses, this section needs to be strengthened significantly.

3) Table 2 is screaming for comparison of MSS to MSI-H, ah there it is in Table 6.

4) In comparing to TCGA there needs to be some description or normalization of cohorts. What fraction of each cohort is POLE, MSI-H, and other (copy number high vs low can be a judgement call so lets ignore it). Then what fraction of POLE, MSI-H and other is DACH1 mutated. This flaw permeates the manuscript and especially figure 8 since the TMB covariate is not controlled for.

5) There are few enough DACH1 mutations that they should all be listed with protein effects. Are these nonsense alterations? Splicing? Silent? Are the amino acid changes consistent with loss of function (e.g. charge switch)?

Minor points:

1) Line 194: p = 0.053 is approaching significance. Saying it is marginally significant makes me think the p value is 0.04999.

2) Figure 2 would look better as a lollipop plot. If the data is formatted properly, cBioportal will make one for you.

3) Figure 3 would benefit from labeling some of the genes called out in the text.

4) Figures 4, 5, 6 have copyright QIAGEN all rights reserved on them. Are the authors allowed to publish these plots in PLOS ONE?

Reviewer #2: The authors have done a thorough job of doing all the relevant data analysis and the manuscript has also been well written. I have no additional comments on the paper and I recommend that the manuscript be accepted.

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Reviewer #1: No

Reviewer #2: No

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DACH1 mutation frequency in endometrial cancer is associated with high tumor mutation burden

PONE-D-20-31424R1

Dear Dr. Kolesar,

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.

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Kind regards,

Sumitra Deb, PhD

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: (No Response)

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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

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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

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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: All comments have been addressed and the data sharing is a satisfactory balance between access and patient privacy.

One minor comment: Line 286, Hochberg is spelled with an 'h'

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Reviewer #1: No