Dear Dr. Sundermann,

Thank you very much for submitting your manuscript "Reconstructing Tumor Evolutionary Histories and Clone Trees in Polynomial-time with SubMARine" for consideration at PLOS Computational Biology.

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Sincerely,

Teresa M. Przytycka

Associate Editor

PLOS Computational Biology

Feilim Mac Gabhann

Editor-in-Chief

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: This manuscript introduces SuBMARine, a method to infer a summary of phylogenetic trees that explain bulk sequencing data of tumors. Basically, given a solution space of trees the maximally-constrained ancestral reconstruction (MAR) designates all ordered pairs (i,j) of mutations as either ancestral (if i is ancestral to j in all trees), not ancestral (if i is not ancestral to j in all trees) or ambiguous (otherwise). Since exhaustive enumeration of the solution is intractable, the authors introduce a relaxation of the MAR, the subMAR,obtained directly from the frequency matrix. The subMAR (just like the MAR) is unique but may contain more ambiguous entries. In addition to the clean problem without CNAs, the authors consider a version of the problem with CNAs. I have two major comment and several minor comments.

Major:

1. Please provide a real data application of the extended SuBMARine algorithm.

While simulations are used to assess the performance of their algorithms in both problems settings, the TRACERx non-small-cell lung cancer data is used to assess only the basic version of the problem without CNAs. I would like to see a real application of the extended SuBMARine algorithm.

2. Dealing with uncertainty

Compared to the conference version, this manuscript contains an extension of the algorithm to account for uncertainty in the frequency matrix. It would be good to include more methodological details in the main text about this. Moreover, it would be good to assess the performance of SuBMARine using simulated data where one accounts for uncertainty in read counts.

Minor:

* Pseudo code:

- Line 1: As \\phi is a matrix, I would not write |\\phi| to indicate the number of rows. Simply define \\phi to be a K by N matrix.

- What is Equation 9? (this equation is also referred to several times in the main text).

* Author summary: "up o 50" => "up to 50"

* Line 140, 144, etc. What is t? Isn't the basic clone tree reconstruction problem defined by phi?

* Line 230. Elaborate on sorting of phi. Do you sort in ascending order of frequencies in first sample? How do you break ties?

Reviewer #2: The authors have significantly improved the manuscript. The methodology is clearly explained and supported by new figures and supplementary materials. The revised version of the paper covers some crucial topics more extensively, such as: 1) The authors have introduced a noise buffer to extend SubMARine to handling some noise in the estimates of subclonal frequency when performing reconstructions; 2) Full comparison of the results with CITUP method.

The changes introduced to the algorithm in this updated version address satisfactorily my concerns in my first round of review. In my opinion the methods and the manuscript have enhanced scientific quality addressing the challenges of clone tree reconstruction.

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Have all data underlying the figures and results presented in the manuscript been provided?

Large-scale datasets should be made available via a public repository as described in the PLOS Computational Biology data availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: No

Reviewer #2: Yes: Alexander Martinez-Fundichely

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Dear Dr. Sundermann,

We are pleased to inform you that your manuscript 'Reconstructing Tumor Evolutionary Histories and Clone Trees in Polynomial-time with SubMARine' 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,

Teresa M. Przytycka

Associate Editor

PLOS Computational Biology

Feilim Mac Gabhann

Editor-in-Chief

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: My comments have been satisfactorily addressed.

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Have all data underlying the figures and results presented in the manuscript been provided?

Large-scale datasets should be made available via a public repository as described in the PLOS Computational Biology data availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.

Reviewer #1: Yes

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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