Interrogating the precancerous evolution of pathway dysfunction in lung squamous cell carcinoma using XTABLE

  1. Matthew Roberts
  2. Julia Ogden
  3. AS Mukarram Hossain
  4. Anshuman Chaturvedi
  5. Alastair RW Kerr
  6. Caroline Dive
  7. Jennifer Ellen Beane
  8. Carlos Lopez-Garcia  Is a corresponding author
  1. Cancer Biomarker Centre, Cancer Research UK Manchester Institute, The University of Manchester, United Kingdom
  2. Cancer Research UK Lung Cancer Centre of Excellence, United Kingdom
  3. Translational Lung Cancer Biology Laboratory, Cancer Research UK Manchester Institute, University of Manchester, United Kingdom
  4. Department of Histopathology, The Christie Hospital, United Kingdom
  5. Boston University School of Medicine, United States

Peer review process

This article was accepted for publication as part of eLife's original publishing model.

History

  1. Version of Record updated
  2. Version of Record published
  3. Accepted Manuscript published
  4. Accepted
  5. Preprint posted
  6. Received

Decision letter

  1. W Kimryn Rathmell
    Senior and Reviewing Editor; Vanderbilt University Medical Center, United States
  2. Sam M Janes
    Reviewer; University College London, United Kingdom

Our editorial process produces two outputs: i) public reviews designed to be posted alongside the preprint for the benefit of readers; ii) feedback on the manuscript for the authors, including requests for revisions, shown below. We also include an acceptance summary that explains what the editors found interesting or important about the work.

Decision letter after peer review:

[Editors’ note: the authors submitted for reconsideration following the decision after peer review. What follows is the decision letter after the first round of review.]

Thank you for submitting the paper "Interrogating the Precancerous Evolution of Pathway Dysfunction in Lung Squamous Cell Carcinoma Using XTABLE" for consideration by eLife. Your article has been reviewed by 2 peer reviewers, and the evaluation has been overseen by a Reviewing Editor and a Senior Editor.

We are sorry to say that, after consultation with the reviewers, we have decided that this work will not be considered further for publication by eLife. There was different opinion among the reviewers, and we sought a third outside opinion to make a final decision. The principal reason is the lack of novelty in this work, the lack of possibility of integration of other datasets of precancerous lesions, and the existence of many other similar applications that are user-friendly. Curation of an early cancer database across multiple cancer types, which provides a user-friendly application to perform integrative analyses across datasets, we suspect would be beyond the scope of this study, and would be necessary to have the user-friendliness of this application carry the novelty. We have included reviewers' comments.

Reviewer #2 (Recommendations for the authors):

Some of the referencing needs careful proofreading. We notice for example that reference 25, Teixeira et al., is labelled as 2019 in the bibliography, 2020 in the text (line 86), and 2018 in Figure 1.

Line 153 – this study used whole genome, not whole exome sequencing.

Figure 2A appears to be an old screenshot as the app is titled "NSCLC" rather than "XTABLE".

https://doi.org/10.7554/eLife.77507.sa1

Author response

[Editors’ note: The authors appealed the original decision. What follows is the authors’ response to the first round of review.]

Reviewer #2 (Recommendations for the authors):

Some of the referencing needs careful proofreading. We notice for example that reference 25, Teixeira et al., is labelled as 2019 in the bibliography, 2020 in the text (line 86), and 2018 in Figure 1.

Line 153 – this study used whole genome, not whole exome sequencing.

Figure 2A appears to be an old screenshot as the app is titled "NSCLC" rather than "XTABLE".

We will address these points accordingly.

All these points have been sorted out according to the reviewer’s comments.

https://doi.org/10.7554/eLife.77507.sa2

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  1. Matthew Roberts
  2. Julia Ogden
  3. AS Mukarram Hossain
  4. Anshuman Chaturvedi
  5. Alastair RW Kerr
  6. Caroline Dive
  7. Jennifer Ellen Beane
  8. Carlos Lopez-Garcia
(2023)
Interrogating the precancerous evolution of pathway dysfunction in lung squamous cell carcinoma using XTABLE
eLife 12:e77507.
https://doi.org/10.7554/eLife.77507

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https://doi.org/10.7554/eLife.77507