PONE-D-19-26430

An evaluation of genetic causes and environmental risks for bilateral optic atrophy

PLOS ONE

Dear Dr. Tarnopolsky,

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A flow chart with of the process from NGS to variant selection would be easily understandable. In addition to that, please read carefully the comments from the reviewer and address them point by point and with any additional experiments if necessary.

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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: Yes

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

Reviewer #1: I Don't Know

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: Yes

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: In this research article by Chen et al., 97 individuals with optic atrophy (OA) were analyzed by NGS of 22 nuclear genes and/or complete mitochondrial DNA (mtDNA) sequencing in order to assess the clinical utility of NGS for the diagnosis of OA; moreover the impact of environmental factors was investigated, identifying ethanol consumption as a potential independent risk study. The manuscript is overall well written and the results are fully explained. However, it is not clear to me what correlation the authors expected to exist between environmental factors such as ethanol consumption and genetics defects associated with OA, as the presence of a causative genetic mutation (and not a susceptibility factor) should be responsible for the development of the disease independently from environmental factors. Moreover, I am not sure that the definition of ethanol consumption as an epigenetic factor is appropriate, as the term epigenetic modification refers to the specific DNA modification (for example, DNA methylation)that can develop as a result of environmental agents; and still it’s not clear why the authors expected an epigenetic factor to interact with a known causative mutation. I think the authors should revise this section and make their hypothesis more understandable. Finally, it should also be clarified how exactly the genes in the panel were selected and why some patients underwent only nuclear genes or mitochondrial DNA sequencing instead of both.

Reviewer #2: Gist/Summary: The authors come up with analysis of variants in patients with optic atrophy and liaise this with environment factors. In this process, they sequence the mitochondrial genomes of the patients by employing a retrospective cohort design. Detecting positive variant in a cohort of samples in the patients with excessive alcohol ( ethanol) intake and smokers augurs well with the proposal. It is certainly the need of the hour for such diseases linking NGS and epigenetics!

Strengths: Well aimed with two diffident objectives for the design. The authors also deliberate well in evaluating the genetic causes and associating LHON and other neuropathies.

Weaknesses: A pictorial methodology would have been nice. The figures could have been bettered. A detailed discussion on associated gene risk , finding variants through epistatic effects could have been very nice!

Lines 69-77: The role of DNA repair genes and a sentence on it could be a good addition.

Lines 84-90: Pretty long sentence., could be split into two!

Lines 117-119: A Table with restrospective design, odds ration, criteria etcs. could be a value addition.

Lines 136-138: The panel details must be elaborated. There are a few open reading frames that are from known unknown regions/unannotated ( c10orf2, c12orf65) encompassing Twinkle helicase/PEO genes. Did the authors find any variants associated with them?

Something similar of this sort, whence presenting Table 1, SLC25A1 gene links WFS1 and Aconitase (ACO2) gene. Did the authors find any variants associated with them. A soft gene interaction map would be a good one ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4746751/ )

Line 204: "Previously" mistyped.

The possibility of variants, be it homozygous dominant or heterozygous mutations in Metabolic syndromes cannot be ruled out. Could the authors discuss these aspects?

A subtle challenge in linking the statistical significance of their environmental study is the lack of inherent samples for ethanol/smoking. Could machine learning heuristics be an answer for this in the future as good number of datasets are available in sequence read archive.

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Reviewer #1: No

Reviewer #2: Yes: Prashanth N Suravajhala

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An evaluation of genetic causes and environmental risks for bilateral optic atrophy

PONE-D-19-26430R1

Dear Dr. Tarnopolsky,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

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With kind regards,

Obul Reddy Bandapalli, MSc, 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)

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: I Don't Know

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: (No Response)

Reviewer #2: Yes

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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: I am satisfied with all the changes rendered by the authors. They could have answered the responses in line, but it's okay.

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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: Yes: Prashanth Suravajhala