PONE-D-23-27333Trans-ethnic analysis in over 799,000 individuals yields new insights into the genetic etiology of colorectal cancerPLOS ONE

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Comments to the Author

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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

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

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Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: 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

Reviewer #3: 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: This manuscript identifies causal relationships between peripheral markers and colorectal cancer. I appreciate the efforts of the authors. In summary, I think that this manuscript would require expansion to be suitable for publication in PLOS ONE.

1. I found the " ethnicity" language quite jarring. Ancestry is a biological category based on shared genetic heritage. While there are several papers in the literature that use these terms interchangeably, I worry that doing so fuels racist narratives about biological differences between groups and racial supremacy. I like to recommend you change "ethnicity" and "ancestry" everywhere."

2. UK Biobank data consists of individual-level data, and I would appreciate more details on how you selected the individuals for your GWAS summary statistics. For instance, did you employ PCA analysis to determine the ancestry? It appears that you focused on the European population, but I'm curious whether you included only white British individuals or if you also encompassed other European ancestries.

3. This manuscript lacks sufficient information regarding the quality control (QC) procedures applied to the UK Biobank (UKBB) genetic data. I would appreciate a comprehensive description of the QC process employed.

You can have a look to the following manuscript

https://www.nature.com/articles/s41467-023-36281-x

4. Did you employ any covariates to adjust phenotypes in the UK Biobank data before conducting GWAS? If so, please provide a detailed explanation, as this would enhance the manuscript."

5. I think collider bias is a potential concern in Mendelian randomization (MR) analysis, how did you handle collider bias in your analysis?

6. In practice, it's often recommended to conduct a sensitivity analysis to assess the impact of including or excluding ambiguous SNPs. This involves running your machine learning analysis with and without these SNPs and comparing the results. If the inclusion of ambiguous SNPs does not substantially affect the outcomes and the models remain stable and reliable, you may choose to keep them. However, if they introduce substantial noise or instability, it's wise to exclude them.

7. How did you handle ambiguous SNPs when comparing data from the UK Biobank (UKBB), Biobank Japan (BBJ), and Finnegan cohorts? Did you ensure that the effect allele for each SNP was matched across all cohorts before conducting the study? Please provide a clear explanation for the readers.

8. In line 108, you mentioned using LD r^2 < 0.001 with a clumping distance cut-off of 10,000kb. Could you explain the rationale behind choosing these specific thresholds for LD r^2 and the window size? Additionally, could you clarify the software or tools you employed to perform this step, such as PRSice or PLINK?

9. In line 114, you stated that you calculated F statistics, but you did not provide an explanation of what R^2 represents. It would be helpful to include the equations for these calculations in the following formats and provide references for both equations.

Please see

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8440862/

https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1003288

https://journals.sagepub.com/doi/full/10.1177/0962280210394459

10. On line 68, please use 'Instrumental variable (IV)' for the first time and then you can use the abbreviation 'IV' later throughout the text."

Reviewer #2: I am pleased to review the manuscript. Here are some comments to the authors:

1. Introduction: In this part, the authors are suggested to introduce some previous Mendelian randomization studies that explored the associations between modifiable factors and CRC (e.g., PMID: 36169182 and 36239790).

2. Methods, line 68: The authors stated this study has a two-sample design. However, from the following content, the authors selected SNPs for exposures from three databases and then extracted the data on outcomes from the same three datasets. Such analyses were more likely to be a one-sample design. The authors should state clearly how did they select the data sources.

3. Genetic instrument of potential risk factors: One of the most important criteria for SNPs is that they were not palindromic SNPs (A/T or C/G) with intermediated EAFs (40-70%). Did the authors apply the criteria when selecting IVs? If yes, relevant descriptions are needed.

4. Figure 3: I think this is a table but not a figure. In addition, the authors are recommended to show other details of the data sources in this table. If it is available, the PubMed ID or DOI of the data sources should be added.

5. Figure 5: From this figure, we can see that there was no association between exposures and outcomes in European populations excepted for WBC.

6. Results: The authors did not mention the results of other MR methods in this part.

7. Discussion, lines 180-181: Need references for the content.

Reviewer #3: Manuscript: Trans-ethnic analysis in over 799,000 individuals yields new insights into the genetic

etiology of colorectal cancer

Manuscript # PONE-D-23-27333

General Comments

This manuscript used summary-level data from the UK Biobank, FinnGen, and BioBank Japan Project cohorts to examine the association of various circulating factors and risk of colorectal cancer. Total cholesterol, eosinophil cell count, red cell distribution width, platelet count, total protein, and C-reactive protein were associated with colorectal cancer risk among all cohorts, while differences in associations were noted when comparing participants of European and Japanese ancestry separately. This is an interesting study, and a few specific comments are listed below.

Specific Comments

1. Introduction: First mention of references #3 and 4 seem incorrect (lines 45 and 47).

2. Methods, Study design: IV (line 68) may need to be defined at the first mention.

3. Results, Trans-ethnic meta-analysis of CRC in three nationwide biobanks: There are some inconsistencies between Figure 4 and Supplementary Tables 8-10. Some markers for the individual cohorts are missing in Figure 4 while values are present in the tables (e.g., EOS for UKBB).

4. Discussion: It seems that the observed differences by ancestry were not really addressed. Can the authors speculate why there may be differences between European vs. East Asian ancestry?

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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Trans-ancestry analysis in over 799,000 individuals yields new insights into the genetic etiology of colorectal cancer

PONE-D-23-27333R1

Dear Dr. Jia,

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,

Yazhou He

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 #2: All comments have been addressed

Reviewer #3: 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 #2: (No Response)

Reviewer #3: Yes

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

Reviewer #2: (No Response)

Reviewer #3: Yes

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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 #2: (No Response)

Reviewer #3: 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 #2: (No Response)

Reviewer #3: 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 #2: (No Response)

Reviewer #3: (No Response)

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Reviewer #2: No

Reviewer #3: No

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