PONE-D-21-08932

Cohort Profile: Epigenetics in Pregnancy (EPIPREG) – population-based sample of European and South Asian pregnant women with epigenome-wide DNA methylation (850k) in peripheral blood leukocytes.

PLOS ONE

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[EPIPREG is supported by the South Eastern Norway Regional Health Authority (grant number: 2019092), and the Norwegian Diabetes Association (grant number: N/A). G.H.M. is supported by the Norwegian Research Council (Post doctoral mobility research grant 287198), and have received funding support by Nils Normans minnegave (grant number: N/A)]. 

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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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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: No

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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: This paper describes a new cohort with pregnancy data on a set of women from two different ethnic groups.

The cohort is of interest however I am disappointed that the authors have not performed any basic analysis with any of the cardio-metabolic traits or other pregnancy related traits. Moreover, none of the methods (experimental nor statistical analysis) are novel therefore this is merely a report of a new collected cohort with some description of demographics.

Reviewer #2: This is an excellent presentation of a very interesting cohort. I have some minor comments which may help to improve the manuscript content.

The authors state several times that the cohort is of a large size although they do also say they have limited statistical power in their limitations section. I would argue the cohort is of modest size, however the quantity and range of data collected on each mother-child pair is sizable and the repeated measures are a major advantage to the cohort design.

Within the introduction the paper would benefit from a justification of why there is value in a cohort collection with 2 ethnic groups.

Additional minor comments:

Suggest referring to the EPIC array as Infinium MethylationEPIC BeadChip kit rather than just MethylationEPIC kit to make the resource more discoverable.

In the introduction there are other citations that the authors could consider including and which support the content presented. For example, there are other large studies showing the association between T2D and methylation eg Juvinao-Quintero DL et al (DOI: 10.1186/s13148-021-01027-3) and some studies which have a multi-ethnic study design relevant to EPIPREG eg Chambers JC et al (doi: 10.1016/S2213-8587(15)00127-8). For smoking citations (#16 or #17) it might be also useful to include eg Joehanes R et al (10.1161/CIRCGENETICS.116.001506), Wiklund P et al (DOI: 10.1186/s13148-019-0683-4) and/or Joubert et al (DOI: 10.1289/ehp.1205412). For alcohol intake there are other published papers that are relevant eg Dugue AP (blood)(DOI: 10.1111/adb.12855) and Xu K (although this is a study in saliva not blood)(DOI: 10.1111/acer.14168). Citation #8 is a review so should be acknowledged as such.

“The population based design and inclusion of a significant number of women with European and South Asian ethnicity allows us to study a wide range of phenotypes.” I would suggest removing the words “significant number” from this sentence as it is subjective.

The introduction is clearly written. It could however be improved by discussing the rationale for inclusion of women of European and South Asian ancestries.

In the “Study Population” section it would be more informative to report the specific participation rates in the two ethnic groups in EPIPREG rather than the range across all groups in STORK G.

Line 134: “…if the last was born outside Europe” suggest changing to “if the latter was born outside Europe”

Line 164: A citation to the Oxford University HOMA Calculator should be included.

Line 173: “intense?” typo ?

Line 186 (and 189): suggest amending “Formalin-fixated- paraffin embedded blocks” to “Formalin-Fixed Paraffin-Embedded (FFPE) blocks”

Line 215: for imputation of genetic data it isn’t clear if imputation was conducted in each ethnic group separately or not (or what reference panel was used).

Line 246: typo “QUIAGEN” -> “QIAGEN”

Line 247: suggest replacing the work “doublet” with “duplicate” since this is a more common way of describing replicates.

Line 248: It is unclear what the unmethylated and methylated controls are. Presumably these are commercially available samples(?) It needs to be made clear the negative control is a sample containing no DNA template (if this is the case).

Line 298: The R2 of 0.98 is misleading as it doesn’t actually tell us anything about correlation between methods on a per CpG basis. There should be 4x R2 measures reported, one for each CpG tested which would give an estimate of agreement between methods for each CpG.

Line 309-310: There are a number of other studies studying epigenetics perinatally (eg members of the PACE consortium https://www.niehs.nih.gov/research/atniehs/labs/epi/pi/genetics/pace/index.cfm) and cohorts who also have South Asian and European ancestry maternal and offspring samples eg Born in Bradford: https://borninbradford.nhs.uk/). I would argue that in terms of sample size EPIPREG is relatively small compared to some of these other cohorts.

Figure 2: There appears to be some population stratification which is particularly noticeable in the South Asian group (two groups are evident on both the 1st and 2nd PCs). It would be useful to comment if this can be explored further.

Figure 3: This figure isn’t very informative given that the CpG sites tested have very different distributions. A 4 panel figure showing the R2 for each of the 4 CpG sites would show the relationship between the two methods tested much more clearly. This plot could also be improved if the scales were labelled the same (ie both 0-1 or 0-100) and the labels were descriptive (eg “% methylation measured by bisulphite pyrosequencing” instead of “BSP”).

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Reviewer #1: No

Reviewer #2: No

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

Reviewer #2: Yes

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Cohort Profile: Epigenetics in Pregnancy (EPIPREG) – population-based sample of European and South Asian pregnant women with epigenome-wide DNA methylation (850k) in peripheral blood leukocytes.

PONE-D-21-08932R1

Dear Dr. Sommer,

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,

Lee-Ling Lim

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

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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: Yes

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

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 #2: 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: 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: The authors have made revisions which satisfy the comments/questions raised in my original review. I have no further comments and recommend this paper for publication.

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Reviewer #2: No