Similar Ehlers–Danlos Syndrome Profiles Produced by Variants in Multiple Collagen Genes

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The authors  comment on "Diverse collagen gene changes produce similar Ehlers-Danlos 2 syndrome profiles"

Abstract: some sentences too long; not really clear

line 34:  explanation not needed

Results and figure can be extensively improved; language no  always clear.

general structure of the paper to be revisited

conclusions, ok in general, but could be shortened and made more clear defining better the points of discussion.

results refer to 4 cases, but then in discussion, the comments on these cases are only a minor part of the discussion.

the reader does not immediately understand if you are willing to discuss EDS in general or report 4 peculiar cases.

a wonderful amount of data which deserves to be better presented

 

Comments on the Quality of English Language

many sentences too long and difficult to read

Author Response

My comments are in the attached file

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The authors have used a large number of participants with Ehlers-Danlos Syndrome (and controls with developmental disability but not EDS) and through whole genome sequencing which was outsourced to a clinical sequencing company. They conclude that variants in different collagen genes can contribute to similar EDS clinical presentations, which could be important for clinicians and genetic councilors in determining which individuals and the widely different phenotypes have EDS versus other conditions. While this type of finding would be important for differential diagnosis, the presentation of the results in the tables make it very difficult to interpret. For example, specific variants in each of the collagen genes are not given, nor whether these are missense, nonsense, splice variants or non-coding variants. In addition, there is not really a grouping of participants and variants—in other words, is it the total number of variants overall or number of variant genes that are being considered. The authors need to reconsider how to present these data to have a more visual interpretation. Individual variant SNP/rs numbers should be provided, and the authors might also consider a visual with the position of the variants within each collagen gene. Otherwise it is very difficult to know if the results presented really show that multiple gene variants in one person lead to similar EDS profile compared to other patients with EDS.

 

In addition, other concerns should be addressed:

 

Title: The title of the paper does not convey the findings which appear to be that variants in multiple collagen genes produce similar EDS profiles. Perhaps a title of “Ehlers-Danlos syndrome profiles produced by variants in multiple collagen genes” would be clear.

 

Abstract: The authors state in the abstract that “Equal or greater numbers of patients with collagen gene variants met criteria for hypermobile EDS, emphasizing that the type of mutation rather than gene determines EDS types (e. g, COL3 mutation ≠ vascular EDS, COL5 mutation ≠ classical EDS). This statement is somewhat unclear as the paper seems to be about the different genes (rather than specific variants or types of variants within the genes).

 

Starting on page 1: The full gene name, followed by the human gene symbol in capital letters and italics should be given for each gene.

 

Page 1, Line 16-should that be “known” variants versus “recurring” variants?

 

Page 1, Starting at Line 34: “these 6-digit McKusick numbers will access information on diseases or 34 genes in the www.omim.org database”-should you instead just write OMIM 147400, and then reference with the webpage from OMIM? This is the suggested format for referncings OMIM from their FAQ page: Online Mendelian Inheritance in Man, OMIM^®. Johns Hopkins University, Baltimore, MD. MIM Number: {MIM number}: {Date last edited}: . World Wide Web URL: https://omim.org/

 

The introduction fails to convey why the authors undertook this study in the first place. Is there difficulty in differential diagnosis of EDS patients, or a lack of knowledge about known gene changes and symptoms or something else?

 

Page 2, Line 17, change “mutations” to “variants” per the American College of Medical Genetics and Genomics, suggestions for referring to changes in the DNA or protein sequence. If the variant is known to be pathogenic, then the term “pathogenic variant” can be used. In addition, the term “patient” should only be used when actively treating an individual. Otherwise, for Human Subject studies, the term “participant” should be used to indicate their involvement in the study. For example, on page 3, “1979 EDS and 735 developmental disability patients” could be changed to The 1979 participants with EDS and the 735 participants with developmental disabilities…” to also include the participant forward or patient forward nomenclature—rather than identification by their disease stat only.

 

Page 3, line 48, the rs numbers for the variants, when available, should be provided.

 

The authors refer to supplemental data in their results, but none of these data were in the review package downloaded from the journal site.

 

The data presentation in Figures 1, 2, and 3 make interpretation difficult.

Figure 1: why is age plotted both on the X and Y axis? The line “age” is not necessary since the graphs are already divided into age categories. It is also unclear why line graphs are used at all to report these findings. Could one instead use bar graphs at each age category?  What is the “N” of patients represented by these line graphs and is there significance?  Standard deviation/error should also be plotted.

Figure 2: Again, the layout of the table/figure is difficult to discern multiple features, and the figure legend is not helping. For example, the top rows make sense indicating those individuals who are diagnosed EDS versus not diagnosed, and separating out categories such as hypermobility, and sex. However, how these categories then relate to the bottom rows is unclear. The authors seem to want to present individual genes (although not the specific variants within the genes) and how presence of a variant relates to the categories along the top row. What isn’t clear is how the second set of rows relates to the different categories in the first set of rows. Perhaps this second set of rows should be its own table, with the EDS/not-EDS; male/female etc as new columns. In addition, the arrows colored red or green and pointing up or down, along with the dots are not defined in the figure legend. They seem to indicate a category where variants in that gene are more or less associated with that symptom or group of symptoms, but again, it is not clear.

 

Figure 3 appears to break down the symptom groups even more with a similar layout to Figure 3, but just the red and green dots, no arrows—which are not defined in the figure legend.

 

In the discussion the authors conclude that different collagen types (fibrillar, versus FACIT versus those types with interrupted triple helices) lead to phenotypically similar EDS presentations. However, a listing of these collagens and the type they represent (even as part of a table with that information as a column) would be useful to help decide if indeed the patients with multiple types show similar presentations.

Author Response

My comments are in the attached file

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

This is a revised version of manuscript DNA-3372452. The authors have been responsive to the reviewers critique of the manuscript. In general, the implemented changes have improved the overall presentation of the data, and background/conclusions for the paper. The authors have made the Figure legends more detailed to include their arrows and dots, which helps in the interpretation. There is one additional suggestion which was not addressed, which are the meaning of the color schemes used in the Figures. Are these simply used to separate categories and visually show a percentage within the rectangle of each value?  Or are the category colors additional information?  If percentage, then this should also be described in the figure legend. If the colors are meant to convey additional meaning, this should be described in the figure legend i.e. skin phenotypes are shown in yellow with percentage represented by the colored bar in each cell of the figure. If there is no meaning to the colors, the authors might consider removing them entirely.

Author Response

This is a revised version of manuscript DNA-3372452. The authors have
been responsive to the reviewers critique of the manuscript. In general,
the implemented changes have improved the overall presentation of the
data, and background/conclusions for the paper. The authors have made
the Figure legends more detailed to include their arrows and dots, which
helps in the interpretation. There is one additional suggestion which
was not addressed, which are the meaning of the color schemes used in
the Figures. Are these simply used to separate categories and visually
show a percentage within the rectangle of each value?  Or are the
category colors additional information?  If percentage, then this should
also be described in the figure legend. If the colors are meant to
convey additional meaning, this should be described in the figure legend
i.e. skin phenotypes are shown in yellow with percentage represented by
the colored bar in each cell of the figure. If there is no meaning to
the colors, the authors might consider removing them entirely.

I have added comments to both figure legends (in red) clarifying that the color bars allow the reader to rapidly compare amounts in each column in Fig. 1 and in each row in Fig. 2. The colors are different for each number set to show that these finding numbers reflect different underlying traits or mechanisms, the Beighton and joint-skeletal findings in Fig. 1 having the same color because they both reflect joint laxity, findings reflecting particular mechanisms in Fig. 2 (i. e., joint laxity, GI issues) having the same color. In Fig. 2 this color code is applied to the findings selected because of historical or management impact in the lower rows, showing for example that child clumsiness and showing off double-jointed tricks derive from the same joint laxity mechanism as the upper 5 findings (subluxations, etc.) by their shared yellow color.