Reviewer’s report
Title: 
Genotype-Phenotype Associations of Polymorphisms within the Gene
Locus of NOD-like Receptor Pyrin Domain Containing 3 in Swiss inflammatory
bowel disease patients
Version: 
0 
Date: 
09 Mar 2021
Reviewer's report:
This is a clearly written, well excecuted study with a concise presentation in the
manuscript. Very well and thorough presentation of the demographic data and
associations between clinical/non-clinical parameters and genetic variation.
Clearly a well phenotyped and well curated cohort. Also the number of
participants in your study is significantly large.
I believe the manuscript could further benefit from addressing the comments
raised below, to maximize clarity and offer to its readers a complete picture of
the emerging associations between IBD and NLRP3 inflammasome-related gene
.
- Can you provide us the minor allele frequency for the general population (swiss
or other ethnically-matched/CEU or Europeans from 1000Genomes, ESP, etc)?
Are there serious MAF deviations for other (non-Swiss, non-CEU) populations
manifesting IBD? You do state that 70-80% of the population (worldwide?) carry
the major alleles but you could be a bit more explicit and use references.
- Can you provide us linkage data (r2/D') for these three linked variants? How far
apart are they? Most importantly, are these three variants linked with coding or
promoter regulatory NLRP3 variants?
- The authors state that these variants lie within a regulatory region downstream
of NLRP3 gene but provide no info (or discussion) as to what kind of regulatory
region this is/may be (transcription factor binding sites, eQTL,? - you could
explore GTEx), being downstream of NLRP3. Simultaneously to having a
regulatory role on NLRP3, the same variants are exonic (rs4353135), intronic
(rs55646866) and upstream (rs10733113) of the OR2B11 gene. How do these
data relate?
- Has any of these variants (or combinations of those) been previously studied in
the context of other inflammatory/autoimmune diseases prognosis parameters
(course, severity, cytokine levels, autoantibodies levels, etc)? Perhaps a comment
in discussion would suffize.
- I find the association of NOD2 - NLRC4 - CASP1 - NLRP3 and the fact that
NLRC4 and NLRP3 may occupy the same inflammasome complex (Man et al.,
PNAS, 2014, PMID= 24803432) very intriguing. Since you seem to have more
genetic data from the same cohort (pg-4, lines 57-59), a combinatorial analysis
of variants in NLRP3 and established IBD NOD2 variants (and NLRC4 variants
if available) would be of interest.
- Finally, is there any observed NLRP3-variant-dependent association between
IBD (CD or UC) gut microbiota status and disease course parameters such as
time of relapse/flare-ups?
Minor comments:
- Please use italics whenever referring to the gene (eg pg-2/line 25, pg-3/lines 8,
62, pg-4/line 55, pg-9/lines 1,52, pg-10/lines 2, 12, etc....many places) - please
check throughout.
- You have a typo mistake in pg-20, Table 2, last line (total TT genotypes,
should be 317, currently is 217) 
- You have a typo on pg-3, line 10 (rs5564866 should be rs55646866) and a typo
on pg-12, line 7 (IL-β instead of IL-1β).
- On pg-13/line 53 you write Nlrp3. Please use capital letters to distinguish from
eg mouse homologue.
Publons Reviewer Recognition
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No
Declaration of competing interests
Please complete a declaration of competing
interests, considering the following questions:
1
. 
Have you in the past five years received reimbursements, fees, funding, or
salary from an organisation that may in any way gain or lose financially
from the publication of this manuscript, either now or in the future?
2
. 
Do you hold any stocks or shares in an organisation that may in any way
gain or lose financially from the publication of this manuscript, either now
or in the future?
3
. 
Do you hold or are you currently applying for any patents relating to the
content of the manuscript?
4
. 
Have you received reimbursements, fees, funding, or salary from an
organization that holds or has applied for patents relating to the content of
the manuscript?
5
. 
Do you have any other financial competing interests?
6
. 
Do you have any non-financial competing interests in relation to this
paper?
If you can answer no to all of the above, write 'I declare that I have no competing
interests' below. If your reply is yes to any, please give details below.
I declare that I have no competing interests
Reviewer Publication Consent.
 I agree for my report to be made available
under an Open Access Creative Commons CC-BY License (
http://creativecommons.org/licenses/by/4.0
) if this manuscript is accepted for
publication. Any comments that I do not wish to be included in the published
report have been included as confidential comments to the editor, which will not
be published.
If you are not happy for us to publish this report, please contact the
editorial office before completing the review.
If you wish, you can include your
name in your published report. Please note you must decide whether to include
your name at the start of the process and confirm this decision whenever
prompted. If you change your decision later, we will not be able to publish your
name.
I agree to the terms of the CC-BY 4.0 license; please 
do not
 publish my name
with my report. (default)
Is the study design appropriate to answer the research question (including the use
of appropriate controls), and are the conclusions supported by the evidence
presented?
Yes
Are the methods sufficiently described to allow the study to be repeated?
Yes
Is the use of statistics and treatment of uncertainties appropriate?
Yes
Is the presentation of the work clear?
Yes
Are the images in this manuscript (including electrophoretic gels and blots) free
from apparent manipulation?
Yes
Reviewer’s report
Title: 
Genotype-Phenotype Associations of Polymorphisms within the Gene
Locus of NOD-like Receptor Pyrin Domain Containing 3 in Swiss inflammatory
bowel disease patients
Version: 
0 
Date: 
09 Mar 2021
Reviewer's report:
This is a clearly written, well excecuted study with a concise presentation in the
manuscript. Very well and thorough presentation of the demographic data and
associations between clinical/non-clinical parameters and genetic variation.
Clearly a well phenotyped and well curated cohort. Also the number of
participants in your study is significantly large.
I believe the manuscript could further benefit from addressing the comments
raised below, to maximize clarity and offer to its readers a complete picture of
the emerging associations between IBD and NLRP3 inflammasome-related gene
.
- Can you provide us the minor allele frequency for the general population (swiss
or other ethnically-matched/CEU or Europeans from 1000Genomes, ESP, etc)?
Are there serious MAF deviations for other (non-Swiss, non-CEU) populations
manifesting IBD? You do state that 70-80% of the population (worldwide?) carry
the major alleles but you could be a bit more explicit and use references.
- Can you provide us linkage data (r2/D') for these three linked variants? How far
apart are they? Most importantly, are these three variants linked with coding or
promoter regulatory NLRP3 variants?
- The authors state that these variants lie within a regulatory region downstream
of NLRP3 gene but provide no info (or discussion) as to what kind of regulatory
region this is/may be (transcription factor binding sites, eQTL,? - you could
explore GTEx), being downstream of NLRP3. Simultaneously to having a
regulatory role on NLRP3, the same variants are exonic (rs4353135), intronic
(rs55646866) and upstream (rs10733113) of the OR2B11 gene. How do these
data relate?
- Has any of these variants (or combinations of those) been previously studied in
the context of other inflammatory/autoimmune diseases prognosis parameters
(course, severity, cytokine levels, autoantibodies levels, etc)? Perhaps a comment
in discussion would suffize.
- I find the association of NOD2 - NLRC4 - CASP1 - NLRP3 and the fact that
NLRC4 and NLRP3 may occupy the same inflammasome complex (Man et al.,
PNAS, 2014, PMID= 24803432) very intriguing. Since you seem to have more
genetic data from the same cohort (pg-4, lines 57-59), a combinatorial analysis
of variants in NLRP3 and established IBD NOD2 variants (and NLRC4 variants
if available) would be of interest.
- Finally, is there any observed NLRP3-variant-dependent association between
IBD (CD or UC) gut microbiota status and disease course parameters such as
time of relapse/flare-ups?
Minor comments:
- Please use italics whenever referring to the gene (eg pg-2/line 25, pg-3/lines 8,
62, pg-4/line 55, pg-9/lines 1,52, pg-10/lines 2, 12, etc....many places) - please
check throughout.
- You have a typo mistake in pg-20, Table 2, last line (total TT genotypes,
should be 317, currently is 217) 
- You have a typo on pg-3, line 10 (rs5564866 should be rs55646866) and a typo
on pg-12, line 7 (IL-β instead of IL-1β).
- On pg-13/line 53 you write Nlrp3. Please use capital letters to distinguish from
eg mouse homologue.
Publons Reviewer Recognition
. Springer Nature can send verification of this
review directly to Publons (a subsidiary of Clarivate Analytics). If you would
like to take advantage of this service, please click on the “Yes” option below.
Your name, email address, title of the reviewed manuscript, name of the journal,
and date of your review submission (the “Review Data”) will then be transmitted
to Publons after the final decision on the manuscript has been made. If you have
already registered at Publons, they will notify you of the receipt of this review
and update your profile 
as per your settings and their policy. If you are not
registered with Publons, you will receive an email from them asking you to
register in order for them to be able to recognize your review on your new
profile page. Publons may use the Review Data to generate derivative metadata
for the benefit of Publons and you as a reviewer, carefully considering the
sensitivity of such information. For example, Publons may verify your record as
a reviewer by updating your profile published on its webservice if you have
registered for such service or help editors to identify candidate reviewers. Please
find the details of processing in Publons’ privacy policy
https://publons.com/about/terms
No
Declaration of competing interests
Please complete a declaration of competing
interests, considering the following questions:
1
. 
Have you in the past five years received reimbursements, fees, funding, or
salary from an organisation that may in any way gain or lose financially
from the publication of this manuscript, either now or in the future?
2
. 
Do you hold any stocks or shares in an organisation that may in any way
gain or lose financially from the publication of this manuscript, either now
or in the future?
3
. 
Do you hold or are you currently applying for any patents relating to the
content of the manuscript?
4
. 
Have you received reimbursements, fees, funding, or salary from an
organization that holds or has applied for patents relating to the content of
the manuscript?
5
. 
Do you have any other financial competing interests?
6
. 
Do you have any non-financial competing interests in relation to this
paper?
If you can answer no to all of the above, write 'I declare that I have no competing
interests' below. If your reply is yes to any, please give details below.
I declare that I have no competing interests
Reviewer Publication Consent.
 I agree for my report to be made available
under an Open Access Creative Commons CC-BY License (
http://creativecommons.org/licenses/by/4.0
) if this manuscript is accepted for
publication. Any comments that I do not wish to be included in the published
report have been included as confidential comments to the editor, which will not
be published.
If you are not happy for us to publish this report, please contact the
editorial office before completing the review.
If you wish, you can include your
name in your published report. Please note you must decide whether to include
your name at the start of the process and confirm this decision whenever
prompted. If you change your decision later, we will not be able to publish your
name.
I agree to the terms of the CC-BY 4.0 license; please 
do not
 publish my name
with my report. (default)
Is the study design appropriate to answer the research question (including the use
of appropriate controls), and are the conclusions supported by the evidence
presented?
Yes
Are the methods sufficiently described to allow the study to be repeated?
Yes
Is the use of statistics and treatment of uncertainties appropriate?
Yes
Is the presentation of the work clear?
Yes
Are the images in this manuscript (including electrophoretic gels and blots) free
from apparent manipulation?
Yes
Please review this paper.
user
Reviewer’s report
Title: 
Genotype-Phenotype Associations of Polymorphisms within the Gene
Locus of NOD-like Receptor Pyrin Domain Containing 3 in Swiss inflammatory
bowel disease patients
Version: 
0 
Date: 
09 Mar 2021
Reviewer's report:
This is a clearly written, well excecuted study with a concise presentation in the
manuscript. Very well and thorough presentation of the demographic data and
associations between clinical/non-clinical parameters and genetic variation.
Clearly a well phenotyped and well curated cohort. Also the number of
participants in your study is significantly large.
I believe the manuscript could further benefit from addressing the comments
raised below, to maximize clarity and offer to its readers a complete picture of
the emerging associations between IBD and NLRP3 inflammasome-related gene
.
- Can you provide us the minor allele frequency for the general population (swiss
or other ethnically-matched/CEU or Europeans from 1000Genomes, ESP, etc)?
Are there serious MAF deviations for other (non-Swiss, non-CEU) populations
manifesting IBD? You do state that 70-80% of the population (worldwide?) carry
the major alleles but you could be a bit more explicit and use references.
- Can you provide us linkage data (r2/D') for these three linked variants? How far
apart are they? Most importantly, are these three variants linked with coding or
promoter regulatory NLRP3 variants?
- The authors state that these variants lie within a regulatory region downstream
of NLRP3 gene but provide no info (or discussion) as to what kind of regulatory
region this is/may be (transcription factor binding sites, eQTL,? - you could
explore GTEx), being downstream of NLRP3. Simultaneously to having a
regulatory role on NLRP3, the same variants are exonic (rs4353135), intronic
(rs55646866) and upstream (rs10733113) of the OR2B11 gene. How do these
data relate?
- Has any of these variants (or combinations of those) been previously studied in
the context of other inflammatory/autoimmune diseases prognosis parameters
(course, severity, cytokine levels, autoantibodies levels, etc)? Perhaps a comment
in discussion would suffize.
- I find the association of NOD2 - NLRC4 - CASP1 - NLRP3 and the fact that
NLRC4 and NLRP3 may occupy the same inflammasome complex (Man et al.,
PNAS, 2014, PMID= 24803432) very intriguing. Since you seem to have more
genetic data from the same cohort (pg-4, lines 57-59), a combinatorial analysis
of variants in NLRP3 and established IBD NOD2 variants (and NLRC4 variants
if available) would be of interest.
- Finally, is there any observed NLRP3-variant-dependent association between
IBD (CD or UC) gut microbiota status and disease course parameters such as
time of relapse/flare-ups?
Minor comments:
- Please use italics whenever referring to the gene (eg pg-2/line 25, pg-3/lines 8,
62, pg-4/line 55, pg-9/lines 1,52, pg-10/lines 2, 12, etc....many places) - please
check throughout.
- You have a typo mistake in pg-20, Table 2, last line (total TT genotypes,
should be 317, currently is 217) 
- You have a typo on pg-3, line 10 (rs5564866 should be rs55646866) and a typo
on pg-12, line 7 (IL-β instead of IL-1β).
- On pg-13/line 53 you write Nlrp3. Please use capital letters to distinguish from
eg mouse homologue.
Publons Reviewer Recognition
. Springer Nature can send verification of this
review directly to Publons (a subsidiary of Clarivate Analytics). If you would
like to take advantage of this service, please click on the “Yes” option below.
Your name, email address, title of the reviewed manuscript, name of the journal,
and date of your review submission (the “Review Data”) will then be transmitted
to Publons after the final decision on the manuscript has been made. If you have
already registered at Publons, they will notify you of the receipt of this review
and update your profile 
as per your settings and their policy. If you are not
registered with Publons, you will receive an email from them asking you to
register in order for them to be able to recognize your review on your new
profile page. Publons may use the Review Data to generate derivative metadata
for the benefit of Publons and you as a reviewer, carefully considering the
sensitivity of such information. For example, Publons may verify your record as
a reviewer by updating your profile published on its webservice if you have
registered for such service or help editors to identify candidate reviewers. Please
find the details of processing in Publons’ privacy policy
https://publons.com/about/terms
No
Declaration of competing interests
Please complete a declaration of competing
interests, considering the following questions:
1
. 
Have you in the past five years received reimbursements, fees, funding, or
salary from an organisation that may in any way gain or lose financially
from the publication of this manuscript, either now or in the future?
2
. 
Do you hold any stocks or shares in an organisation that may in any way
gain or lose financially from the publication of this manuscript, either now
or in the future?
3
. 
Do you hold or are you currently applying for any patents relating to the
content of the manuscript?
4
. 
Have you received reimbursements, fees, funding, or salary from an
organization that holds or has applied for patents relating to the content of
the manuscript?
5
. 
Do you have any other financial competing interests?
6
. 
Do you have any non-financial competing interests in relation to this
paper?
If you can answer no to all of the above, write 'I declare that I have no competing
interests' below. If your reply is yes to any, please give details below.
I declare that I have no competing interests
Reviewer Publication Consent.
 I agree for my report to be made available
under an Open Access Creative Commons CC-BY License (
http://creativecommons.org/licenses/by/4.0
) if this manuscript is accepted for
publication. Any comments that I do not wish to be included in the published
report have been included as confidential comments to the editor, which will not
be published.
If you are not happy for us to publish this report, please contact the
editorial office before completing the review.
If you wish, you can include your
name in your published report. Please note you must decide whether to include
your name at the start of the process and confirm this decision whenever
prompted. If you change your decision later, we will not be able to publish your
name.
I agree to the terms of the CC-BY 4.0 license; please 
do not
 publish my name
with my report. (default)
Is the study design appropriate to answer the research question (including the use
of appropriate controls), and are the conclusions supported by the evidence
presented?
Yes
Are the methods sufficiently described to allow the study to be repeated?
Yes
Is the use of statistics and treatment of uncertainties appropriate?
Yes
Is the presentation of the work clear?
Yes
Are the images in this manuscript (including electrophoretic gels and blots) free
from apparent manipulation?
Yes
assistant