Reviewer ’s report  
 
Title: The 1000IBD project: multi -omics data of 1000 infla mmatory bowel disease patients; 
Data release 1  
 
Version: 0 Date: 24 Aug 2018  
 
Reviewer: James John Ashton  
 
Reviewer's report:  
 
Background - 
 
The authors present a succinct overview of the importance of developing multi -omic data in IBD  
in order to move to a systems biology and personalised medicine approach to disease. It would 
be interesting to discuss the recent publications from the RISK cohort where use of these data 
has enabled modelling to take a first step towards precision medic ine in IBD. I feel this would 
place the 1000IBD project in context and emphasise it's importance.  
 
 
What will be the arrangements for publication of any results developed from these data by 
institutions external to Groningen? Will co -authorship be required  or just citation?  
 
 
Methods - This is clearly an extremely ambitious and important project, with very important data 
likely to be generated by this work (and already developed). Whilst I do not include specific 
comments about the outputs yet several questio ns do arise which would be important to answer 
prior to using these data. Additionally the use of patient -based reporting systems has previous 
had flaws (reporting bias, subjective etc.) but also represents a very interesting way of collecting 
data.  
 
 
What  were the ages of the patients included? Were paediatric samples included?  
 
 
Were the two new questionnaires developed for this study validated, reviewed externally or 
piloted prior to use? The importance of the quality of the clinical phenotypic data here cannot be 
understated  
 
 
Will all raw fastq files from the WES, microbiome and transcriptomic sequencing be available to 
run through custom pipelines?  
 
 
RNAseq and microbiome (MGS) data is notorious for being subject to batch effects, could the 
authors commen t on how the 300 samples where grouped and how batch effect was minimised?  
How quickly were biopsies snap -frozen after sampling? Previous studies have used RNAlater to 
preserve bacterial DNA and human RNA to prevent degradation, did the authors consider this?  
 
 
Similarly how many of the stool samples were frozen within 15 minutes?  The exact conditions 
for samples is important in determining the quality of the output data  
 
 
At what point in the disease course were patients recruited? Are any treatment naive? Are any 
followed longitudinally with multiple samples available?  
 
 
Overall - This is a good report and the publication would benefit researchers to understand the 
access to these data, clearly further work is ongoing.  
 
 
There are several typos that should be corrected including - 
 
 
Page 10, line 43 - GENERATION OF DIETART AND ENVIRO NMENTAL DATA  
 
 
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary controls?  
If not, please specify which controls are required in your comments to the autho rs. 
 
No 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
Are you able to assess any statistics in the manus cript or would you recommend an 
additional statistical review?  
If an additional statistical review is recommended, please speci fy what aspects require further 
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
 
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Needs some language corrections before being published  
 
 
 
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, f ees, funding, or salary from an 
organisation that may in any way gain or lose financial ly from the publication of this 
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares  in an organisation t hat 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 recei ved 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  
 
I agree to the open peer review policy o f the journal. I understan d that my name will be included 
on my report to the authors and, if the manuscript is accepted f or publication, my named report 
including any attachments I upload will be posted on the website along with the authors' 
responses. 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/ ). I understand that any com ments 
which I do not wish to be included in my named report can be included as confidential  comments 
to the editor s, which will not be published.  
 
I agree to the open peer review policy of the journal  
 
Reviewer ’s report  
 
Title: The 1000IBD project: multi -omics data of 1000 infla mmatory bowel disease patients; 
Data release 1  
 
Version: 0 Date: 24 Aug 2018  
 
Reviewer: James John Ashton  
 
Reviewer's report:  
 
Background - 
 
The authors present a succinct overview of the importance of developing multi -omic data in IBD  
in order to move to a systems biology and personalised medicine approach to disease. It would 
be interesting to discuss the recent publications from the RISK cohort where use of these data 
has enabled modelling to take a first step towards precision medic ine in IBD. I feel this would 
place the 1000IBD project in context and emphasise it's importance.  
 
 
What will be the arrangements for publication of any results developed from these data by 
institutions external to Groningen? Will co -authorship be required  or just citation?  
 
 
Methods - This is clearly an extremely ambitious and important project, with very important data 
likely to be generated by this work (and already developed). Whilst I do not include specific 
comments about the outputs yet several questio ns do arise which would be important to answer 
prior to using these data. Additionally the use of patient -based reporting systems has previous 
had flaws (reporting bias, subjective etc.) but also represents a very interesting way of collecting 
data.  
 
 
What  were the ages of the patients included? Were paediatric samples included?  
 
 
Were the two new questionnaires developed for this study validated, reviewed externally or 
piloted prior to use? The importance of the quality of the clinical phenotypic data here cannot be 
understated  
 
 
Will all raw fastq files from the WES, microbiome and transcriptomic sequencing be available to 
run through custom pipelines?  
 
 
RNAseq and microbiome (MGS) data is notorious for being subject to batch effects, could the 
authors commen t on how the 300 samples where grouped and how batch effect was minimised?  
How quickly were biopsies snap -frozen after sampling? Previous studies have used RNAlater to 
preserve bacterial DNA and human RNA to prevent degradation, did the authors consider this?  
 
 
Similarly how many of the stool samples were frozen within 15 minutes?  The exact conditions 
for samples is important in determining the quality of the output data  
 
 
At what point in the disease course were patients recruited? Are any treatment naive? Are any 
followed longitudinally with multiple samples available?  
 
 
Overall - This is a good report and the publication would benefit researchers to understand the 
access to these data, clearly further work is ongoing.  
 
 
There are several typos that should be corrected including - 
 
 
Page 10, line 43 - GENERATION OF DIETART AND ENVIRO NMENTAL DATA  
 
 
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary controls?  
If not, please specify which controls are required in your comments to the autho rs. 
 
No 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
Are you able to assess any statistics in the manus cript or would you recommend an 
additional statistical review?  
If an additional statistical review is recommended, please speci fy what aspects require further 
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
 
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Needs some language corrections before being published  
 
 
 
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, f ees, funding, or salary from an 
organisation that may in any way gain or lose financial ly from the publication of this 
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares  in an organisation t hat 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 recei ved 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  
 
I agree to the open peer review policy o f the journal. I understan d that my name will be included 
on my report to the authors and, if the manuscript is accepted f or publication, my named report 
including any attachments I upload will be posted on the website along with the authors' 
responses. 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/ ). I understand that any com ments 
which I do not wish to be included in my named report can be included as confidential  comments 
to the editor s, which will not be published.  
 
I agree to the open peer review policy of the journal  
 
Please review this paper.
user
Reviewer ’s report  
 
Title: The 1000IBD project: multi -omics data of 1000 infla mmatory bowel disease patients; 
Data release 1  
 
Version: 0 Date: 24 Aug 2018  
 
Reviewer: James John Ashton  
 
Reviewer's report:  
 
Background - 
 
The authors present a succinct overview of the importance of developing multi -omic data in IBD  
in order to move to a systems biology and personalised medicine approach to disease. It would 
be interesting to discuss the recent publications from the RISK cohort where use of these data 
has enabled modelling to take a first step towards precision medic ine in IBD. I feel this would 
place the 1000IBD project in context and emphasise it's importance.  
 
 
What will be the arrangements for publication of any results developed from these data by 
institutions external to Groningen? Will co -authorship be required  or just citation?  
 
 
Methods - This is clearly an extremely ambitious and important project, with very important data 
likely to be generated by this work (and already developed). Whilst I do not include specific 
comments about the outputs yet several questio ns do arise which would be important to answer 
prior to using these data. Additionally the use of patient -based reporting systems has previous 
had flaws (reporting bias, subjective etc.) but also represents a very interesting way of collecting 
data.  
 
 
What  were the ages of the patients included? Were paediatric samples included?  
 
 
Were the two new questionnaires developed for this study validated, reviewed externally or 
piloted prior to use? The importance of the quality of the clinical phenotypic data here cannot be 
understated  
 
 
Will all raw fastq files from the WES, microbiome and transcriptomic sequencing be available to 
run through custom pipelines?  
 
 
RNAseq and microbiome (MGS) data is notorious for being subject to batch effects, could the 
authors commen t on how the 300 samples where grouped and how batch effect was minimised?  
How quickly were biopsies snap -frozen after sampling? Previous studies have used RNAlater to 
preserve bacterial DNA and human RNA to prevent degradation, did the authors consider this?  
 
 
Similarly how many of the stool samples were frozen within 15 minutes?  The exact conditions 
for samples is important in determining the quality of the output data  
 
 
At what point in the disease course were patients recruited? Are any treatment naive? Are any 
followed longitudinally with multiple samples available?  
 
 
Overall - This is a good report and the publication would benefit researchers to understand the 
access to these data, clearly further work is ongoing.  
 
 
There are several typos that should be corrected including - 
 
 
Page 10, line 43 - GENERATION OF DIETART AND ENVIRO NMENTAL DATA  
 
 
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary controls?  
If not, please specify which controls are required in your comments to the autho rs. 
 
No 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
Are you able to assess any statistics in the manus cript or would you recommend an 
additional statistical review?  
If an additional statistical review is recommended, please speci fy what aspects require further 
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
 
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Needs some language corrections before being published  
 
 
 
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, f ees, funding, or salary from an 
organisation that may in any way gain or lose financial ly from the publication of this 
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares  in an organisation t hat 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 recei ved 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  
 
I agree to the open peer review policy o f the journal. I understan d that my name will be included 
on my report to the authors and, if the manuscript is accepted f or publication, my named report 
including any attachments I upload will be posted on the website along with the authors' 
responses. 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/ ). I understand that any com ments 
which I do not wish to be included in my named report can be included as confidential  comments 
to the editor s, which will not be published.  
 
I agree to the open peer review policy of the journal  
 
assistant