Review for 10.1186/s12876-018-0917-5 (2019)

Reviewer ’s report  
 
Title: The 1000IBD project: multi -omics data of 1000 infla mmatory bowel disease patients; 
Data release 1  
 
Version: 0 Date: 07 Aug 2018  
 
Reviewer: Nicholas Kennedy  
 
Reviewer's report:  
 
This paper provides a basic description of the phenotype and genotype data gener ated as part of 
the 1000IBD project. It does not, in itself, contain any new findings, but the cohort described will 
no doubt be used by the submitting authors and others to generate a wide range of interesting 
analyses.  
 
I have a few specific questions:  
 
1. It's not clear to me why only a subset of the data generated is being released at this stage 
(e.g. 314 of the 1015 patients with Immunochip data). This could be better explained in 
the manuscript.  
 
 
2. The website for EGA is https://ega -archive.org (i.e. w ithout the www)  
 
 
3. The website https://1000ibd.org  is not live. The Molgenis github page 
(https://github.com/molgenis/molgenis -projects ) suggests the address should be 
https://1000ibd.com , but again this is not live.  
 
 
4. I would have liked to see some top -level summary statistics of the cohort presented (e.g. 
diagnoses, age at diagnosis, sex, Montreal classification, disease duration at recruitment, 
medication exposure, disease activity, etc.)  
 
 
5. As new, unpublished instruments, details on the FFQ and enviro nmental questionnaire is 
rather limited.  
 
 
6. When are these patients recruited? At diagnosis? Opportunistically? How are they 
selected? What are the inclusion/exclusion criteria?  
 
 
7. Are patients recallable for resampling? If so, is this available to externa l researchers, or 
just to the UMCG group?  
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. 
 
Unable to assess  
 
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.  
 
Not relevant to this manuscript  
 
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
 
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.  
 
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