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NIHR IBD BioResource: SNP chip data
Population Size
Not reported
Years
2016
Associated BioSamples
DNA
Plasma
Geographic coverage
United Kingdom
Lead time
Not applicable
Summary
In order to do recall by genotype, participants have their DNA tested using one the SNP chip arrays from eg. Illumina and Affymetrix (now Thermosfisher). The current iteration is the UK Biobank v2.1 from Thermofisher, which measures ~820k markers.
Documentation
The NIHR IBD Bioresource comprises ~34k participants with Inflammatory Bowel Disease (IBD). The NIHR IBD BioResource extracts DNA from blood and saliva samples taken at recruitment, and measures a panel of SNPs on each DNA sample, using a commodity SNP genotyping array from e.g. Illumina or Affymetrix (now Thermofisher). This is used to pre-screen or match participants when inviting them to take part in experimental medicine studies. De-identified versions of this data is available to researchers investigating the feasibility of future studies. The Technical Metadata describes a SNP annotation file – i.e. what the chip is measuring. The file itself has as many rows as there are SNPs represented on the chip, and is proprietary to the manufacturer, although deeply familiar to researchers.
Dataset type
Health and disease, Omics
Dataset sub-type
Oral and gastrointestinal
Keywords
IBD, Crohn's, colitis, recall, SNP chip, Thermofisher, cohort discovery
Observations
Observed Node | Disambiguating Description | Measured Value | Measured Property | Observation Date |
|---|---|---|---|---|
Events | SNP genotyping array chips processed | 11787 | Count | 01 Sep 2021 |
Events | Approximate number of variants on a SNP chip | 780000 | COUNT | 01 Sep 2021 |
Provenance
Purpose of dataset collection
Study
Source of data extraction
Machine generated
Collection source setting
Other
Image contrast
Not stated
Biological sample availability
DNA,Plasma,Serum
Structural Metadata
Details
Publishing frequency
Quarterly
Version
4.0.0
Modified
08/10/2024
Distribution release date
31/03/2021
Citation Requirements
NIHR BioResource. Acknowledgement text: "We thank NIHR BioResource volunteers for their participation, and gratefully acknowledge NIHR BioResource centres, NHS Trusts and staff for their contribution. We thank the National Institute for Health Research, NHS Blood and Transplant, and Health Data Research UK as part of the Digital Innovation Hub Programme. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care."
Coverage
Start date
13/01/2016
Time lag
2-6 months
Geographic coverage
United Kingdom
Minimum age range
18
Maximum age range
85
Follow-up
1 - 10 Years
Accessibility
Language
en
Controlled vocabulary
OTHER
Format
text/plink, text/vcf
Data Access Request
Dataset pipeline status
Not available
Access rights
Time to dataset access
Not applicable
Access request cost
Access method category
TRE/SDE
Access service description
Some de-identified data may be released to researchers in a platform-independent filetype (e.g. CSV). However, access to any data acquired via NHS Digital is subject to strict restrictions governing where data may be accessed and from which locale - access in a Trustworthy Research Environment (TRE) at AIMES secure data centre (https://aimes.uk/). It is also intended that SNP data be available from the European Genome-Phenome Archive (EBI's EGA) via managed access - https://ega-archive.org/
Jurisdiction
GB-GB
Data use limitation
Research use only
Data use requirements
Institution-specific restrictions,Project-specific restrictions,Return to database or resource,Time limit on use,User-specific restriction
Data Controller
Cambridge University Hospitals NHS Foundation Trust (CUH)
Data Processor
Data processors are NIHR BioResource staff, others with Letters of Access to CUH and approved members of staff at the data centre (AIMES, https://aimes.uk/)