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NIHR BioResource: SNP chip data

Population Size

Not reported
Population Size statistic card

Years

2019

Years statistic card

Associated BioSamples

DNA

Plasma

Associated BioSamples statistic card

Geographic coverage

United Kingdom

Geographic coverage statistic card

Lead time

2-6 months

Lead time statistic card

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 Bioresource consists of several groups of participants: ~70k from the general population and blood donors (COMPARE, INTERVAL and STRIDES studies); ~19k with one of ~50 rare diseases (RD) including a ~5k pilot for GEL; ~30k with Inflammatory Bowel Disease (IBD) which include the members of Gut Reaction, the Health Data Research Hub for IBD; and ~20k with Anxiety or depression (GLAD study). It intends to extend recruitment in all areas, and to other rare and common disease groups, with a target of ~300k by 2022. The NIHR 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

Keywords

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

1.0.0

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

15/07/2019

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

https://bioresource.nihr.ac.uk/using-our-bioresource

Time to dataset access

2-6 months

Access request cost

https://bioresource.nihr.ac.uk/using-our-bioresource/industry-researchers/industry-bioresource-usage-costs/

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 is currently via an experimental safe haven built in Microsoft Azure. 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-GBN

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/)

Dataset Types: Health and disease

Collection Sources: Other

Relationships: