UK Infrastructure for Large-scale Clinical Genomics Research

Lead Research Organisation: Queen Mary, University of London

Abstract

The UK 100,000 Genomes Project will accelerate the application of whole genome sequencing (WGS) into routine care for the National Health Service. The genome is the genetic material of an organism (either in DNA or, for many types of viruses, in RNA). WGS provides the most comprehensive inventory of an individual's genetic variation. By incorporating this into routine care it will transform the health services people receive, changing the processes of diagnosis and management. The UK 100,000 Genomes Project seeks to drive this change by sequencing 100,000 genomes of individuals affected by rare diseases and cancer (and their families) and infectious disease pathogens.

Technical Summary

This proposal to the MRC will establish a shared, secure, high performance data and compute infrastructure as a platform for large-scale clinical genomics research based on the data flows of the UK 100,000 Genomes project.

Samples and data from patients with cancer and rare, inherited disorders will be provided by NHS England, working in collaboration with Cancer Research UK and programmes funded by the NIHR and the MRC. Genomics England, a company wholly owned by the Department of Health, will pay for the generation of whole genome sequence data.

Genomics England will pay also for the generation of summary reports, based upon clinical annotations of this data, and will return these to the NHS to support patient care. Genomics England will make anonymised, redacted versions of the data available for industrial research strictly within a secure, managed environment.

The proposed infrastructure will provide a similar environment for academic research, with a more comprehensive collection of genomic and patient data, including the read-level data used for the generation of variant calls and summary reports. The infrastructure will include software tools to support the production of 'research-ready' data sets, the effective management of patient and genomic data, and the delivery of collaborative clinical research.

The project partners have experience in infrastructure development and clinical genomics research, and will be able to re-use designs, procedures, and software developed and tested within existing programmes and organisations, including UK Biobank and the European Bioinformatics Institute.

A formal mechanism will be established for engagement with public, charitable, and philanthropic funders, and with the clinical research projects that they fund. Subject to capacity constraints, projects that add appropriate value to the Genomics England programme will be provided with access to the compute infrastructure at no charge.

Publications

10 25 50
 
Description Chief Scientist Genomics England
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
URL http://www.genomicsengland.co.uk
 
Description Chief Scientist Genomics England
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
URL http://www.genomicsengland.co.uk
 
Description Chief Scientist Genomics England
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
URL http://www.genomicsengland.co.uk
 
Description Chief Scientist Genomics England
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
URL http://www.genomicsengland.co.uk
 
Description Transformation of the NHS Genomic Medicine Service
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact I co-chaired the NHS Transition groups in rare disease cancer and pharmaco-genomics which has created a national test directory adjusting 750k genomic tests in the NHS to offer, for the first time, an equitable NHS genomics medicine service across England from Oct '18.
URL http://www.genomicsengland.co.uk
 
Description UK Clinical Genomics Infrastructure: Co-lead for the preparation for commissioning in the NHS of a National Genomic Health service
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
 
Description UK Clinical Genomics Infrastructure: Member of the Topol Review of Digital, Genomics and Artificial Intelligence implications for workforce planning.
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
 
Description UK Clinical Genomics Research Data Infrastructure
Amount £2,700,000 (GBP)
Organisation Department of Health (DH) 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2021
 
Title The UK Clinical Genomics Infrastructure: Clinical Data 
Description Improvement to the wider UK Clinical Genomics Infrastructure 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? Yes  
Impact The infrastructure now holds 1.6 billion data points on 94,000 participants and 91,000 whole genomes and recently cancer registry and mortality data (2141 participants with cause of death). 
URL https://www.genomicsengland.co.uk/
 
Description Genomics England - 100k Genome Project (Multiple National & International Talks 2015-2018) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Multiple talks about the 100k Genomes project as GEL Chief Scientist
Year(s) Of Engagement Activity 2015,2016,2017,2018
URL http://www.genomicsengland.co.uk
 
Description The Genomics Conversation 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Activities:
•Events took place all over the country and a big thank you goes to the teams in Lincoln, York and Nottingham for their awareness raising activities.
•We launched our new nursing video - 'Nursing in the Genomic Era'
•We hosted our fifth WeNurses chat on 'Nursing and Ethics in the Genomic Era'
•Ran a competition using the Genomics Game to conclude the week.
•Four #GenomicsConversation podcasts were launched on SoundCloud to introduce nurses and midwives to genomics.
•We held our first ever #GenomicsConversation Thunderclap to launch the weeks activities.
•We organised a social media pledge campaign with enthusiasts spreading the message far and wide on social media.

Engagement:
•During the course of the week the website received over 12,000 page views.
•Our first ever Thunderclap was a great success delivering a huge social reach with influential supporters from nursing including WeNurses, AgencyNurse and 6CsLive!.
•Our four #GenomicsConversation podcasts were streamed over 80 times during week.
•We received over 1000 views of our videos.
Year(s) Of Engagement Activity 2018
URL https://www.genomicseducation.hee.nhs.uk/woa-18/