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100,000 Genomes Project

(Redirected from 100,000 genome project)
Not to be confused with 100K Pathogen Genome Project or 1000 Genomes Project.

The 100,000 Genomes Project is a now-completed UK Government project managed by Genomics England that is sequencing whole genomes from National Health Service patients. The project is focusing on rare diseases, some common types of cancer, and infectious diseases.[1][2] Participants give consent for their genome data to be linked to information about their medical condition and health records. The medical and genomic data is shared with researchers to improve knowledge of the causes, treatment, and care of diseases.[3] The project has received over £300 million from public and private investment.[4]

100,000 Genomes Project
Project typeGovernment
Funding agency
Referencedoi:10.1136/bmj.k1687
Project coordinatorGenomics England
Partners
DurationJuly 2013 – December 2018
Websitewww.genomicsengland.co.uk/about-genomics-england/the-100000-genomes-project/

History

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The project was first announced by UK Prime Minister David Cameron in December 2012.[5] The Government set up a new company Genomics England to oversee the project[2] with the plan to focus on rare diseases, cancer, and infectious diseases announced by Health Secretary Jeremy Hunt in July 2013. The project was also made possible by the National Institute for Health and Care Research (NIHR), NHS England, Public Health England, and Health Education England. In 2015, Northern Ireland[6] and Scotland[7] also joined the project with plans to start work the following year. In 2016, the Welsh government issued a statement of intent[8] and is considering participating in the 100,000 Genomes Project.[7]

The initial participants were recruited from Cambridge University Hospitals, University College London Partners, and Newcastle upon Tyne NHS Foundation Trust. The following medical centres joined the project a short time later: Central Manchester University Hospitals NHS Foundation Trust, Great Ormond Street Hospital, Guy's and St Thomas' NHS Foundation Trust, Moorfields Eye Hospital NHS Foundation Trust and Oxford University Hospitals NHS Trust.[9] In total, the coordination of recruitment for the 100,000 Genome Project was overseen by 13 Genomic Medicine Centers that have been established across 85 NHS Trusts in England, Northern Ireland, and Scotland.[10]

In September 2015, Genomics England announced it had contracted with interpretation partners Congenica and Omicia. This is in addition to ongoing work with sequencing partner Illumina.[11]

As of 1 October 2018, the 100,000 Genomes Project had completed the sequencing of 87,231 whole genomes in England[12] and results are in the process of being returned to NHS Genomic Medicine Centres and ultimately back to participants; the first diagnoses from the Project were returned to patients in spring 2015 and over 2,000 families' results have been returned to the NHS in the rare disease programme to date (July 2017).[13]

In December 2018, the full 100,000 genomes milestone was reached.[14]

In July 2019, Genomics England announced Data Release 7, which included the 100,000th whole genome made available to researchers.[15]

A 2019 review identified the initiative as an 'exemplar' in involving the public in genomic research.[16]

In June 2020, Lifebit, a UK-based biotechnology company, was announced as the provider of the trusted research environment that will link the genomic data gathered as part of the 100,000 Genome Project with academic research institutions.[17][18]

NHS Genomic Medicine Centres

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Main article: Genomics_England § NHS_Genomic_Medicine_Centres

Research

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The Genomics England Clinical Interpretation Partnership (GeCIP) includes 2,500 UK and international clinicians and scientists from approximately 300 institutions in 24 countries. There are plans to increase this number. Researchers are organised in "domains" formed around particular conditions, cancer types and research areas such as Machine Learning and Health Economics. The partnership is integrated with the NHS and the aims include improving the use of genotype and phenotype data in healthcare, and providing a platform for genomic research collaborations to add to the knowledge base for genetic disorders.[19][20]

GenOMICC study on COVID-19

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The 100,000 Genomes Project provided a pre-COVID reference set in the GenOMICC study on COVID-19. Genomics England worked in partnership with the GenOMICC consortium, led by the University of Edinburgh, to analyse the whole genome sequences of approximately 20,000 people who have been severely affected by COVID-19. This data was compared with 15,000 other genomes from people who were only mildly affected. It was combined with data set which now includes more than 120,000 genomes (from the "100,000 Genomes" Project). The 100,000 Genomes Project was referred to as the "incredibly important" pre-COVID reference set.[21]

See also

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References

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  1. ^ Ramesh, Randeep (5 July 2013). "Jeremy Hunt launches genomics body to oversee healthcare revolution". The Guardian. Retrieved 12 September 2014.
  2. ^ a b Department of Health and Social Care (5 July 2013). "DNA mapping to better understand cancer, rare diseases and infectious diseases" (Press release). UK Government. Archived from the original on 20 March 2016. Retrieved 26 May 2016.
  3. ^ "Data access, security and privacy". Genomics England. 10 March 2015. Archived from the original on 5 June 2016. Retrieved 6 June 2016.
  4. ^ McKee, Selina (1 August 2014). "£300m for UK 100,000 genomes project - PharmaTimes". pharmatimes.com. Archived from the original on 12 January 2024. Retrieved 12 January 2024.
  5. ^ "DNA tests to revolutionise fight against cancer and help 100,000 NHS patients". UK Government. 10 December 2012. Archived from the original on 3 June 2016. Retrieved 26 May 2016.
  6. ^ "Northern Ireland joins the 100,000 Genomes Project". Genomics England. 29 October 2015. Archived from the original on 19 August 2016. Retrieved 8 September 2016.
  7. ^ a b "Scottish investment in genomic medicine". Genomics England. 1 March 2016. Archived from the original on 14 September 2016. Retrieved 8 September 2016.
  8. ^ "Written Statement -Statement of Intent for Genomics and Precision Medicine". The Welsh Government. Archived from the original on 13 September 2016. Retrieved 8 September 2016.
  9. ^ The 100,000 Genomes Project Pilot Investigators (11 November 2021). "100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care — Preliminary Report". New England Journal of Medicine. 385 (20): 1868–1880. doi:10.1056/NEJMoa2035790. ISSN 0028-4793. PMC 7613219. PMID 34758253.{{cite journal}}: CS1 maint: numeric names: authors list (link)
  10. ^ Wheway, Gabrielle; Genomics England Research Consortium; Mitchison, Hannah M.; Ambrose, J. C.; Baple, E. L.; Bleda, M.; Boardman-Pretty, F.; Boissiere, J. M.; Boustred, C. R.; Caulfield, M. J.; Chan, G. C.; Craig, C. E. H.; Daugherty, L. C.; de, Burca A.; Devereau, A. (2019). "Opportunities and Challenges for Molecular Understanding of Ciliopathies–The 100,000 Genomes Project". Frontiers in Genetics. 10: 127. doi:10.3389/fgene.2019.00127. ISSN 1664-8021. PMC 6421331. PMID 30915099.
  11. ^ "Genomics England announces interpretation partners and expands industry engagement | Genomics England". 30 September 2015. Archived from the original on 9 October 2016. Retrieved 16 September 2016.
  12. ^ "The 100,000 Genomes Project by numbers". Genomics England. Archived from the original on 9 December 2018. Retrieved 2 October 2018.
  13. ^ First children diagnosed in DNA project Archived 6 July 2018 at the Wayback Machine by James Gallagher published by BBC News on 12 January 2016
  14. ^ Fergus Walsh: Faster diagnosis from 'transformational' gene project Archived 5 December 2018 at the Wayback Machine 5 December 2018, bbc.co.uk/news, accessed 5 December 2018
  15. ^ "Over 100,000 whole genome sequences now available for approved researchers | Genomics England". 31 July 2019. Archived from the original on 24 June 2021. Retrieved 16 June 2021.
  16. ^ Lacaze, Paul; Fransquet, Peter; Tiller, Jane; Nunn, Jack S. (2019). "Public Involvement in Global Genomics Research: A Scoping Review". Frontiers in Public Health. 7: 79. doi:10.3389/fpubh.2019.00079. ISSN 2296-2565. PMC 6467093. PMID 31024880.
  17. ^ "Genomics England launches next-generation research platform central to UK COVID-19 response". 29 June 2020. Archived from the original on 15 May 2023. Retrieved 3 February 2023.
  18. ^ Versel, Neil (8 February 2022). "Lifebit Counting on New UK Partnerships to Develop, Validate Federated Data Model". Archived from the original on 3 February 2023. Retrieved 3 February 2023.
  19. ^ "Written evidence submitted by Genomics England (GEN0015)". Committees. January 2017. Retrieved 25 June 2024.
  20. ^ "Evidence on Genomics and genome-editing". Committees. 1 April 2017. Retrieved 25 June 2024.
  21. ^ "GenOMICC COVID-19 study | Genomics England". 4 May 2020. Archived from the original on 4 October 2021. Retrieved 4 October 2021.
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