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Personal Genome Project UK (PGP-UK): a research and citizen science hybrid project in support of personalized medicine

PGP-UK Consortium. BMC Med Genomics. .

Abstract

Background: Molecular analyses such as whole-genome sequencing have become routine and are expected to be transformational for future healthcare and lifestyle decisions. Population-wide implementation of such analyses is, however, not without challenges, and multiple studies are ongoing to identify what these are and explore how they can be addressed.

Methods: Defined as a research project, the Personal Genome Project UK (PGP-UK) is part of the global PGP network and focuses on open data sharing and citizen science to advance and accelerate personalized genomics and medicine.

Results: Here we report our findings on using an open consent recruitment protocol, active participant involvement, open access release of personal genome, methylome and transcriptome data and associated analyses, including 47 new variants predicted to affect gene function and innovative reports based on the analysis of genetic and epigenetic variants. For this pilot study, we recruited 10 participants willing to actively engage as citizen scientists with the project. In addition, we introduce Genome Donation as a novel mechanism for openly sharing previously restricted data and discuss the first three donations received. Lastly, we present GenoME, a free, open-source educational app suitable for the lay public to allow exploration of personal genomes.

Conclusions: Our findings demonstrate that citizen science-based approaches like PGP-UK have an important role to play in the public awareness, acceptance and implementation of genomics and personalized medicine.

Keywords: Citizen science; Genome app; Genome donation; Genome reports; Open access; Open consent; Personal genomics.

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Conflict of interest statement

Authors’ information

Consortium members

Stephan Beck1, 2, 3, Alison M Berner1, Graham Bignell4, Maggie Bond4, Martin J Callanan4, Olga Chervova1, Lucia Conde5, Manuel Corpas4, 6, Simone Ecker1, Hannah R Elliott7, 8, Silvana A Fioramonti1, Adrienne M Flanagan9, Ricarda Gaentzsch10, David Graham11, Deirdre Gribbin4, José Afonso Guerra-Assunção5, Rifat Hamoudi12, 13, Vincent Harding14, Paul L Harrison15, Javier Herrero5, Jana Hofmann16, Erica Jones4, Saif Khan12, Jane Kaye17, 18, Polly Kerr19, Emanuele Libertini1, Lauren Marks20, Laura McCormack21, Ismail Moghul1, Nikolas Pontikos4, Sharmini Rajanayagam22, Kirti Rana5, Momodou Semega-Janneh4, Colin P Smith4, 23, Louise Strom24, Sevgi Umur1, Amy P Webster1, Elizabeth H Williams10, Karen Wint4, John N Wood4,25.

Affiliations

1Medical Genomics, UCL Cancer Institute, London WC1E 6BT, UK.

2Institute of Digital Health, University College London, London WC1E 6BT, UK.

3Institute for Precision Medicine, University College London, London WC1E 6BT, UK.

4UK Citizen.

5Bill Lyons Informatics Centre, UCL Cancer Institute, London WC1E 6BT, UK.

6Cambridge Precision Medicine Ltd., Future Business Centre, King’s Hedges Road, Cambridge CB4 2HY, UK.

7MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK.

8Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1TH, UK.

9Head of Pathology, UCL Cancer Institute, London WC1E 6BT, UK.

10Seven Bridges Genomics Inc., 1 Main St, 5th Floor, Suite 500, Cambridge MA 02142, USA.

11University College London Hospital, 235 Euston Road, London, NW1 2BU, UK.

12Division of Surgery and Interventional Science, University College London, London WC1E 6BT, UK.

13Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, UAE.

14UCL Health Creatives, 30 Guilford Street, London WC1N 1EH, UK.

15Visual Research Centre, Duncan of Jordanstone College of Art and Design, University of Dundee DD1 4DY, UK.

16Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, DE.

17Centre for Health, Law and Emerging Technologies (HeLEX), Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK.

18Melbourne Law School, University of Melbourne, 185 Pelham Street, Carlton Victoria 3053, Australia.

19NIHR Oxford Biomedical Research Centre, The Churchill Hospital, Oxford OX3 7LE, UK.

20Division of Biosciences, University College London, London WC1E 6BT, UK.

21Permanent UK Resident.

22The Royal Australian College of General Practitioners, 100 Wellington Parade, East Melbourne, VIC 3002, AU.

23School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, BN2 4GJ, UK.

24Arnold & Porter Kaye Scholer LLP, London WC2B 5PQ, UK.

25Molecular Nociception Group, WIBR, University College London, London WC1E 6BT, UK.

Project coordination

Stephan Beck, Olga Chervova, Lucia Conde, José Afonso Guerra-Assunção, Rifat Hamoudi, Paul L Harrison, Javier Herrero, Erica Jones, Jane Kaye, Ismail Moghul, Amy P Webster.

IT systems

Olga Chervova, Ricarda Gaentzsch, Javier Herrero, Rifat Hamoudi, Vincent Harding, Ismail Moghul, Sevgi Umur, Elizabeth H Williams.

Data Analysis

Lucia Conde, Simone Ecker, Silvana A Fioramonti, José Afonso Guerra-Assunção, Rifat Hamoudi, Javier Herrero, Emanuele Libertini, Ismail Moghul, Nikolas Pontikos, Kirti Rana, Amy P Webster.

Support

Alison M Berner, Hannah R Elliott, Adrienne M Flanagan, David Graham, Jana Hofmann, Saif Khan, Polly Kerr, Lauren Marks, Sharmini Rajanayagam, Louise Strom.

Citizen science

Graham Bignell, Maggie Bond, Martin J Callanan, Manuel Corpas, Deirdre Gribbin, Laura McCormack, Nikolas Pontikos, Momodou Semega-Janneh, Colin P Smith, Karen Wint, John N Wood.

Manuscript

Stephan Beck wrote the manuscript with contributions from all authors. All authors have approved the manuscript. Corresponding author: Stephan Beck (s.beck@ucl.ac.uk).

Links

PGP-UK: https://www.personalgenomes.org.uk/

PGP-UK Data: https://www.personalgenomes.org.uk/data/

GenoME app: https://itunes.apple.com/gb/app/genome/id1358680703?mt=8

Global PGP Network: https://www.personalgenomes.org.uk/global-network

Open Humans: https://www.openhumans.org/

DNA.Land https://dna.land/

EBI: http://www.ebi.ac.uk/

Ensembl Glossary: https://www.ensembl.org/Help/Glossary?id=535

Repositive: https://discover.repositive.io/collections/

Seven Bridges Genomics: https://www.sevenbridges.com/

PGP-UK data in Seven Bridges Genomics cloud:

https://docs.cancergenomicscloud.org/docs/personal-genome-project-uk-pgp-uk-pilot-dataset

1000 Genomes Project: www.internationalgenome.org/

SNPedia: www.snpedia.com/

ExAC: http://exac.broadinstitute.org/

gnomAD: http://gnomad.broadinstitute.org/.

GetEvidence: http://evidence.pgp-hms.org/

ClinVar: www.ncbi.nlm.nih.gov/clinvar/

PGP-UK social media:

Twitter: www.twitter.com/PGPUK_genomes

Facebook: www.facebook.com/PGPUK/

YouTube: www.youtube.com/channel/UCosCFqd5LftftvYX8bD_Q0g

Blog: www.pgpukblog.wordpress.com

Ethics approval and consent to participate

The research conformed to the requirements of the Declaration of Helsinki, UK national laws and to UK regulatory requirements for medical research. All participants were informed, consented, subjected to an online entrance exam and enrolled as described on the PGP-UK sign-up web site (www.personalgenomes.org.uk/sign-up). The study was approved by the UCL Research Ethics Committee (ID Number 4700/001) and is subject to annual reviews and renewals. PGP-UK participants uk35C650, uk33D02F, uk481F67 and uk4CA868 all self-identified and consented for their names, photos, videos and data to be used in the manuscript and GenoME app.

Consent for publication

All authors have approved the manuscript for publication. In addition, PGP-UK participant uk35C650 has self-identified and consented for his photo to be used.

Competing interests

All authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Venn diagram of private SNVs from the 10 PGP-UK pilot participants. Only coding SNVs were selected for effect prediction using the four orthogonal prediction methods indicated. See Abbreviations section for description of acronyms
Fig. 2
Fig. 2
Time series (a-c) of screens showing how GenoME communicates genetic SNVs associated with the participant’s eye colour. PGP-UK participant uk35C650 self-identified and consented for his photos to be used
Fig. 3
Fig. 3
Time series (a-c) of screens showing how GenoME communicates epigenetic SNVs associated with the participant’s smoking status. PGP-UK participant uk35C650 self-identified and consented for his photos to be used
See this image and copyright information in PMC

References

    1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921. doi: 10.1038/35057062. - DOI - PubMed
    1. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, et al. The sequence of the human genome. Science. 2001;291:1304–1351. doi: 10.1126/science.1058040. - DOI - PubMed
    1. Stephens ZD, Lee SY, Faghri F, Campbell RH, Zhai C, Efron MJ, Iyer R, Schatz MC, Sinha S, Robinson GE. Big Data: Astronomical or Genomical? PLoS Biol. 2015;13:e1002195. doi: 10.1371/journal.pbio.1002195. - DOI - PMC - PubMed
    1. Peplow M. The 100,000 genomes project. BMJ. 2016;353:i1757. doi: 10.1136/bmj.i1757. - DOI - PubMed
    1. Collins FS, Varmus H. A new initiative on precision medicine. N Engl J Med. 2015;372:793–795. doi: 10.1056/NEJMp1500523. - DOI - PMC - PubMed

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