Abstract

Improved sequencing technologies offer unprecedented opportunities for investigating the role of rare genetic variation in common disease. However, there are considerable challenges with respect to study design, data analysis and replication1. Using pooled next-generation sequencing of 507 genes implicated in the repair of DNA in 1,150 samples, an analytical strategy focused on protein-truncating variants (PTVs) and a large-scale sequencing case–control replication experiment in 13,642 individuals, here we show that rare PTVs in the p53-inducible protein phosphatase PPM1D are associated with predisposition to breast cancer and ovarian cancer. PPM1D PTV mutations were present in 25 out of 7,781 cases versus 1 out of 5,861 controls (P = 1.12 × 10−5), including 18 mutations in 6,912 individuals with breast cancer (P = 2.42 × 10−4) and 12 mutations in 1,121 individuals with ovarian cancer (P = 3.10 × 10−9). Notably, all of the identified PPM1D PTVs were mosaic in lymphocyte DNA and clustered within a 370-base-pair region in the final exon of the gene, carboxy-terminal to the phosphatase catalytic domain. Functional studies demonstrate that the mutations result in enhanced suppression of p53 in response to ionizing radiation exposure, suggesting that the mutant alleles encode hyperactive PPM1D isoforms. Thus, although the mutations cause premature protein truncation, they do not result in the simple loss-of-function effect typically associated with this class of variant, but instead probably have a gain-of-function effect. Our results have implications for the detection and management of breast and ovarian cancer risk. More generally, these data provide new insights into the role of rare and of mosaic genetic variants in common conditions, and the use of sequencing in their identification.

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Acknowledgements

We thank all the subjects and families that participated in the research and D. Dudakia, J. Bull and R. Linger for their assistance in recruitment. We are indebted to M. Stratton for discussions of the data and to A. Strydom for editorial assistance. We thank the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics, Oxford (funded by Wellcome Trust grant reference 090532/Z/09/Z and Medical Research Council (MRC) Hub grant G0900747 91070) for the generation of the phase 1 sequencing data. This work was funded by the Institute of Cancer Research, The Wellcome Trust, Cancer Research UK and Breakthrough Breast Cancer. We acknowledge support by the RMH-ICR National Institute for Health Research (NIHR) Specialist Biomedical Research Centre for Cancer. We acknowledge the use of DNA from the British 1958 Birth Cohort collection funded by the MRC grant G0000934 and the Wellcome Trust grant 068545/Z/02. A.C.A. is a Cancer Research UK Senior Cancer Research Fellow (C12292/A11174). P.Do. is supported by a Wolfson-Royal Society Merit Award. K.S. is supported by the Michael and Betty Kadoorie Cancer Genetics Research Programme.

Author information

Author notes

    • Elise Ruark
    • , Katie Snape
    •  & Peter Humburg

    These authors contributed equally to this work.

Affiliations

  1. Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton SM2 5NG, UK

    • Elise Ruark
    • , Katie Snape
    • , Chey Loveday
    • , Anthony Renwick
    • , Sheila Seal
    • , Emma Ramsay
    • , Silvana Del Vecchio Duarte
    • , Margaret Warren-Perry
    • , Anna Zachariou
    • , Sandra Hanks
    • , Anne Murray
    • , Naser Ansari Pour
    • , Jenny Douglas
    • , Richard Houlston
    • , Clare Turnbull
    •  & Nazneen Rahman
  2. The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK

    • Peter Humburg
    • , Manuel A. Rivas
    • , Lorna Gregory
    • , Andrew Rimmer
    • , Mark I. McCarthy
    •  & Peter Donnelly
  3. The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK

    • Ilirjana Bajrami
    • , Rachel Brough
    • , Daniel Nava Rodrigues
    • , Adriana Campion-Flora
    • , Jorge S. Reis-Filho
    • , Alan Ashworth
    •  & Christopher J. Lord
  4. Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK

    • Rachel Brough
  5. Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7LD, UK

    • Manuel A. Rivas
  6. Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0XY, UK

    • Neil M. Walker
    •  & John A. Todd
  7. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

    • Tsun-Po Yang
    •  & Panagiotis Deloukas
  8. Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds LS7 4SA, UK

    • Julian W. Adlard
  9. Leicestershire Genetics Centre, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK

    • Julian Barwell
  10. Human Genetics, Division of Medical Sciences, University of Dundee, Dundee DD1 9SY, UK

    • Jonathan Berg
  11. NW Thames Regional Genetics Service, Kennedy Galton Centre, London HA1 3UJ, UK

    • Angela F. Brady
  12. Peninsula Regional Genetics Service, Royal Devon & Exeter Hospital, Exeter EX1 2ED, UK

    • Carole Brewer
  13. SW Thames Regional Genetics Service, St George’s Hospital, London SW17 0RE, UK

    • Glen Brice
  14. West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham B15 2TG, UK

    • Cyril Chapman
  15. Sheffield Regional Genetics Service, Sheffield Children’s NHS Foundation Trust, Sheffield S10 2TH, UK

    • Jackie Cook
  16. West of Scotland Regional Genetics Service, Laboratory Medicine, Southern General Hospital, Glasgow G51 4TF, UK

    • Rosemarie Davidson
  17. South Western Regional Genetics Service, University Hospitals of Bristol NHS Foundation Trust, Bristol BS2 8EG, UK

    • Alan Donaldson
  18. Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle NE1 3BZ, UK

    • Fiona Douglas
    •  & Alex Henderson
  19. Faculty of Medicine, University of Southampton, Southampton University Hospitals NHS Trust, Southampton SO16 5YA, UK

    • Diana Eccles
  20. Genetic Medicine, Manchester Academic Health Science Centre, St Mary’s Hospital, Manchester M13 9WL, UK

    • D. Gareth Evans
  21. Merseyside and Cheshire Clinical Genetics Service, Liverpool Women’s NHS Foundation Trust, Liverpool L8 7SS, UK

    • Lynn Greenhalgh
  22. SE Thames Regional Genetics Service, Guy’s and St Thomas NHS Foundation Trust, London SE1 9RT, UK

    • Louise Izatt
  23. NE Thames Regional Genetics Service, Great Ormond St Hospital, London WC1N 3JH, UK

    • Ajith Kumar
  24. University Department of Medical Genetics & Regional Genetics Service, St Mary’s Hospital, Manchester M13 9WL, UK

    • Fiona Lalloo
  25. University of Aberdeen and North of Scotland Clinical Genetics Service, Aberdeen Royal Infirmary, Aberdeen AB25 2ZA, UK

    • Zosia Miedzybrodzka
  26. Northern Ireland Regional Genetics Service, Belfast HSC Trust, Department of Medical Genetics, Queen’s University Belfast, Belfast BT9 7AB, UK

    • Patrick J. Morrison
  27. East Anglian Regional Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK

    • Joan Paterson
  28. South East of Scotland Clinical Genetics Service, Western General Hospital, Edinburgh EH4 2XU, UK

    • Mary Porteous
  29. All Wales Medical Genetics Service, University Hospital of Wales, Cardiff CF14 4XW, UK

    • Mark T. Rogers
  30. Department of Cancer Genetics, Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK

    • Susan Shanley
    • , Clare Turnbull
    •  & Nazneen Rahman
  31. Oxford Regional Genetics Service, Oxford University Hospitals NHS Trust, Oxford OX3 7LJ, UK

    • Lisa Walker
  32. Department of Gynaecologic Oncology, Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK

    • Martin Gore
  33. University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane 4102, Australia

    • Matthew A. Brown
  34. Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK

    • Mark J. Caufield
  35. Oxford Centre for Diabetes, Endocrinology and Medicine, University of Oxford, Churchill Hospital, Oxford OX3 7LI, UK

    • Mark I. McCarthy
  36. Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford OX3 7LI, UK

    • Mark I. McCarthy
  37. Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK

    • Antonis C. Antoniou
  38. Department of Statistics, University of Oxford, Oxford OX1 3TG, UK

    • Peter Donnelly

Consortia

  1. The Breast and Ovarian Cancer Susceptibility Collaboration

    Lists of participants and their affiliations appear in the Supplementary Information.

  2. Wellcome Trust Case Control Consortium

    Lists of participants and their affiliations appear in the Supplementary Information.

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Contributions

E.R., K.S., P.H., N.M.W., T.-P.Y., M.A.B., M.J.C., C.T., J.T., M.I.M., P.De., P.Do. and N.R. (chair) are the Wellcome Trust Case Control Consortium (WTCCC) exon-resequencing group who devised and funded phase 1. J.W.A., J.Ba., J.Be., A.F.B., C.B., G.B., C.C., J.C., R.D., A.D., F.D., D.E., D.G.E., L.G., A.H., L.I., A.K., F.L., Z.M., P.J.M., J.P., M.P., M.T.R., S.Sh., L.W. and N.R. are centre leads of the Breast and Ovarian Cancer Susceptibility Collaboration (BOCS), which is coordinated by M.W.-P. and A.Z. A full list of the WTCCC and BOCS consortia is in the Supplementary Information. R.H. and M.G. assembled the unselected ovarian cancer series. L.G. coordinated phase 1 sequencing. P.H., M.R. and P.Do. undertook analysis of the pooled DNA repair panel. J.D., A.M., S.Se., S.H. and E.R. undertook NGS sequencing and analysis. S.Se. E.R., S.D.V.S., N.A.P., A.Re., K.S., C.L. and J.D. undertook Sanger sequencing, MLPA and tumour microsatellite analysis. E.R. undertook sample selection and data analyses with C.T. A.C.A. wrote the risk analysis software and oversaw the penetrance analysis that was performed by E.R. A.Ri. provided and optimized Platypus. D.N.R., A.C.-F. and J.S.R.-F. undertook histopathological analyses and performed microdissections. I.B., R.B., C.J.L. and A.A. undertook functional analyses. E.R., K.S. and N.R. managed and oversaw all aspects of the study and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Nazneen Rahman.

Supplementary information

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    Supplementary Information

    This file contains Supplementary Figures 1-8 and details of the WTCCC and BOCS consortia.

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  1. 1.

    Supplementary Tables

    This file contains Supplementary Tables 1-8.

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https://doi.org/10.1038/nature11725

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