Mutagenesis in Medicine
Early Cancer Institute, University of Cambridge
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Dr. Helen Davies

Senior Research Associate

Helen is a molecular biologist by training with over 25 years of experience in human genetics. She completed her PhD on the Molecular Genetics of Androgen Insensitivity Syndrome at the University of Cambridge in 1996. After a period working for a genomics start-up company, she joined the Cancer Genome Project based at the Wellcome Sanger Institute in 2000. During her 18 years at the Sanger Institute, Helen’s research involved the identification of novel cancer genes including BRAF and UTX and the cataloguing of driver mutations and genome wide genetic changes in a number of tumour types, most notably breast cancer.

Helen began working with Serena Nik-Zainal whilst at the Sanger Institute, working together on the ICGC breast cancer project. She went on to join Serena’s team at the University of Cambridge in 2018.

Working closely with the bioinformaticians in the team, Helen specialises in the biological interpretation of cancer whole genome sequencing data and the investigation of the clinical utility of mutational signatures.

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Published Works

  • Chopra, N., Tovey, H., Pearson, A., Cutts, R., Toms, C., Proszek, P., Hubank, M., Dowsett, M., Dodson, A., Daley, F., Kriplani, D., Gevensleben, H., Davies, H. R., Degasperi, A., Roylance, R., Chan, S., Tutt, A., Skene, A., Evans, A., Bliss, J. M., … Turner, N. C. (2020). Homologous recombination DNA repair deficiency and PARP inhibition activity in primary triple negative breast cancer. Nature communications, 11(1), 2662. https://doi.org/10.1038/s41467-020-16142-7
  • Degasperi, A., Amarante, T. D., Czarnecki, J., Shooter, S., Zou, X., Glodzik, D., Morganella, S., Nanda, A. S., Badja, C., Koh, G., Momen, S. E., Georgakopoulos-Soares, I., Dias, J. M. L., Young, J., Memari, Y., Davies, H., & Nik-Zainal, S. (2020). A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies. Nature cancer, 1(2), 249–263. https://doi.org/10.1038/s43018-020-0027-5
  • ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020). Pan-cancer analysis of whole genomes. Nature, 578(7793), 82–93. https://doi.org/10.1038/s41586-020-1969-6
  • Nik-Zainal, S., Memari, Y., & Davies, H. R. (2020). Holistic cancer genome profiling for every patient. Swiss medical weekly, 150, w20158. https://doi.org/10.4414/smw.2020.20158
  • Davies, H. R., Hodgson, K., Schwalbe, E., Coxhead, J., Sinclair, N., Zou, X., Cockell, S., Husain, A., Nik-Zainal, S., & Rajan, N. (2019). Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome. Nature communications, 10(1), 4717. https://doi.org/10.1038/s41467-019-12746-w
  • Momen, S., Fassihi, H., Davies, H. R., Nikolaou, C., Degasperi, A., Stefanato, C. M., Dias, J. M. L., Dasgupta, D., Craythorne, E., Sarkany, R., Papa, S., & Nik-Zainal, S. (2019). Dramatic response of metastatic cutaneous angiosarcoma to an immune checkpoint inhibitor in a patient with xeroderma pigmentosum: whole-genome sequencing aids treatment decision in end-stage disease. Cold Spring Harbor molecular case studies, 5(5), a004408. https://doi.org/10.1101/mcs.a004408
  • Staaf, J., Glodzik, D., Bosch, A., Vallon-Christersson, J., Reuterswärd, C., Häkkinen, J., Degasperi, A., Amarante, T. D., Saal, L. H., Hegardt, C., Stobart, H., Ehinger, A., Larsson, C., Rydén, L., Loman, N., Malmberg, M., Kvist, A., Ehrencrona, H., Davies, H. R., Borg, Å., … Nik-Zainal, S. (2019). Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study. Nature medicine, 25(10), 1526–1533. https://doi.org/10.1038/s41591-019-0582-4
  • Maura, F., Degasperi, A., Nadeu, F., Leongamornlert, D., Davies, H., Moore, L., Royo, R., Ziccheddu, B., Puente, X. S., Avet-Loiseau, H., Campbell, P. J., Nik-Zainal, S., Campo, E., Munshi, N., & Bolli, N. (2019). A practical guide for mutational signature analysis in hematological malignancies. Nature communications, 10(1), 2969. https://doi.org/10.1038/s41467-019-11037-8
  • Brinkman, A. B., Nik-Zainal, S., Simmer, F., Rodríguez-González, F. G., Smid, M., Alexandrov, L. B., Butler, A., Martin, S., Davies, H., Glodzik, D., Zou, X., Ramakrishna, M., Staaf, J., Ringnér, M., Sieuwerts, A., Ferrari, A., Morganella, S., Fleischer, T., Kristensen, V., Gut, M., … Stunnenberg, H. G. (2019). Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation. Nature communications, 10(1), 1749. https://doi.org/10.1038/s41467-019-09828-0
  • Smid, M., Wilting, S. M., Uhr, K., Rodríguez-González, F. G., de Weerd, V., Prager-Van der Smissen, W. J. C., van der Vlugt-Daane, M., van Galen, A., Nik-Zainal, S., Butler, A., Martin, S., Davies, H. R., Staaf, J., van de Vijver, M. J., Richardson, A. L., MacGrogan, G., Salgado, R., van den Eynden, G. G. G. M., Purdie, C. A., Thompson, A. M., … Martens, J. W. M. (2019). The circular RNome of primary breast cancer. Genome research, 29(3), 356–366. https://doi.org/10.1101/gr.238121.118
  • Zou, X., Morganella, S., Glodzik, D., Davies, H., Li, Y., Stratton, M. R., & Nik-Zainal, S. (2017). Short inverted repeats contribute to localized mutability in human somatic cells. Nucleic acids research, 45(19), 11213–11221. https://doi.org/10.1093/nar/gkx731
  • Davies, H., Morganella, S., Purdie, C. A., Jang, S. J., Borgen, E., Russnes, H., Glodzik, D., Zou, X., Viari, A., Richardson, A. L., Børresen-Dale, A. L., Thompson, A., Eyfjord, J. E., Kong, G., Stratton, M. R., & Nik-Zainal, S. (2017). Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency. Cancer research, 77(18), 4755–4762. https://doi.org/10.1158/0008-5472.CAN-17-1083
  • Ju, Y. S., Martincorena, I., Gerstung, M., Petljak, M., Alexandrov, L. B., Rahbari, R., Wedge, D. C., Davies, H. R., Ramakrishna, M., Fullam, A., Martin, S., Alder, C., Patel, N., Gamble, S., O'Meara, S., Giri, D. D., Sauer, T., Pinder, S. E., Purdie, C. A., Borg, Å., … Stratton, M. R. (2017). Somatic mutations reveal asymmetric cellular dynamics in the early human embryo. Nature, 543(7647), 714–718. https://doi.org/10.1038/nature21703
  • Davies, H., Glodzik, D., Morganella, S., Yates, L. R., Staaf, J., Zou, X., Ramakrishna, M., Martin, S., Boyault, S., Sieuwerts, A. M., Simpson, P. T., King, T. A., Raine, K., Eyfjord, J. E., Kong, G., Borg, Å., Birney, E., Stunnenberg, H. G., van de Vijver, M. J., Børresen-Dale, A. L., … Nik-Zainal, S. (2017). HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures. Nature medicine, 23(4), 517–525. https://doi.org/10.1038/nm.4292
  • Glodzik, D., Morganella, S., Davies, H., Simpson, P. T., Li, Y., Zou, X., Diez-Perez, J., Staaf, J., Alexandrov, L. B., Smid, M., Brinkman, A. B., Rye, I. H., Russnes, H., Raine, K., Purdie, C. A., Lakhani, S. R., Thompson, A. M., Birney, E., Stunnenberg, H. G., van de Vijver, M. J., … Nik-Zainal, S. (2017). A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers. Nature genetics, 49(3), 341–348. https://doi.org/10.1038/ng.3771
  • Jones, D., Raine, K. M., Davies, H., Tarpey, P. S., Butler, A. P., Teague, J. W., Nik-Zainal, S., & Campbell, P. J. (2016). cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data. Current protocols in bioinformatics, 56, 15.10.1–15.10.18. https://doi.org/10.1002/cpbi.20
  • Smid, M., Rodríguez-González, F. G., Sieuwerts, A. M., Salgado, R., Prager-Van der Smissen, W. J., Vlugt-Daane, M. V., van Galen, A., Nik-Zainal, S., Staaf, J., Brinkman, A. B., van de Vijver, M. J., Richardson, A. L., Fatima, A., Berentsen, K., Butler, A., Martin, S., Davies, H. R., Debets, R., Gelder, M. E., van Deurzen, C. H., … Martens, J. W. (2016). Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration. Nature communications, 7, 12910. https://doi.org/10.1038/ncomms12910
  • Behjati, S., Gundem, G., Wedge, D. C., Roberts, N. D., Tarpey, P. S., Cooke, S. L., Van Loo, P., Alexandrov, L. B., Ramakrishna, M., Davies, H., Nik-Zainal, S., Hardy, C., Latimer, C., Raine, K. M., Stebbings, L., Menzies, A., Jones, D., Shepherd, R., Butler, A. P., Teague, J. W., … Campbell, P. J. (2016). Mutational signatures of ionizing radiation in second malignancies. Nature communications, 7, 12605. https://doi.org/10.1038/ncomms12605
  • Shlien, A., Raine, K., Fuligni, F., Arnold, R., Nik-Zainal, S., Dronov, S., Mamanova, L., Rosic, A., Ju, Y. S., Cooke, S. L., Ramakrishna, M., Papaemmanuil, E., Davies, H. R., Tarpey, P. S., Van Loo, P., Wedge, D. C., Jones, D. R., Martin, S., Marshall, J., Anderson, E., … Campbell, P. J. (2016). Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer. Cell reports, 16(7), 2032–2046. https://doi.org/10.1016/j.celrep.2016.07.028
  • Morganella, S., Alexandrov, L. B., Glodzik, D., Zou, X., Davies, H., Staaf, J., Sieuwerts, A. M., Brinkman, A. B., Martin, S., Ramakrishna, M., Butler, A., Kim, H. Y., Borg, Å., Sotiriou, C., Futreal, P. A., Campbell, P. J., Span, P. N., Van Laere, S., Lakhani, S. R., Eyfjord, J. E., … Nik-Zainal, S. (2016). The topography of mutational processes in breast cancer genomes. Nature communications, 7, 11383. https://doi.org/10.1038/ncomms11383
  • Nik-Zainal, S., Davies, H., Staaf, J., Ramakrishna, M., Glodzik, D., Zou, X., Martincorena, I., Alexandrov, L. B., Martin, S., Wedge, D. C., Van Loo, P., Ju, Y. S., Smid, M., Brinkman, A. B., Morganella, S., Aure, M. R., Lingjærde, O. C., Langerød, A., Ringnér, M., Ahn, S. M., … Stratton, M. R. (2016). Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature, 534(7605), 47–54. https://doi.org/10.1038/nature17676
  • Raine, K. M., Hinton, J., Butler, A. P., Teague, J. W., Davies, H., Tarpey, P., Nik-Zainal, S., & Campbell, P. J. (2015). cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing. Current protocols in bioinformatics, 52, 15.7.1–15.7.12. https://doi.org/10.1002/0471250953.bi1507s52
  • Menzies, A., Teague, J. W., Butler, A. P., Davies, H., Tarpey, P., Nik-Zainal, S., & Campbell, P. J. (2015). VAGrENT: Variation Annotation Generator. Current protocols in bioinformatics, 52, 15.8.1–15.8.11. https://doi.org/10.1002/0471250953.bi1508s52
  • Yates, L. R., Gerstung, M., Knappskog, S., Desmedt, C., Gundem, G., Van Loo, P., Aas, T., Alexandrov, L. B., Larsimont, D., Davies, H., Li, Y., Ju, Y. S., Ramakrishna, M., Haugland, H. K., Lilleng, P. K., Nik-Zainal, S., McLaren, S., Butler, A., Martin, S., Glodzik, D., … Campbell, P. J. (2015). Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nature medicine, 21(7), 751–759. https://doi.org/10.1038/nm.3886
  • Ju, Y. S., Tubio, J. M., Mifsud, W., Fu, B., Davies, H. R., Ramakrishna, M., Li, Y., Yates, L., Gundem, G., Tarpey, P. S., Behjati, S., Papaemmanuil, E., Martin, S., Fullam, A., Gerstung, M., ICGC Prostate Cancer Working Group, ICGC Bone Cancer Working Group, ICGC Breast Cancer Working Group, Nangalia, J., Green, A. R., … Stratton, M. R. (2015). Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells. Genome research, 25(6), 814–824. https://doi.org/10.1101/gr.190470.115
  • Ju, Y. S., Alexandrov, L. B., Gerstung, M., Martincorena, I., Nik-Zainal, S., Ramakrishna, M., Davies, H. R., Papaemmanuil, E., Gundem, G., Shlien, A., Bolli, N., Behjati, S., Tarpey, P. S., Nangalia, J., Massie, C. E., Butler, A. P., Teague, J. W., Vassiliou, G. S., Green, A. R., Du, M. Q., … Campbell, P. J. (2014). Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer. eLife, 3, e02935. https://doi.org/10.7554/eLife.02935
  • Tubio, J. M. C., Li, Y., Ju, Y. S., Martincorena, I., Cooke, S. L., Tojo, M., Gundem, G., Pipinikas, C. P., Zamora, J., Raine, K., Menzies, A., Roman-Garcia, P., Fullam, A., Gerstung, M., Shlien, A., Tarpey, P. S., Papaemmanuil, E., Knappskog, S., Van Loo, P., Ramakrishna, M., … ICGC Prostate Cancer Group (2014). Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science (New York, N.Y.), 345(6196), 1251343. https://doi.org/10.1126/science.1251343
  • Nik-Zainal, S., Wedge, D. C., Alexandrov, L. B., Petljak, M., Butler, A. P., Bolli, N., Davies, H. R., Knappskog, S., Martin, S., Papaemmanuil, E., Ramakrishna, M., Shlien, A., Simonic, I., Xue, Y., Tyler-Smith, C., Campbell, P. J., & Stratton, M. R. (2014). Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer. Nature genetics, 46(5), 487–491. https://doi.org/10.1038/ng.2955
  • Cooke, S. L., Shlien, A., Marshall, J., Pipinikas, C. P., Martincorena, I., Tubio, J. M., Li, Y., Menzies, A., Mudie, L., Ramakrishna, M., Yates, L., Davies, H., Bolli, N., Bignell, G. R., Tarpey, P. S., Behjati, S., Nik-Zainal, S., Papaemmanuil, E., Teixeira, V. H., Raine, K., … ICGC Breast Cancer Group (2014). Processed pseudogenes acquired somatically during cancer development. Nature communications, 5, 3644. https://doi.org/10.1038/ncomms4644
  • Behjati, S., Tarpey, P. S., Presneau, N., Scheipl, S., Pillay, N., Van Loo, P., Wedge, D. C., Cooke, S. L., Gundem, G., Davies, H., Nik-Zainal, S., Martin, S., McLaren, S., Goodie, V., Robinson, B., Butler, A., Teague, J. W., Halai, D., Khatri, B., Myklebost, O., … Flanagan, A. M. (2013). Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone. Nature genetics, 45(12), 1479–1482. https://doi.org/10.1038/ng.2814
  • Alexandrov, L. B., Nik-Zainal, S., Wedge, D. C., Aparicio, S. A., Behjati, S., Biankin, A. V., Bignell, G. R., Bolli, N., Borg, A., Børresen-Dale, A. L., Boyault, S., Burkhardt, B., Butler, A. P., Caldas, C., Davies, H. R., Desmedt, C., Eils, R., Eyfjörd, J. E., Foekens, J. A., Greaves, M., … Stratton, M. R. (2013). Signatures of mutational processes in human cancer. Nature, 500(7463), 415–421. https://doi.org/10.1038/nature12477
  • Stephens, P. J., Davies, H. R., Mitani, Y., Van Loo, P., Shlien, A., Tarpey, P. S., Papaemmanuil, E., Cheverton, A., Bignell, G. R., Butler, A. P., Gamble, J., Gamble, S., Hardy, C., Hinton, J., Jia, M., Jayakumar, A., Jones, D., Latimer, C., McLaren, S., McBride, D. J., … Futreal, P. A. (2013). Whole exome sequencing of adenoid cystic carcinoma. The Journal of clinical investigation, 123(7), 2965–2968. https://doi.org/10.1172/JCI67201
  • Tarpey, P. S., Behjati, S., Cooke, S. L., Van Loo, P., Wedge, D. C., Pillay, N., Marshall, J., O'Meara, S., Davies, H., Nik-Zainal, S., Beare, D., Butler, A., Gamble, J., Hardy, C., Hinton, J., Jia, M. M., Jayakumar, A., Jones, D., Latimer, C., Maddison, M., … Futreal, P. A. (2013). Frequent mutation of the major cartilage collagen gene COL2A1 in chondrosarcoma. Nature genetics, 45(8), 923–926. https://doi.org/10.1038/ng.2668
  • Nik-Zainal, S., Van Loo, P., Wedge, D. C., Alexandrov, L. B., Greenman, C. D., Lau, K. W., Raine, K., Jones, D., Marshall, J., Ramakrishna, M., Shlien, A., Cooke, S. L., Hinton, J., Menzies, A., Stebbings, L. A., Leroy, C., Jia, M., Rance, R., Mudie, L. J., Gamble, S. J., … Breast Cancer Working Group of the International Cancer Genome Consortium (2012). The life history of 21 breast cancers. Cell, 149(5), 994–1007. https://doi.org/10.1016/j.cell.2012.04.023
  • Stephens, P. J., Tarpey, P. S., Davies, H., Van Loo, P., Greenman, C., Wedge, D. C., Nik-Zainal, S., Martin, S., Varela, I., Bignell, G. R., Yates, L. R., Papaemmanuil, E., Beare, D., Butler, A., Cheverton, A., Gamble, J., Hinton, J., Jia, M., Jayakumar, A., Jones, D., … Stratton, M. R. (2012). The landscape of cancer genes and mutational processes in breast cancer. Nature, 486(7403), 400–404. https://doi.org/10.1038/nature11017
  • Papaemmanuil, E., Cazzola, M., Boultwood, J., Malcovati, L., Vyas, P., Bowen, D., Pellagatti, A., Wainscoat, J. S., Hellstrom-Lindberg, E., Gambacorti-Passerini, C., Godfrey, A. L., Rapado, I., Cvejic, A., Rance, R., McGee, C., Ellis, P., Mudie, L. J., Stephens, P. J., McLaren, S., Massie, C. E., … Chronic Myeloid Disorders Working Group of the International Cancer Genome Consortium (2011). Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. The New England journal of medicine, 365(15), 1384–1395. https://doi.org/10.1056/NEJMoa1103283
  • van Haaften, G., Dalgliesh, G. L., Davies, H., Chen, L., Bignell, G., Greenman, C., Edkins, S., Hardy, C., O'Meara, S., Teague, J., Butler, A., Hinton, J., Latimer, C., Andrews, J., Barthorpe, S., Beare, D., Buck, G., Campbell, P. J., Cole, J., Forbes, S., … Futreal, P. A. (2009). Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer. Nature genetics, 41(5), 521–523. https://doi.org/10.1038/ng.349
  • Davies, H., Bignell, G. R., Cox, C., Stephens, P., Edkins, S., Clegg, S., Teague, J., Woffendin, H., Garnett, M. J., Bottomley, W., Davis, N., Dicks, E., Ewing, R., Floyd, Y., Gray, K., Hall, S., Hawes, R., Hughes, J., Kosmidou, V., Menzies, A., … Futreal, P. A. (2002). Mutations of the BRAF gene in human cancer. Nature, 417(6892), 949–954. https://doi.org/10.1038/nature00766

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Prof. Serena Nik-Zainal
Early Cancer Institute
University of Cambridge
Hutchison Research Centre
Box 197
Cambridge Biomedical Campus
Cambridge
United Kingdom
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sn206@cam.ac.uk