David Wedge

David Wedge, BA, PGCE, MSc, PhD

Professor of Cancer Genomics and Data Science

 https://orcid.org/0000-0002-7572-3196

Personal profile

Biography

The focus of my research is cancer evolution and heterogeneity. Cancers are made up of a heterogeneous mix of cells, each bearing a different set of mutations in its DNA. We aim to characterise groups of cells, or ‘subclones’, according to their mutational profiles and to study the interaction between subclones.

Tumours are difficult to treat because they change over time, gaining mutations that enable them to metastasise to distant organs or that result in resistance to treatment. By comparing multiple samples, we can identify those mutations that cause relapse and progression. Using genetic markers, we can also track the spread of disease, giving us insights into the mechanisms and processes involved in cancer growth and metastasis.

We have developed software packages for the purpose of studying tumour evolution and heterogeneity, including:

  • The Battenberg algorithm, which identifies clonal and subclonal copy number aberrations. The Battenberg package may be downloaded from here.
  • DPClust clusters mutations into subclones, identifying the Cancer Cell Fraction (CCF) and number of mutations within each subclones. DPClust may be downloaded from here.
  • Octopus, a mapping-based variant caller that calls single nucleotide variants (SNVs) and small insertions and deletions (indels) using a haplotype-aware framework. Octopus may be downloaded from here.

Job vacancies

We currently have no posts available. However, we regularly advertise posts on the University of Manchester Jobs pages.

https://www.jobs.manchester.ac.uk/Home/Job

 

My group

The Wedge lab is made up of a talented team of researchers. To find out more about the team and the projects that we're involved in, please look at the Wedge group website. 

Expertise related to UN Sustainable Development Goals

In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):

  • SDG 3 - Good Health and Well-being
  • SDG 9 - Industry, Innovation, and Infrastructure
  • SDG 10 - Reduced Inequalities

Areas of expertise

  • RC0254 Neoplasms. Tumors. Oncology (including Cancer)
  • QH426 Genetics
  • QA76 Computer software

Research Beacons, Institutes and Platforms

  • Cancer
  • Global inequalities
  • Digital Futures
  • Christabel Pankhurst Institute
  • Manchester Cancer Research Centre
  • Healthier Futures

Keywords

  • cancer genomics
  • tumour evolution
  • Computational Biology

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Collaborations and top research areas from the last five years

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  • An integrative multiparametric approach stratifies putative distinct phenotypes of blast phase chronic myelomonocytic leukemia

    Gurashi, K., Wang, Y.-H., Amaral, F. M. R., Spence, K., Cant, R., Yao, C.-Y., Lin, C.-C., Wirth, C., Wedge, D. C., Montalban-Bravo, G., Colla, S., Tien, H.-F., Somervaille, T. C. P., Batta, K. & Wiseman, D. H., 31 Jan 2025, (E-pub ahead of print) In: Cell reports. Medicine. 101933.

    Research output: Contribution to journal › Article › peer-review

    Open Access

  • APOBEC affects tumor evolution and age at onset of lung cancer in smokers

    Zhang, T., Sang, J., Hoang, P. H., Zhao, W., Rosenbaum, J., Johnson, K. E., Klimczak, L. J., McElderry, J., Klein, A., Wirth, C., Bergstrom, E. N., Díaz-Gay, M., Vangara, R., Colon-Matos, F., Hutchinson, A., Lawrence, S. M., Cole, N., Zhu, B., Przytycka, T. M. & Shi, J. & 11 others, Caporaso, N. E., Homer, R., Pesatori, A. C., Consonni, D., Imielinski, M., Chanock, S. J., Wedge, D. C., Gordenin, D. A., Alexandrov, L. B., Harris, R. S. & Landi, M. T., 21 May 2025, In: Nature Communications. 16, 1, p. 4711

    Research output: Contribution to journal › Article › peer-review

  • Causes of evolutionary divergence in prostate cancer

    Esentürk, E., Sahli, A., Haberland, V., Ziuboniewicz, A., Wirth, C., Bova, G. S., Bristow, R. G., Brook, M. N., Brors, B., Butler, A., Cancel-Tassin, G., Cheng, K. C., Cooper, C. S., Corcoran, N. M., Cussenot, O., Eeles, R. A., Favero, F., Gerhauser, C., Gihawi, A. & Girma, E. G. & 35 others, Gnanapragasam, V. J., Gruber, A. J., Hamid, A., Hayes, V. M., He, H. H., Hovens, C. M., Imada, E. L., Jakobsdottir, G. M., Jung, C.-H., Khani, F., Kote-Jarai, Z., Lamy, P., Leeman, G., Loda, M., Lutsik, P., Marchionni, L., Molania, R., Papenfuss, A. T., Pellegrina, D., Pope, B., Queiroz, L. R., Rausch, T., Reimand, J., Robinson, B., Schlomm, T., Sørensen, K. D., Uhrig, S., Weischenfeldt, J., Xu, Y., Yamaguchi, T. N., Zanettini, C., Lynch, A. G., Wedge, D. C., Brewer, D. S. & Woodcock, D. J., 17 Mar 2025, Cornell University, (arXiv).

    Research output: Preprint/Working paper › Preprint

  • Chromothripsis-associated chromosome 21 amplification orchestrates transformation to blast-phase MPN through targetable overexpression of DYRK1A

    Brierley, C. K., Yip, B. H., Orlando, G., Wen, J., Wen, S., Goyal, H., Levine, M., Jakobsdottir, G. M., Tapinos, A., Cornish, A. J., Rodriguez-Romera, A., Rodriguez-Meira, A., Bashton, M., Hamblin, A., Clark, S. A., Hamley, J. C., Fox, O., Giurgiu, M., O'Sullivan, J. & Murphy, L. & 21 others, Adamo, A., Olijnik, A. A., Cotton, A., Hendrix, E., Narina, S., Pruett-Miller, S. M., Enshaei, A., Harrison, C., Drummond, M., Knapper, S., Tefferi, A., Antony-Debré, I., Davies, J., Henssen, A. G., Thongjuea, S., Wedge, D. C., Constantinescu, S. N., Papaemmanuil, E., Psaila, B., Crispino, J. D. & Mead, A. J., Jun 2025, In: Nature Genetics. 57, 6, p. 1478-1492 15 p.

    Research output: Contribution to journal › Article › peer-review

  • Deciphering lung adenocarcinoma evolution and the role of LINE-1 retrotransposition

    Zhang, T., Zhao, W., Wirth, C., Díaz-Gay, M., Yin, J., Cecati, M., Marchegiani, F., Hoang, P. H., Leduc, C., Baine, M. K., Travis, W. D., Sholl, L. M., Joubert, P., Sang, J., McElderry, J. P., Klein, A., Khandekar, A., Hartman, C., Rosenbaum, J. & Colón-Matos, F. J. & 47 others, Miraftab, M., Saha, M., Lee, O. W., Jones, K. M., Caporaso, N. E., Wong, M. P., Leung, K. C., Agnes Hsiung, C., Chen, C.-Y., Edell, E. S., Martínez Santamaría, J., Schabath, M. B., Yendamuri, S. S., Manczuk, M., Lissowska, J., Świątkowska, B., Mukeria, A., Shangina, O., Zaridze, D., Holcatova, I., Mates, D., Milosavljevic, S., Savic, M., Bossé, Y., Gould Rothberg, B. E., Christiani, D. C., Gaborieau, V., Brennan, P., Liu, G., Hofman, P., Homer, R., Yang, S.-R., Pesatori, A. C., Consonni, D., Yang, L., Zhu, B., Shi, J., Brown, K., Rothman, N., Chanock, S. J., Alexandrov, L. B., Choi, J., Cardelli, M., Lan, Q., Nowak, M. A., Wedge, D. C. & Landi, M. T., 16 Mar 2025, In: bioRxiv.

    Research output: Contribution to journal › Article › peer-review

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