A systems-epigenomics approach to cancer risk prediction

Andrew Teschendorff (primary)
Department of Women’s Cancer
University College London
Martin Widschwendter (secondary)
Department of Women’s Cancer
University College London

Abstract

Epigenetic changes, and specifically, alterations to the DNA methylome, are believed to play an important role in the earliest stages of cancer development.  Measuring DNA methylation changes in relevant tissues may thus be informative of cancer risk. This PhD project will use a novel system-epigenomic approach to construct cancer risk prediction models for women specific cancers. It will draw on extensive knowledge of epigenomics, stem-cell biology and cancer, and will use advanced methods from statistics, machine learning and physics to integrate multi-dimensional omic datasets. Corresponding data is already available and data generation will be ongoing throughout the duration of the project via our European partners.


References

  1. Teschendorff AE, Gao Y, Jones A, Ruebner M, Beckmann MW, Wachter DL, Fasching PA, Widschwendter M. DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer. Nat Commun. 2016 Jan 29;7:10478.
  2. Jiao Y, Widschwendter M, Teschendorff AE. A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control. Bioinformatics. 2014 Aug 15;30(16):2360-6.
  3. Teschendorff AE, Jones A, Fiegl H, Sargent A, Zhuang JJ, Kitchener HC, Widschwendter M. Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation. Genome Med. 2012 Mar 27;4(3):24.
  4. Jenkinson G, Pujadas E, Goutsias J, Feinberg AP. Potential energy landscapes identify the information-theoretic nature of the epigenome. Nat Genet. 2017 May;49(5):719-729.
  5. Vanderkraats ND, Hiken JF, Decker KF, Edwards JR. Discovering high-resolution patterns of differential DNA methylation that correlate with gene expression changes. Nucleic Acids Res. 2013 Aug;41(14):6816-27.

BBSRC Area
Animal disease, health and welfare
Area of Biology
Cell BiologyGenetics
Techniques & Approaches
BioinformaticsEngineeringGeneticsMathematics / StatisticsMolecular BiologySimulation / Modelling