Cutting-edge technologies to improve treatment for women with breast and ovarian cancers

About the Project

The Epigenetics for Female Personalised Cancer Care – or EpiFemCare – project used cutting edge technologies from the field of epigenetics to investigate the potential for improving clinical pathways for women with breast and ovarian cancers. Epigenetic tags are found on top of the DNA and the patterns of epigenetic tags in cancer cells can be abnormal. In fact, these abnormal patterns are thought to occur very early in the development of cancer. As a tumour grows, it releases DNA into the bloodstream. The EpiFemCare project aimed to find tumour DNA in blood by identifying characteristic patterns of epigenetic tags.

The project has developed new methods for finding these patterns and has made progress towards identifying new blood tests that could:

  • Detect breast and ovarian cancers earlier
  • Monitor the efficacy of breast and ovarian cancer treatments
  • Distinguish benign from malignant pelvic masses

For more information on epigenetics and the EpiFemCare project, please download our flyer or watch our explanatory video.

Our Aims

Breast and ovarian cancers affect thousands of women in the EU each year and although clinical pathways are already in place unsolved challenges still remain. The EpiFemCare project aimed to improve the following aspects of these established pathways:

Screening: There is no screening programme for ovarian cancer and improved methods are needed for breast cancer (see Mammography Fact Box for further information).

Diagnosis: Ovarian cancer is often discovered only when the disease has spread to other parts of the body and is difficult to treat. New methods are needed to distinguish ovarian cancer from other benign, non-cancerous conditions.

Personalised Care: Chemotherapy is prescribed for most women with cancer, but each woman will differ in her response to a specific treatment. It is currently not possible to predict which women would benefit most from receiving which drugs. As every woman is an individual it makes more sense to attempt to personalise their treatment where possible.

These pathways are explored further in this video created by the EpiFemCare project.

Results

The EpiFemCare team explored two different methods to identify epigenetic markers released by tumour cells into the blood stream: the Illumina Methyl 450K array and Reduced Representation Bisulfite Sequencing (RRBS). During the project, we also developed a new method based on analysis of patterns of DNA methylation within single sequencing reads with the aim of maximising the specificity of the test.

GATC - Optimised Liquid Biopsy

The sequencing of several thousands of cell-free DNA samples within the EpiFemCare project led to the optimisation of highly standardised workflows for oncology products at GATC and contributed to the launch of the GATCLIQUID service line. GATC has developed specialised protocols for cell-free DNA extraction that are capable of handling the very low concentrations and highly fragmented nature of the cell-free DNA, as well as protocols for RRBS and targeted bisulfite sequencing of the EpiFemCare samples.

Read More

GeneData - Finding Solutions for EpiFemCare

Detecting highly diluted tumor-specific DNA fragments in blood samples is very challenging. Working with the Genedata Profiler™ platform, the Genedata scientists working on the EpiFemCare project solved this problem by developing new algorithms for scanning RRBS data for single read methylation patterns that are unique to tumor samples, providing superior specificity and sensitivity for both the discovery and clinical utility of DNA methylation markers. The scientists then ranked the resulting patterns to isolate cancer-specific candidate biomarkers for clinical diagnostics.

New Biomarkers for Screening, Diagnosis and Personalised Care

We identified new biomarkers for breast and ovarian cancers and validation of these markers in all contexts is ongoing. Methods and sample sets used for biomarker discovery and validation in the ovarian cancer case are shown below.

Publications

Perspectives on Women’s Involvement in Research

The gynaecology team at Charles University collected large numbers of samples from women with breast and ovarian cancers and healthy volunteers to support biomarker development during the project. Their clinical team was particularly successful in this regard and they also conducted research to better understand women’s perspectives on their involvement in the research. Their findings will be published when available.

Outlook/Future Research

The EpiFemCare project was supported by the European Union’s Framework Programme 7 under grant agreement number 305428. The project completed in April 2016. However, the consortium partners will continue to investigate these markers and to validate them for use in clinical practice where possible. Please check out our consortium partners’ websites for further information.

The Consortium

  • University College London
  • London, UK
  • GATC Biotech AG
  • Konstanz, Germany
  • Genedata AG
  • Basel, Switzerland
  • Euram Ltd
  • Nottingham, UK
  • Ludwig-Maximilians-Universität
  • Munich, Germany
  • Universita Karlova V Praze
  • Prague, Czech Republic

'First and foremost I would like to wholeheartedly say that my team and I have immensely enjoyed working with our consortium partners and it was a massive privilege and pleasure to lead the consortium. It was amazing to witness how people from diverse backgrounds were willing to leave their comfort zones in order to make a very tangible difference to women with cancer by detecting cancers earlier and monitoring the treatment. We have gained hugely invaluable insights and will undoubtedly soon be evaluating a clinical test based on our EpiFemCare findings. The excellent results we have attained in the last 3.5 years only go to reflect what can be achieved when academia and industry join forces on a pan-European scale.'
Martin Widschwendter, Project Coordinator, UCL

'This is definitely one of the most focused and success oriented collaborative projects I’ve been working in. There’s great team spirit: I’ve been looking forward to every single project meeting, be it a consortium meeting or with a smaller group.'
Timo Wittenberger, Business Development Manager, Genedata

'Cancer is a very complex disease and new approaches for an earlier and more precise detection are urgently needed. The EpiFemCare consortium with its talented team of clinicians and scientists aimed to develop a new blood test for the screening and the diagnosis of lethal pathologies such as breast and ovary cancer, allowing a huge step forward in cancer care. Inspired by a common vision and a common goal, our team at Ludwig-Maximilians-University took part to the EpiFemCare project with great enthusiasm, having recruited in the study more than 300 breast cancer patients in the study and providing several hundreds of serum samples obtained from breast cancer patients enrolled in the SUCCESS study. Being part of this consortium has been a true honour and a great experience for us, especially because we are confident that all the efforts will contribute to improving the quality of patients' treatment in a very near future. And this is what counts at the end.'
The Ludwig-Maximilians-Universität Team