Large-scale changes to the structure of the genome are often seen in cancer cells. Scientists at the Babraham Institute in Cambridge, UK, have found a way to detect these changes, which could enhance cancer diagnosis and aid the use of targeted treatments.
The report, in the journal Genome Biology, outlines a new application of a technique called Hi-C, which allows scientists to map how genetic material is arranged inside cells. By analysing this information, researchers can reliably identify major genetic changes that other methods may miss. This all comes at a lower cost than standard DNA sequencing methods.
Hi-C can detect chromosome rearrangements – where large sections of DNA are exchanged or moved between pieces of the genome called chromosomes – and also copy number variation – where genetic material gets copied or deleted. Both of these changes can have drastic effects on how the cell behaves.
First author on the paper, Dr Louise Harewood, said: “Chromosomal rearrangements are seen both in the general population and in the majority of cancers. Detection of chromosome rearrangements in patients can be troublesome and many can be missed. This can be detrimental, particularly in oncology where rearrangements can play both diagnostic and prognostic roles.”
The scientists, led by Professor Peter Fraser, used Hi-C to examine the genome of cancer cells from six people with brain tumours. They were able to identify major genome changes, often with pinpoint accuracy. Uniquely, this approach allows doctors and scientists to study genetic changes in the wider context of the whole genome. Hi-C could become a powerful tool for understanding the complex genetic changes found in many cancers.
Professor Fraser, said: “Hi-C could play a pivotal role in the detection of chromosomal abnormalities and may aid the discovery of new fusion genes. The technique works with much lower quality samples than current techniques and has the additional advantage of being able to provide copy number information from the same data. This all comes at a significantly lower cost than standard methods that use DNA sequencing.”
Harewood L, Kishore K, Eldridge MD, Wingett S, Pearson D, Schoenfelder S, Collins VP, Fraser P (2017) Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours. Genome Biology 18:125. https://doi.org/10.1186/s13059-017-1253-8
This work was supported by the Biotechnology and Biological Science Research Council, Cancer Research UK and the University of Cambridge.
Hi-C could replace DNA sequencing as a cheaper, faster way to detect large-scale genome changes in cancer.
Image by Shaury Nash via Flickr, CC-BY-SA license.
Affiliated Authors (in author order):
Louise Harewood, Nuclear Dynamics Programme, Babraham Institute
Steven Wingett, Nuclear Dynamics Programme, Babraham Institute
Stefan Schoenfelder, Nuclear Dynamics Programme, Babraham Institute
Peter Fraser, Group Leader, Nuclear Dynamics Programme, Babraham Institute
About the Babraham Institute:
The Babraham Institute receives strategic funding from the Biotechnology and Biological Sciences Research Council (BBSRC) to undertake world-class life sciences research. Its goal is to generate new knowledge of biological mechanisms underpinning ageing, development and the maintenance of health. Research focuses on signalling, gene regulation and the impact of epigenetic regulation at different stages of life. By determining how the body reacts to dietary and environmental stimuli and manages microbial and viral interactions, we aim to improve wellbeing and support healthier ageing.
04 July 2017