New method opens opportunities for large-scale studies of cancer development

Cancer is caused by mutations in DNA. In order to study these mutations is important to analyse the DNA of large numbers of cancer patients. Researchers from the University Medical Center Groningen (UMCG) have now developed a new method for doing this and were able to analyse data from more than 16,000 cancer patients. Their research is therefore one of the world’s largest oncological studies to date. Today’s edition of the leading journal Nature Genetics includes an article by the researchers on the subject.

Over the past fifteen years, thousands of laboratories across the world studied the gene expression (or the RNA profile) of tumours, because studying the DNA of large groups of patients was prohibitively expensive. The UMCG researchers have found a special new way of re-analysing the data from gene expression and using the RNA profiles to identify abnormalities in the DNA. This has created opportunities for new studies into the development of cancer using huge volumes of data on DNA.

Re-use statistical data

The new method was developed by a research team led by geneticist Prof. Lude Franke: ‘Compiling systematic analyses of the DNA of 16,000 tumours would be a very expensive business. However, the data from the extensive work on gene expression carried out over the past fifteen years is freely available. We have developed a new statistical method that allows us to re-use this data. In this way, we have been able to identify the changes present in DNA taken from more than 16,000 tumours. We saw a high incidence of particular abnormalities in the DNA, but noted that other abnormalities only presented themselves in specific tumours, such as breast cancer.’

New starting points for therapies

Medical oncologist Dr Rudolf Fehrmann thinks that this new method will give analysts a new take on the gene expression profiles compiled over the past fifteen years. ‘It has, for example, led us to potential new starting points for therapies for particularly resilient cancers (those where the DNA shows a lot of abnormalities). Experiments are currently being carried out in the laboratory to explore their potential.’

Substantial savings

Developing this method involved studying 80,000 expression profiles. A ‘big data’ approach of this magnitude was previously unthinkable, but is now possible thanks to the advent of better computers and new mathematical technology. Large volumes of data, once collected for totally different reasons, can now be used to gain a better understanding of how cancer develops. It has created opportunities for new studies in the field, and could result in substantial savings.

To theNature Genetics publication: Gene expression analysis identifies global gene dosage sensitivity in cancer

Source: press release UMCG/RUG