Coloured graphs reveal hidden gene variants

13 January 2012

In an exciting breakthrough for the application of algorithms, scientists can now access complex genetic variants that have previously escaped detection.

Mathematician Zam Iqbal and computer scientist Mario Caccamo have created an innovative method to analyse genomes, called coloured de Bruijin graphs. This new approach to de novo assembly could yield insights of major medical importance, for example in infectious disease analysis where the complexity of genetic mutations and rearrangement makes mapping unreliable.

Moreover, with the associated Cortex software, scientists can, for the first time, analyse multiple genomes whilst retaining information about individual ones, allowing comparison between genomes.

Already, they’ve revealed that each person has on average 1.4 million DNA bases that are highly divergent from anything found in the reference sequence, a significant proportion of which occur within coding gene sequences and may therefore affect biological function.

"What's exciting about this method is that it opens up new ways of looking at how genomes change, from the development of cancerous tumours to the study of drug resistance in bacteria", says Professor Gil McVean, who has supervised the project since Zam moved to work in his Oxford-based group two years ago.

The paper is published today in Nature Genetics