CNR developed an algorithm which identifies DNA alterations in cancer
A number of diseases, including tumour, neurodegenerative, developmental and cardiovascular diseases, are associated with the presence of DNA abnormalities. The researchers of the Institute of Informatics and Telematics of the Research Area of Pisa of the National Research Council (CNR), in collaboration with the Department of Experimental and Clinical Medicine of the University of Florence, have developed a mathematical algorithm to identify these abnormalities.
Excavator2 – this is the name given by researchers to the algorithm, to highlight its ability to deeply “excavate” huge amounts of complex data – was presented in the scientific journal Nucleic Acids Research of the editorial group Oxford Journals in a paper entitled: “Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2”.
“The underlying idea of this algorithm – explained CNR researchers –,which uses data from second-generation sequencing technology with a completely innovative approach, is to include in the analysis data that, so far, have been considered as waste sequences; these sequences, appropriately processed, give us the opportunity to assess the presence of chromosomal abnormalities on the entire genome by sequencing 1% only, with a considerable reduction in experimental costs”.
Application tests of Excavator2 on large population databases, such as Progetto 1000 Genomi, and databases of patients with cancer available at the Centro Nacional de Investigaciones Oncologicas (CNIO) of Madrid, Spain, have confirmed that the software developed by the CNR is able to produce “surprising results, with performances markedly higher than any other available methods”, proudly said the Italian researchers.
How will the algorithm be applied in the future? Researchers are already talking about new national and international collaborations with the major bodies in this sector, such as Alleanza Contro il Cancro, for the screening of cancer patients, and Qatar Genomes Poject, which is currently the largest and important sequencing project in the world, with a database of information from over 350,000 people.