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27/10/2016

CEXS-UPF: A web tool to help detect cancer mutations

CEXS-UPF: A web tool to help detect cancer mutations


News from CEXS-UPF


The correct treatment and diagnosis of cancer increasingly depends on the genetic analysis of patients. Scientists look for mutations, which may have diagnostic, prognostic or therapeutic value for the disease. In order to identify these mutations, tumor DNA sequencing is required, either covering the whole genome, its exome (ie, the functional part of the genome) or only certain genes or gene regions, that are included in panels. Panel sequencing has advantages over whole genome/exome sequencing, as well as apart from having a better ratio of cost / benefit, the panels detect fewer false positives thanks to its higher sensitivity.

There are sequencing panels predesigned and marketed by several companies, but they are commonly unspecific panels, designed to sequence any type of tumor. The cost / benefit of these panels for answering specific questions is usually low, since most of the genomic regions included are irrelevant. Clinicians increasingly decide to design specific tailored panels and they need to search in previous studies and integrate information from databases. Moreover, it is difficult to estimate in advance the ratio of cost / benefit of the panel designed .

To solve these problems, the group on Biomedical Genomics of GRIB (UPF-IMIM), have developed OncoPaD , the first web tool open to the entire scientific community for the design of cancer sequencing panels taking into account the relevant prior knowledge about the type of tumor and whose estimated cost / benefit ratio can be adjusted by the researchers. 

More information:
CEXS-UPF website

Reference work:
Rubio-Pérez et al . Rational design of cancer gene panels with OncoPaD. Genome Medicine. 2016 Oct 3.