Free Software Quickly Detects Gene Mutations Associated with Breast, Other Cancers

Free Software Quickly Detects Gene Mutations Associated with Breast, Other Cancers

Free, easy-to-use software called DECoN can detect gene mutations in breast, ovarian, and other cancers that previously needed to be identified by a separate test.

DECoN, developed by researchers at The Institute of Cancer Research in London and the Wellcome Trust Centre for Human Genetics in Oxford, accurately detects changes in exons — copy number of blocks of DNA — which could improve the genetic mutations involved in breast cancer.

The study reporting the development of the software, “Accurate clinical detection of exon copy number variants in a targeted NGS panel using DECoN,” was published in the journal Wellcome Open Research.

Most gene mutations are small DNA changes within an exon. These small changes are readily detected by targeted next generation sequencing (NGS) tests. However, accurate detection of deletions or duplications of whole exons, also known as exon copy number variants (exon CNVs), has proven to be problematic in targeted NGS data, particularly detection of single exon CNVs.

Accurately detecting these gene variants is critical, as they represent the underlying cause of diseases. In the case of breast and ovarian cancer, about 10 percent of BRCA1 mutations are exon CNVs. The researchers developed DECoN (Detection of Exon Copy Number variants), as a cost-saving software tool that quickly and accurately detects deletions or duplications of exon.

The researchers tested the performance of DECoN using 96 samples with independently validated exon CNV data. They then performed evaluations of the tool in 1,919 BRCA samples, and found that the software was able to detect BRCA exon CNVs with 100 percent sensitivity and 99 percent specificity.

“DECoN has transformed our gene testing pipeline, making it more efficient and more effective, whilst also making it much faster and cheaper,” study leader Prof. Nazneen Rahman, head of cancer genetics at The Institute of Cancer Research, London, and The Royal Marsden Hospital Foundation Trust, said in a news release.

“Previously we had to do an additional slow and expensive test to detect these tricky mutations. Now they are automatically detected by DECoN during the data analysis process,” he said.

Prof. Gerton Lunter, leader of the software development at the Wellcome Trust Centre for Human Genetics at Oxford, described DECon as “an outstanding collaboration for us. It is hugely rewarding to see our work having a real impact for patients.”

Rahman added that it’s important “that our work can be as impactful as possible.”

He said a free easy-to-use version of DECoN is available at, and the source code is also available.