A New Approach to Finding Copy Number Aberrations

An advance article in Bioinformatics discusses a new approach, called Correlation Matrix Diagonal Segmentation, that identifies recurrent DNA copy number aberration using a between-chromosomal-site correlation analysis. At MassGenomics, Dan Koboldt, a co-worker of the authors, describes how they evaluated the tool with lung adenocarcinoma and glioblastoma datasets from the Tumor Sequencing Project and the Cancer Genome Atlas. The researchers were able to call 39 recurrent copy number aberration regions in lung cancer and 37 in brain cancer — all of which had previously reported. Kobolt adds that the Correlation Matrix Diagonal Segmentation is fast: “The R version of CMDS finished in 13 seconds. The other algorithms took more than 300 times longer on the same dataset, indicating that CMDS represents a substantial performance gain. There’s also a C version of CMDS that runs even faster.”