A Linear-Time Algorithm for Analyzing Array CGH Data Using Log Ratio Triangulation

DNA copy number is the number of replicates of a contiguous segment of DNA on the genome. Copy number alteration (CNA) is a genetic abnormality in which the number of these segments differs from the normal copy number, which is two for human chromosomal DNA. The association of CNA with cancer has led to a proliferation of research into algorithmic methods for detecting these regions of genetic abnormality. We propose a linear-time algorithm to identify chromosomal change points using array comparative genomic hybridization (aCGH) data. This method treats log-2 ratio values as points in a triangle and segments the genome into regions of equal copy number by exploiting the properties of log-2 ratio values often seen at segment boundaries. Applying our method to real and simulated aCGH datasets shows that the triangulation method is fast and is robust for data with low to moderate noise levels.