Circular binary segmentation for the analysis of array-based DNA copy number data

TLDR

DNA copy number denotes the number of DNA copies at a genomic region, and alterations in copy number are common in cancer progression; microarray technologies now enable simultaneous measurement of copy number at thousands of sites. The study introduces circular binary segmentation to convert noisy intensity measurements into contiguous regions of equal copy number. This modification of binary segmentation is applied to array‑based DNA copy number data. The method was evaluated by simulation and demonstrated on cell line data with known copy number alterations and on a breast cancer cell line dataset.

Abstract

DNA sequence copy number is the number of copies of DNA at a region of a genome. Cancer progression often involves alterations in DNA copy number. Newly developed microarray technologies enable simultaneous measurement of copy number at thousands of sites in a genome. We have developed a modification of binary segmentation, which we call circular binary segmentation, to translate noisy intensity measurements into regions of equal copy number. The method is evaluated by simulation and is demonstrated on cell line data with known copy number alterations and on a breast cancer cell line data set.