Circular binary segmentation for the analysis of array-based DNA copy number data.
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.
Olshen
Adam B
AB
Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA. olshena@mskcc.org
Venkatraman
E S
ES
Lucito
Robert
R
Wigler
Michael
M
D001943:Breast Neoplasms / Q000235:genetics; D045744:Cell Line, Tumor; D003198:Computer Simulation; D005260:Female; D018628:Gene Dosage; D015894:Genome, Human; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*