CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays
1 Affymetrix, Inc. 3420 Central Expressway, Santa Clara CA 95051, USA
2 University of Tokyo, Genome Science Division Research Center for Advanced Science and Technology, 4-6-1 Komaba, Meguro, 153-8904, Tokyo
BMC Bioinformatics 2006, 7:83 doi:10.1186/1471-2105-7-83Published: 21 February 2006
DNA copy number alterations are one of the main characteristics of the cancer cell karyotype and can contribute to the complex phenotype of these cells. These alterations can lead to gains in cellular oncogenes as well as losses in tumor suppressor genes and can span small intervals as well as involve entire chromosomes. The ability to accurately detect these changes is central to understanding how they impact the biology of the cell.
We describe a novel algorithm called CARAT (
Overall, CARAT automatically detects regions with copy number variations and assigns a significance score to each alteration as well as generating allele-specific output. When coupled with SNP genotype calls from the same array, CARAT provides additional detail into the structure of genome wide alterations that can contribute to allelic imbalance.