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CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays

Jing Huang1*, Wen Wei1, Joyce Chen1, Jane Zhang1, Guoying Liu1, Xiaojun Di1, Rui Mei1, Shumpei Ishikawa2, Hiroyuki Aburatani2, Keith W Jones1 and Michael H Shapero1

Author Affiliations

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

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BMC Bioinformatics 2006, 7:83  doi:10.1186/1471-2105-7-83

Published: 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 (

opy Number
nalysis with
ree) that uses probe intensity information to infer copy number in an allele-specific manner from high density DNA oligonuceotide arrays designed to genotype over 100, 000 SNPs. Total and allele-specific copy number estimations using CARAT are independently evaluated for a subset of SNPs using quantitative PCR and allelic TaqMan reactions with several human breast cancer cell lines. The sensitivity and specificity of the algorithm are characterized using DNA samples containing differing numbers of X chromosomes as well as a test set of normal individuals. Results from the algorithm show a high degree of agreement with results from independent verification methods.


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.