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

BMC Bioinformatics
Jing HuangMichael H Shapero

Abstract

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 (Copy Number Analysis with Regression And Tree) 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 ...Continue Reading

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Jul 20, 2007·Human Genetics·George ZogopoulosSteven Gallinger
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Datasets Mentioned

BETA
NA12814
NA17279

Methods Mentioned

BETA
PCR
genotyping
chip
chips

Software Mentioned

dCHIP
Primer Express
CARAT
TaqMan
Sequence Detector
R
MathType
CNAG
QPCR
CARAT ( C Number A nalysis with R egression A nd T ree )

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