CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays. Results: We describe a novel algorithm called CARAT (C opy Number A nalysis with R egression A nd T 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. Conclusion: 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.

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  1. Scharpf, Robert B.; Ruczinski, Ingo; Carvalho, Benilton; Doan, Betty; Chakravarti, Aravinda: A multilevel model to address batch effects in copy number estimation using SNP arrays (2011)
  2. Wang, Quan; Qu, Jianghan; Cheng, Xiaoxing; Kang, Yongjian; Wan, Lin; Qian, Minping; Deng, Minghua: A study of biases of DNA copy number estimation based on PICR model (2011)
  3. Greenman, Chris D.; Bignell, Graham; Butler, Adam; Edkins, Sarah; Hinton, Jon: PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data (2010)
  4. Rueda, Oscar M.; Díaz-Uriarte, Ramón: Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously (2009) ioport
  5. Scharpf, Robert B.; Parmigiani, Giovanni; Pevsner, Jonathan; Ruczinski, Ingo: Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays (2008)
  6. Rueda, Oscar M.; Diaz-Uriarte, Ramon: A response to yu et al. ’A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array’, BMC bioinformatics 2007, 8: 145 (2007) ioport