ArticleBMC bioinformatics2006
CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 65 citations in OpenAlex.
- Penalized weighted low-rank approximation for robust recovery of recurrent copy number variations.BMC bioinformatics · 2015Article
- HaplotypeCN: copy number haplotype inference with Hidden Markov Model and localized haplotype clustering.PloS one · 2014Article
- Bayesian hierarchical mixture modeling to assign copy number from a targeted CNV array.Genetic epidemiology · 2011Article
- GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays.Nucleic acids research · 2011Article
- A multilevel model to address batch effects in copy number estimation using SNP arrays.Biostatistics (Oxford, England) · 2011Article
- Model-integrated estimation of normal tissue contamination for cancer SNP allelic copy number data.Cancer informatics · 2011Article
- Statistics and bioinformatics in nutritional sciences: analysis of complex data in the era of systems biology.The Journal of nutritional biochemistry · 2010Review
- An integrated Bayesian analysis of LOH and copy number data.BMC bioinformatics · 2010Article
- PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data.Biostatistics (Oxford, England) · 2010Article
- R classes and methods for SNP array data.Methods in molecular biology (Clifton, N.J.) · 2010Article
- Cancer gene discovery in mouse and man.Biochimica et biophysica acta · 2009Review
- Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations.PloS one · 2009Article
- Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously.BMC bioinformatics · 2009Article
- Hybridization modeling of oligonucleotide SNP arrays for accurate DNA copy number estimation.Nucleic acids research · 2009Article
- Integrated study of copy number states and genotype calls using high-density SNP arrays.Nucleic acids research · 2009Article
- Quantification of normal cell fraction and copy number neutral LOH in clinical lung cancer samples using SNP array data.PloS one · 2009Article
- A flexible rank-based framework for detecting copy number aberrations from array data.Bioinformatics (Oxford, England) · 2009Article
- Hybrids of aneuploid human cancer cells permit complementation of simple and complex cancer defects.Cancer biology & therapy · 2009Article
- Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.Genome biology · 2009Article
- A large-scale survey of genetic copy number variations among Han Chinese residing in Taiwan.BMC genetics · 2008Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA 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.
resultsWe 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.
conclusionOverall, 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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.