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BMC Genomics

, 13:591

Human and rodent genomic


BackgroundCancer progression is associated with genomic instability and an accumulation of gains and losses of DNA. The growing variety of tools for measuring genomic copy numbers, including various types of array-CGH, SNP arrays and high-throughput sequencing, calls for a coherent framework offering unified and consistent handling of single- and multi-track segmentation problems. In addition, there is a demand for highly computationally efficient segmentation algorithms, due to the emergence of very high density scans of copy number.

ResultsA comprehensive Bioconductor package for copy number analysis is presented. The package offers a unified framework for single sample, multi-sample and multi-track segmentation and is based on statistically sound penalized least squares principles. Conditional on the number of breakpoints, the estimates are optimal in the least squares sense. A novel and computationally highly efficient algorithm is proposed that utilizes vector-based operations in R. Three case studies are presented.

ConclusionsThe R package copynumber is a software suite for segmentation of single- and multi-track copy number data using algorithms based on coherent least squares principles.

KeywordsCopy numberaCGHSegmentationAllele-specific segmentationPenalized regressionLeast squaresBioconductorAbbreviationsaCGHArray Comparative Genomic Hybridization

AICAkaikes Information Criterion. ASCAT: Allele-Specific Copy number Analysis of Tumors

BACBacterial Artificial Chromosome

BAFB-Allele Frequency

BICSchwarzs Bayesian Information Criterion

CBSCircular Binary Segmentation

CNVCopy Number Variation

DTCDisseminated Tumor Cells

FLFused Lasso

HTSHigh-Throughput Sequencing

IQRInterquartile Range

MADMedian Absolute Deviation

MLPAMultiplex Ligation-dependent Probe Amplification

PCFPiecewise Constant Fitting the method used for segmentation in this paper

ROCReceiver Operating Characteristic curve

SNPSingle-nucleotide Polymorphism.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-13-591 contains supplementary material, which is available to authorized users.

Gro Nilsen, Knut Liestl contributed equally to this work.

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Autor: GroNilsen - KnutLiestl - PeterVan Loo - HansKristianMoen Vollan - MarianneBEide - OscarMRueda - Suet-FeungChin - RoslinRussell - L


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