Copynumber: Efficient algorithms for single- and multi-track copy number segmentation

• Published in: BMC genomics Vol. 13; no. 1; p. 591
• Main Authors: Nilsen, Gro, Liestøl, Knut, Van Loo, Peter, Moen Vollan, Hans Kristian, Eide, Marianne B, Rueda, Oscar M, Chin, Suet-Feung, Russell, Roslin, Baumbusch, Lars O, Caldas, Carlos, Børresen-Dale, Anne-Lise, Lingjærde, Ole Christian
• Format: Journal Article
• Language: English
• Published: London BioMed Central 04.11.2012; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: aCGH; Algorithms; Allele-specific segmentation; Analysis; Animal Genetics and Genomics; Artificial chromosomes; Bioconductor; Biomedical and Life Sciences; Biomedical research; Breakpoints; Cancer; Case studies; Computer programs; Copy number; Copy number variations; Cytogenetics; Data processing; Development and progression; DNA; DNA - genetics; DNA Copy Number Variations; Dynamic programming; Gene Dosage; Genetic aspects; Genetics; Genome, Human; Genomes; Genomic Instability; Genomics; Human and rodent genomic; Humans; Least squares; Life Sciences; Lymphoma, Follicular - genetics; Medical research; Methods; Microarrays; Microbial Genetics and Genomics; Neoplasms - genetics; Oligonucleotide Array Sequence Analysis - methods; Penalized regression; Plant Genetics and Genomics; Polymorphism, Single Nucleotide; Programming languages; Proteomics; Segmentation; Single-nucleotide polymorphism; Software; Studies; Norway; Bioconductor; Segmentation; Copy number; Least squares; Penalized regression; aCGH; Allele-specific segmentation
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-13-591

Background Cancer 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. Results A 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. Conclusions The 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.