title: Preprocessing and downstream analysis of microarray DNA copy number profiles.
abstract: Analysis of DNA copy number profiles requires methods tailored to the specific nature of these data. The number of available data analysis methods has grown enormously in the last 5 years. We discuss the typical characteristics of DNA copy number data, as measured by microarray technology and review the extensive literature on preprocessing methods such as segmentation and calling. Subsequently, the focus narrows to applications of DNA copy number in cancer, in particular, several downstream analyses of multi-sample data sets such as testing, clustering and classification. Finally, we look ahead: what should we prepare for and which methodology-related topics may deserve attention in the near future?
authors.affiliation: Department of Epidemiology & Biostatistics, VU University Medical Center, Amsterdam, The Netherlands. mark.vdwiel@vumc.nl
authors.forename: Mark A
authors.initials: MA
authors.lastname: van de Wiel
authors.forename: Franck
authors.initials: F
authors.lastname: Picard
authors.forename: Wessel N
authors.initials: WN
authors.lastname: van Wieringen
authors.forename: Bauke
authors.initials: B
authors.lastname: Ylstra
mesh_terms: D055028:Comparative Genomic Hybridization; D019295:Computational Biology / Q000379:methods*; D056915:DNA Copy Number Variations; D020869:Gene Expression Profiling / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*