title: CGHcall: calling aberrations for array CGH tumor profiles.
abstract: CGHcall achieves high calling accuracy for array CGH data by effective use of breakpoint information from segmentation and by inclusion of several biological concepts that are ignored by existing algorithms. The algorithm is validated for simulated and verified real array CGH data. By incorporating more than three classes, CGHcall improves detection of single copy gains and amplifications. Moreover, it allows effective inclusion of chromosome arm information.
  
  
  BACKGROUND
  An R-package (GUI), a manual and an example data set are available at http://www.few.vu.nl/~mavdwiel/CGHcall.html.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Pathology, VU University Medical Center, PO Box 7057, 1007MB Amsterdam, The Netherlands. mark.vdwiel@vumc.nl
authors.forename: Mark A
authors.initials: MA
authors.lastname: van de Wiel
authors.forename: Kyung In
authors.initials: KI
authors.lastname: Kim
authors.forename: Sjoerd J
authors.initials: SJ
authors.lastname: Vosse
authors.forename: Wessel N
authors.initials: WN
authors.lastname: van Wieringen
authors.forename: Saskia M
authors.initials: SM
authors.lastname: Wilting
authors.forename: Bauke
authors.initials: B
authors.lastname: Ylstra
mesh_terms: D000465:Algorithms; D002869:Chromosome Aberrations; D002874:Chromosome Mapping / Q000379:methods*; D004273:DNA, Neoplasm / Q000235:genetics*; D018628:Gene Dosage / Q000235:genetics*; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
chemical_list: D004273:DNA, Neoplasm