title: Smoothing waves in array CGH tumor profiles.
abstract: BACKGROUND
  Many high-resolution array comparative genomic hybridization tumor profiles contain a wave bias, which makes accurate detection of breakpoints in such profiles more difficult.
  
  
  RESULTS
  An efficient and highly effective algorithm that largely removes the wave bias from tumor profiles by regressing the tumor profile data on data of profiles from the clinical genetics practice. Results are illustrated on two independent datasets. The algorithm is shown to be robust against the presence of true copy number aberrations. Moreover, the smoothed profiles are able to recapitulate the aberration location and signal for simulated tumor profiles.
  
  
  BACKGROUND
  Easy-to-use R scripts, user instructions and data are available from http://www.few.vu.nl/~mavdwiel/nowaves.html.
  
  
  BACKGROUND
  Supplementary information are available at Bioinformatics online.
authors.affiliation: Department of Epidemiology & Biostatistics, 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: Rebecca
authors.initials: R
authors.lastname: Brosens
authors.forename: Paul H C
authors.initials: PH
authors.lastname: Eilers
authors.forename: Candy
authors.initials: C
authors.lastname: Kumps
authors.forename: Gerrit A
authors.initials: GA
authors.lastname: Meijer
authors.forename: Björn
authors.initials: B
authors.lastname: Menten
authors.forename: Erik
authors.initials: E
authors.lastname: Sistermans
authors.forename: Frank
authors.initials: F
authors.lastname: Speleman
authors.forename: Marieke E
authors.initials: ME
authors.lastname: Timmerman
authors.forename: Bauke
authors.initials: B
authors.lastname: Ylstra
mesh_terms: D055028:Comparative Genomic Hybridization / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D018628:Gene Dosage; D020869:Gene Expression Profiling / Q000379:methods; D009369:Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software