title: CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array.
abstract: The Illumina Infinium HumanMethylation450 BeadChip (450k) is widely used for the evaluation of DNA methylation levels in large-scale datasets, particularly in cancer. The 450k design allows copy number variant (CNV) calling using existing bioinformatics tools. However, in cancer samples, numerous large-scale aberrations cause shifting in the probe intensities and thereby may result in erroneous CNV calling. Therefore, a baseline correction process is needed. We suggest the maximum peak of probe segment density to correct the shift in the intensities in cancer samples.
  
  
  
  CopyNumber450kCancer is implemented as an R package. The package with examples can be downloaded at http://cran.r-project.org
  
  
  
  nour.marzouka@medsci.uu.se
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory.
authors.forename: Nour-Al-Dain
authors.initials: NA
authors.lastname: Marzouka
authors.affiliation: Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory.
authors.forename: Jessica
authors.initials: J
authors.lastname: Nordlund
authors.affiliation: Department of Medical Sciences, Cancer Pharmacology and Computational Medicine and.
authors.forename: Christofer L
authors.initials: CL
authors.lastname: Bäcklin
authors.affiliation: Department of Women's and Children's Health, Pediatric Oncology, Uppsala University, Uppsala, Sweden.
authors.forename: Gudmar
authors.initials: G
authors.lastname: Lönnerholm
authors.affiliation: Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory.
authors.forename: Ann-Christine
authors.initials: AC
authors.lastname: Syvänen
authors.affiliation: Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory.
authors.forename: Jonas
authors.initials: J
authors.lastname: Carlsson Almlöf
mesh_terms: D018899:CpG Islands; D019175:DNA Methylation; D004273:DNA, Neoplasm; D015894:Genome, Human; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software
chemical_list: D004273:DNA, Neoplasm