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Updated: Mar 30, 2026
Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array
Nour-Al-Dain Marzouka1, Jessica Nordlund1, Christofer L Bäcklin2
1Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory.
Unlabelled:
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.
Availability And Implementation:
CopyNumber450kCancer is implemented as an R package. The package with examples can be downloaded at http://cran.r-project.org
Contact:
nour.marzouka@medsci.uu.se
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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