CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array.

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Marzouka NA, Nordlund J, Bäcklin CL, Lönnerholm G, Syvänen AC, Carlsson Almlöf J

Bioinformatics 32 (7) 1080-1082 [2016-04-01; online 2015-11-09]

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.

Bioinformatics Support for Computational Resources [Service]

NGI Uppsala (SNP&SEQ Technology Platform) [Technology development]

National Genomics Infrastructure [Technology development]

PubMed 26553913

DOI 10.1093/bioinformatics/btv652

Crossref 10.1093/bioinformatics/btv652

pii: btv652
pmc: PMC4896365