CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 26553913.
- Also identified by DOI 10.1093/bioinformatics/btv652 and PMC identifier 4896365.
- Licence recorded as CC BY-NC.
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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.
Medical subject headings
- CpG Islands
- DNA Methylation
- Neoplasms
- Software