CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array
2016 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 32, no 7, 1080-1082 p.Article in journal (Refereed) PublishedText
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.
Place, publisher, year, edition, pages
2016. Vol. 32, no 7, 1080-1082 p.
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
IdentifiersURN: urn:nbn:se:uu:diva-296859DOI: 10.1093/bioinformatics/btv652ISI: 000374236400016PubMedID: 26553913OAI: oai:DiVA.org:uu-296859DiVA: diva2:940170
FunderSwedish Cancer Society, CAN2010/592Swedish Research Council, 90559401Swedish Foundation for Strategic Research , RBc08-008