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CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Cancer Pharmacology and Computational Medicine.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Pediatrics.
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2016 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 32, no 7, 1080-1082 p.Article in journal (Refereed) Published
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Abstract [en]

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.
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
URN: urn:nbn:se:uu:diva-296859DOI: 10.1093/bioinformatics/btv652ISI: 000374236400016PubMedID: 26553913OAI: oai:DiVA.org:uu-296859DiVA: diva2:940170
Funder
Swedish Cancer Society, CAN2010/592Swedish Research Council, 90559401Swedish Foundation for Strategic Research , RBc08-008
Available from: 2016-06-20 Created: 2016-06-20 Last updated: 2017-11-28Bibliographically approved

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Marzouka, Nour-al-dainNordlund, JessicaBäcklin, Christofer L.Lönnerholm, GudmarSyvänen, Ann-ChristineAlmlöf, Jonas Carlsson

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Marzouka, Nour-al-dainNordlund, JessicaBäcklin, Christofer L.Lönnerholm, GudmarSyvänen, Ann-ChristineAlmlöf, Jonas Carlsson
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Molecular MedicineCancer Pharmacology and Computational MedicinePediatrics
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Bioinformatics
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)

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