swan subset-quantile within array normalization for illumina infinium humanmethylation450 beadchips天鹅subset-quantile在数组正常化illumina公司英飞纳姆humanmethylation450 beadchips.pdfVIP

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swan subset-quantile within array normalization for illumina infinium humanmethylation450 beadchips天鹅subset-quantile在数组正常化illumina公司英飞纳姆humanmethylation450 beadchips.pdf

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swan subset-quantile within array normalization for illumina infinium humanmethylation450 beadchips天鹅subset-quantile在数组正常化illumina公司英飞纳姆humanmethylation450 beadchips

Maksimovic et al. Genome Biology 2012, 13:R44 /2012/13/6/R44 METHOD Open Access SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips * Jovana Maksimovic, Lavinia Gordon and Alicia Oshlack Abstract DNA methylation is the most widely studied epigenetic mark and is known to be essential to normal development and frequently disrupted in disease. The Illumina HumanMethylation450 BeadChip assays the methylation status of CpGs at 485,577 sites across the genome. Here we present Subset-quantile Within Array Normalization (SWAN), a new method that substantially improves the results from this platform by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package. Background HumanMethylation27 (27k) BeadChip [12,19]. More DNA methylation, which is the addition of a methyl recently, the genomic coverage of the array was dramati- group to the cytosine of a CpG dinucleotide, is one of cally increased, leading to the production of the Infi- the most widely studied epigenetic modifications in nium HumanMethylation450 (450k) BeadChip, which human development and disease. Changes in DNA interrogates the methylation status of 485,577 CpGs in methylation are vital for normal development and differ- the human genome. The Infinium assay detects methy- entiation [1], whilst aberrant methylation is involved in lation status with single base resolution, without the diseases such as diabetes, schizophrenia, multiple sclero- need for methylated DNA capture, thereby avoiding sis a