%0 Journal Article
%T SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips
%A Jovana Maksimovic
%A Lavinia Gordon
%A Alicia Oshlack
%J Genome Biology
%D 2012
%I BioMed Central
%R 10.1186/gb-2012-13-6-r44
%X DNA methylation, which is the addition of a methyl group to the cytosine of a CpG dinucleotide, is one of the most widely studied epigenetic modifications in human development and disease. Changes in DNA methylation are vital for normal development and differentiation [1], whilst aberrant methylation is involved in diseases such as diabetes, schizophrenia, multiple sclerosis and cancer [2-4]. As interest in epigenetics, and particularly DNA methylation, has increased, analysis methods have had to evolve in scale and resolution. Currently, several microarray and next-generation sequencing technologies are available that allow the interrogation of DNA methylation on a genome-wide scale [5-14]. Each of these approaches has inherent strengths and weaknesses, which have been compared and discussed in several recent reviews [15-18]. As sequencing-based DNA methylation assays become more affordable, it is anticipated that they will be more widely used in this arena; at present, however, they are still too costly for most studies, particularly those that involve large numbers of samples. Consequently, methylation arrays are a popular alternative for high-throughput DNA methylation analyses.DNA methylation profiling using Illumina's Infinium technology was first utilized on the Infinium HumanMethylation27 (27k) BeadChip [12,19]. More recently, the genomic coverage of the array was dramatically increased, leading to the production of the Infinium HumanMethylation450 (450k) BeadChip, which interrogates the methylation status of 485,577 CpGs in the human genome. The Infinium assay detects methylation status with single base resolution, without the need for methylated DNA capture, thereby avoiding capture-associated biases. The 50 bp Infinium methylation probes query a [C/T] polymorphism created by bisulfite conversion of unmethylated cytosines in the genome. However, the Infinium 450k methylation platform is unique in that it uses a combination of two distinct probe types, Infi
%U http://genomebiology.com/2012/13/6/R44