Complete pipeline for Infinium ® Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation

摘要: Background: Huge progress has been made in the development of array- or sequencing-based technologies for DNA methylation ana lysis. The Illumina Infinium ® Human Methylation 450K BeadChip (Illumina Inc., CA, USA) allows simultaneous quantitative monitoring more than 480,000 CpG positions, enabling large-scale epigenotyping studies. However, assay combines two different chemistries, which may cause a bias lysis if all signals are merged as unique source measurement. Materials & methods: We confirm three data sets that I stable and cover wider dynamic range values II signals. evaluated profile probes obtained with normalization protocols compared these results subset CpGs analyzed by pyrosequencing. Results: developed quantile approach processing BeadChips. were used ‘anchors’ to normalize at level probe coverage categories. Our outperformed alternative correction approaches terms signal estimation. further implemented complete preprocessing protocol solves most issues currently raised array users. Conclusion: pipeline using an original performs both sample efficient I/II shift correction. scripts, being freely available from authors, will allow researchers concentrate on biological data, such identification signatures.