Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data

Methods. 2015 Jan 15;72:3-8. doi: 10.1016/j.ymeth.2014.08.011. Epub 2014 Sep 16.

Abstract

The Illumina HumanMethylation450 BeadChip has become a popular platform for interrogating DNA methylation in epigenome-wide association studies (EWAS) and related projects as well as resource efforts such as the International Cancer Genome Consortium (ICGC) and the International Human Epigenome Consortium (IHEC). This has resulted in an exponential increase of 450k data in recent years and triggered the development of numerous integrated analysis pipelines and stand-alone packages. This review will introduce and discuss the currently most popular pipelines and packages and is particularly aimed at new 450k users.

Keywords: 450k BeadChip; Analysis pipelines; DNA methylation; EWAS; Epigenetics; HumanMethylation450.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • CpG Islands*
  • DNA Methylation*
  • Epigenomics / methods
  • Genome
  • Genome, Human
  • Humans
  • Oligonucleotide Array Sequence Analysis / methods*
  • Software