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Open Access Methodology article

Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array

Haroon Naeem17*, Nicholas C Wong26, Zac Chatterton2, Matthew K H Hong3, John S Pedersen45, Niall M Corcoran3, Christopher M Hovens3 and Geoff Macintyre17

Author Affiliations

1 NICTA Victoria Research Laboratory, Department of Electrical and Electronic Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia

2 Cancer, Disease and Developmental Epigenetics, Murdoch Childrens Research Institute, Royal Children’s Hospital, Department of Paediatrics, The University of Melbourne, Melbourne, Australia

3 Australian Prostate Cancer Research Centre Epworth, Richmond, Australia and Division of Urology, Department of Surgery, University of Melbourne, Royal Melbourne Hospital, Parkville, Australia

4 TissuPath Specialist Pathology, Mount Waverley, Victoria 3149, Melbourne, Australia

5 Faculty of Medicine, Nursing and Health Sciences, Monash University, Victoria 3800, Australia

6 Current Address: Ludwig Institute of Cancer Research, Olivia Newton John Cancer and Wellness Centre, Austin Hospital, Heidelberg, Victoria, Australia

7 Department of Computing and Information Systems, Melbourne School of Engineering, The University of Melbourne, Melbourne, Victoria 3010, Australia

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BMC Genomics 2014, 15:51  doi:10.1186/1471-2164-15-51

Published: 22 January 2014

Abstract

Background

The Illumina HumanMethylation450 BeadChip (HM450K) measures the DNA methylation of 485,512 CpGs in the human genome. The technology relies on hybridization of genomic fragments to probes on the chip. However, certain genomic factors may compromise the ability to measure methylation using the array such as single nucleotide polymorphisms (SNPs), small insertions and deletions (INDELs), repetitive DNA, and regions with reduced genomic complexity. Currently, there is no clear method or pipeline for determining which of the probes on the HM450K bead array should be retained for subsequent analysis in light of these issues.

Results

We comprehensively assessed the effects of SNPs, INDELs, repeats and bisulfite induced reduced genomic complexity by comparing HM450K bead array results with whole genome bisulfite sequencing. We determined which CpG probes provided accurate or noisy signals. From this, we derived a set of high-quality probes that provide unadulterated measurements of DNA methylation.

Conclusions

Our method significantly reduces the risk of false discoveries when using the HM450K bead array, while maximising the power of the array to detect methylation status genome-wide. Additionally, we demonstrate the utility of our method through extraction of biologically relevant epigenetic changes in prostate cancer.

Keywords:
HumanMethylation450K BeadChip; SNPs; INDELS; Repetitive regions of DNA; SNP arrays; HM450K bead array; Epigenome-wide association studies; EWAS; Cancer; Epigenetics