Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array
Haroon Naeem, Nicholas C Wong, Zac Chatterton, Matthew KH Hong, John S Pedersen, Niall M Corcoran, Christopher M Hovens, Geoff Macintyre
BMC GENOMICS | BMC | Published : 2014
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, IND..View full abstract
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Awarded by NHMRC
We thank the Australian Genome Research Facility for their services in the hybridization of samples to the HM450K bead array and generation of raw intensity data. This work is supported by NICTA. NICTA is funded by the Australian Government as represented by the Department of Broadband, Communications and the Digital Economy and the Australian Research Council through the ICT Centre of Excellence program. NW has been supported by Victorian Cancer Agency grant, National Health and Medical Research Council Grant. NW is also supported by My Room and the Children's Cancer Centre Foundation. MCRI is supported by the Victorian Government's Operational Infrastructure Support Program. The Australian Prostate Cancer Centre Epworth is supported by a federal grant from the Department of Health and Aging, Australia. This study was partly funded by NHMRC project grant 1047581.