Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array

Abstract

BackgroundMeasurement of genome-wide DNA methylation (DNAm) has become an important avenue for investigating potential physiologically-relevant epigenetic changes. Illumina Infinium (Illumina, San Diego, CA, USA) is a commercially available microarray suite used to measure DNAm at many sites throughout the genome. However, it has been suggested that a subset of array probes may give misleading results due to issues related to probe design. To facilitate biologically significant data interpretation, we set out to enhance probe annotation of the newest Infinium array, the HumanMethylation450 BeadChip (450 k), with >485,000 probes covering 99% of Reference Sequence (RefSeq) genes (National Center for Biotechnology Information (NCBI), Bethesda, MD, USA). Annotation that was added or expanded on includes: 1) documented SNPs in the probe target, 2) probe binding specificity, 3) CpG classification of target sites and 4) gene feature classification of target sites.ResultsProbes with documented SNPs at the target CpG (4.3% of probes) were associated with increased within-tissue variation in DNAm. An example of a probe with a SNP at the target CpG demonstrated how sample genotype can confound the measurement of DNAm. Additionally, 8.6% of probes mapped to multiple locations in silico. Measurements from these non-specific probes likely represent a combination of DNAm from multiple genomic sites. The expanded biological annotation demonstrated that based on DNAm, grouping probes by an alternative high-density and intermediate-density CpG island classification provided a distinctive pattern of DNAm. Finally, variable enrichment for differentially methylated probes was noted across CpG classes and gene feature groups, dependant on the tissues that were compared.ConclusionDNAm arrays offer a high-throughput approach for which careful consideration of probe content should be utilized to better understand the biological processes affected. Probes containing SNPs and non-specific probes may affect the assessment of DNAm using the 450 k array. Additionally, probe classification by CpG enrichment classes and to a lesser extent gene feature groups resulted in distinct patterns of DNAm. Thus, we recommend that compromised probes be removed from analyses and that the genomic context of DNAm is considered in studies deciphering the biological meaning of Illumina 450 k array data.

Comparison of DNA methylation measured by Illumina 450K and EPIC BeadChips in blood of newborns and 14-year-old children

“…Cross-reactive probes have been previously identified [15] and were removed according to Chen et al (n  =  27,167) [16]. Probes where 95% of samples had detection P values >0.01 were also dropped (cord n  = 834; 14yr n = 561).…”

DNA methylation levels and long-term trihalomethane exposure in drinking water: an epigenome-wide association study

“…In addition, 2 other technical biases are possible: probes that cross-hybridize, and probes mapping in polymorphic residues. 50,51 Probes that cross-hybridize account for about 8.6% of the 450K array. Methylation levels measured in these probes likely reflect a combination of levels of methylation at the various locations to which these probes hybridize.…”

Racial differences in genome-wide methylation profiling and gene expression in breast tissues from healthy women

“…We further excluded probes including SNPs in the target CpG (n D 115,996) or within 10 base pairs (bps) of the target CpGs (n D 145,116) based on NCBI dbSNP build 138 to avoid any potential effect of SNPs. In addition, problematic probes (non-specific probes) described in 2 recent studies to hybridize to multiple genomic locations by in silico analysis were excluded 23,24 in order to remove potential bias measurements of DNA methylation. GRCh37/hg19 (Human Genome version 19) was used as reference genome for this study.…”