Computational protocol: Genome- and epigenome-wide association study of hypertriglyceridemic waist in Mexican American families

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Protocol publication

[…] DNA samples (500 ng) obtained from peripheral blood cells were bisulfite-converted using the EZ-96 DNA Methylation™ Kit (Zymo Research, Irvine, CA) and were subjected to methylation profiling using the Illumina Infinium HumanMethylation450 BeadChip assay (Illumina, San Diego, CA). The array interrogated 485,577 CpG sites across the genome and incorporated both Infinium I and Infinium II bead types. The Illumina iScan was used to scan the BeadChips and raw data was imported into GenomeStudio (V2011.1) to extract image intensities, following background subtraction and normalization to inbuilt controls on the arrays.Methylation at each CpG site was quantified on a scale from zero (representing fully unmethylated) to one (representing fully methylated) as a methylation score (β). Probes that were located on the sex chromosomes (n = 11,648), that were non-CpG loci (n = 2,994) or that analyzed SNPs (n = 65) were excluded. To correct for differences due to Infinium I and Infinium II probe designs, we used the BMIQ method implemented in the R-based software, BMIQ [].We included only those probes for which heritability analyses could be successfully completed without convergence failures. For 12,154 (2.5 %) probes SOLAR was unable to achieve convergence, leaving a total of 458,716 CpG sites available for analysis. Of these, 1385 probes had detection p values >0.01 in >5 % of the samples and therefore we excluded these probes leaving a total of 457,331 CpG sites that were finally included in this study. To minimize loss of informative associations, we did not exclude SNP-containing or cross-reactive probes but rather investigated whether the significantly associated CpG sites could have been confounded due to these characteristics. […]

Pipeline specifications

Software tools GenomeStudio, BMIQ
Application DNA methylation array analysis
Organisms Homo sapiens
Diseases Cardiovascular Diseases, Diabetes Mellitus, Type 2, Metabolic Diseases
Chemicals Fatty Acids, Glucose