The DNA methylation profiling was based on the Illumina Infinium HumanMethylation450K BeadChip in the FHS and WHI cohort and was based on the Illumina Infinium EPIC 850K BeadChip in the JHS cohort. To ensure future use with EPIC arrays, we focused on the subset of 450,161 CpGs that were present on both platforms. We kept the original normalization methods to ensure consistency with previous publications. The WHI BA23 were normalized using the background correction method implemented in the software GenomeStudio. WHI EMPC were normalized based on BMIQ [57 (link)] for beta-mixture quantile normalization. The JHS data were normalized using the "noob" normalization method implemented in the minfi R package [58 (link),59 (link)].
Lu A.T., Seeboth A., Tsai P.C., Sun D., Quach A., Reiner A.P., Kooperberg C., Ferrucci L., Hou L., Baccarelli A.A., Li Y., Harris S.E., Corley J., Taylor A., Deary I.J., Stewart J.D., Whitsel E.A., Assimes T.L., Chen W., Li S., Mangino M., Bell J.T., Wilson J.G., Aviv A., Marioni R.E., Raj K, & Horvath S. (2019). DNA methylation-based estimator of telomere length. Aging (Albany NY), 11(16), 5895-5923.
Corresponding Organization : University of California, Los Angeles
Other organizations :
University of Edinburgh, King's College London, Chang Gung University, Chang Gung Memorial Hospital, Peking University, Tulane University, Fred Hutch Cancer Center, National Institute on Aging, National Institutes of Health, Northwestern University, Columbia University, University of North Carolina at Chapel Hill, VA Palo Alto Health Care System, Stanford University, Children's Minnesota, University of Mississippi Medical Center, Jackson Memorial Hospital, Rutgers, The State University of New Jersey, Public Health England
Subset of 450,161 CpGs that were present on both the Illumina Infinium HumanMethylation450K BeadChip and the Illumina Infinium EPIC 850K BeadChip
Original normalization methods to ensure consistency with previous publications
Background correction method implemented in the software GenomeStudio for WHI BA23
BMIQ (beta-mixture quantile normalization) for WHI EMPC
Noob normalization method implemented in the minfi R package for JHS data
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