A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies
We developed a comprehensive analysis pipeline to conduct Epigenome-wide Association Studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on data from 2,664 individuals, and 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment, and demonstrate that these improve data-quality. Using permutation testing we establish a null hypothesis for EWAS, show how it can be affected by...
Provenance — who produced it, who reused it
Linked to 22 papers in the literature. Roles are inferred factual signals (who deposited the data vs who reused it), with counts — never a judgement about any author.
- DunedinPACE, a DNA methylation biomarker of the pace of aging 2022 · 945 cites
- DNA Methylation Profiling of Uniparental Disomy Subjects Provide... 2016 · 122 cites
- Refining epigenetic prediction of chronological and biological a... 2023 · 115 cites
- Aging clocks based on accumulating stochastic variation 2024 · 112 cites
- New targeted approaches for epigenetic age predictions 2020 · 98 cites
- A survey of inter-individual variation in DNA methylation identi... 2018 · 79 cites
14 further papers cite this accession but reuse could not be confirmed.
Deep data QC
metadata only · no data-level QC for this typeStandardized, field-standard QC computed by touching the data — every metric states how it was obtained
No quantitative QC rubric exists for this data type yet, so it is deliberately left unscored — this is an honest "not applicable", not a poor rating.
measured = computed from the data · extrapolated/reported = derived or from the repository · dq-1.0 · provisional — verify independently