Replication and expansion of epigenome-wide association literature in a black South African population

H. Toinét Cronjé, Hannah R Elliott, Cornelie Nienaber-Rousseau, Marlien Pieters

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DNA methylation is associated with non-communicable diseases (NCDs) and related traits. Methylation data on continental African ancestries are currently scarce even though there are known genetic and epigenetic differences between ancestral groups and a high burden of NCDs in Africans. Furthermore, the degree to which current literature can be extrapolated to the understudied African populations, who have limited resources to conduct independent large-scale analysis, is not yet known. To this end, this study examines the reproducibility of previously published epigenome-wide association studies (EWASs) of DNA methylation conducted in different ethinicities, on factors related to NCDs, by replicating findings in 120 South African Batswana men aged 45 to 88 years. In addition, novel associations between methylation and the NCD-related factors are investigated using the Illumina EPIC BeadChip.

Up to 86% of previously identified epigenome-wide associations with NCD-related traits (alcohol consumption, smoking, body mass index, waist circumference, C-reactive protein, blood lipids and age) overlapped with those observed here and a further 13% were directionally consistent. Only 1% of the replicated associations presented with effects opposite to findings in other ancestral groups. The majority of these inconcistencies were associated with population-specific genomic variance. In addition, we identified eight new 450K array CpG associations, not previously reported in other ancestries and eleven novel EPIC CpG associations with alcohol consumption.

The successful replication of existing EWAS findings in this African population demonstrates that blood-based 450K EWAS findings from commonly investigated ancestries can largely be extrapolated to ethnicities for whom epigenetic data is not yet available. Possible population-specific differences in 14% of the tested associations does, however, motivate the need to include a diversity of ethnic-groups in future epigenetic research. The novel associations found with the enhanced coverage of the Illumina EPIC array support its usefulness to expand epigenetic literature.
Original languageEnglish
Article number6 (2020)
Number of pages13
JournalClinical Epigenetics
Publication statusPublished - 7 Jan 2020


  • ancestry
  • DNAm
  • EPIC
  • epigenetic epidemiology
  • EWAS
  • methylation
  • NCD
  • PURE

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