Positional Effects Revealed in Illumina Methylation Array and The Impact on Analysis

Abstract

Aim: We aimed to prove the existence of positional effects in the Illumina methylation beadchip data and to find an optimal correction method. Materials & methods: Three HumanMethylation450, three HumanMethylation27 datasets and two EPIC datasets were analyzed. ComBat, linear regression, functional normalization and single-sample Noob were used for minimizing positional effects. The corrected results were evaluated by four methods. Results: We detected 52,988 CpG loci significantly associated with sample positions, 112 remained after ComBat correction in the primary dataset. The pre- and postcorrection comparisons indicate the positional effects could alter the measured methylation values and downstream analysis results. Conclusion: Positional effects exist in the Illumina methylation array and may bias the analyses. Using ComBat to correct positional effects is recommended.

Keywords::

• ComBat
• DNA methylation
• epigenetics
• epigenomics
• Illumina Infinium MethylationEPIC BeadChip
• Infinium Methylation 450K
• Infinium Methylation 27K
• positional effects

Supplementary data

To view the supplementary data that accompany this paper, please visit the journal website at:www.tandfonline.com/doi/suppl/10.2217/epi-2017-0105

Acknowledgements

We sincerely thank Chicago Biomedical Consortium for its supports (to C Liu) as well. We are grateful to Z Chen and Y Jiang for editing the manuscript. All the data contributors are also sincerely thanked for data submitted in the GEO, particularly G Klein and DA Bennett for sharing their data of Religious Orders Study and Memory and Aging Project (ROSMAP).

Financial & competing interests disclosure

This work was supported by NIH (grant numbers: 1 U01 MH103340-01, 1R01ES024988 to C Liu); and National Natural Science Foundation of China (grant numbers: 81401114, 31571312 to C Chen). Funding for open access charge: NIH and National Natural Science Foundation of China. The National Key Plan for Scientific Research and Development of China, Innovation-Driven Project of Central South University (no. 2015CXS034,2018CX033; to C Chen). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

This work was supported by NIH (grant numbers: 1 U01 MH103340-01, 1R01ES024988 to C Liu); and National Natural Science Foundation of China (grant numbers: 81401114, 31571312 to C Chen). Funding for open access charge: NIH and National Natural Science Foundation of China. The National Key Plan for Scientific Research and Development of China, Innovation-Driven Project of Central South University (no. 2015CXS034,2018CX033; to C Chen). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.