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Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
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Evaluation of the pooled sample method in Infinium MethylationEPIC BeadChip array by comparison with individual
Shota Nishitani1,2,3, Takashi X Fujisawa4,5,6, Akiko Yao4
1Research Center for Child Mental Development, University of Fukui, Fukui, Japan. nshota@u-fukui.ac.jp.
Clinical Epigenetics
|August 28, 2023
Summary
The pooled sample method effectively replicates DNA methylation values for epigenome-wide association studies (EWAS) in differentially methylated regions (DMRs). This cost-effective approach is suitable for screening when considering its limitations.
Area of Science:
- Epigenetics
- Genomics
- Bioinformatics
Background:
- The pooled sample method is a cost-effective screening approach in epigenomic research, particularly for limited DNA amounts.
- Previous studies validated methylation level replication using pooled samples on the 450K array but lacked epigenome-wide association study (EWAS) statistics.
- Current DNA quantification and potential batch effects require re-evaluation for pooled sample epigenomic studies.
Purpose of the Study:
- To evaluate the utility of the pooled sample method for EWAS statistics on the updated 850K methylation array.
- To compare EWAS statistics for differentially methylated positions (DMPs) and regions (DMRs) between individual and pooled samples.
- To assess the reproducibility of methylation levels and EWAS results using pooled samples.
Main Methods:
- Four pooled DNA samples were created from 44 individual samples.
- Epigenome-wide association study (EWAS) statistics for DMPs and DMRs were calculated for both individual and pooled samples.
- Methylation levels were compared across the entire dataset and for top CpG sites.
Main Results:
- Methylation levels were well-reproduced in pooled samples, consistent with prior 450K array findings.
- EWAS statistics for DMPs were not replicated in pooled samples.
- EWAS statistics for DMRs showed replicability in pooled samples, particularly for regions with substantial effect sizes on chromosome 20.
Conclusions:
- The pooled sample method is reliable for replicating methylation values and can be applied to EWAS for DMRs.
- This method offers sample amount and cost-effectiveness for screening in epigenomic studies.
- Effective use of the pooled sample method requires understanding its advantages, disadvantages, and integration with candidate gene analyses.
