Evaluation of the pooled sample method in Infinium MethylationEPIC BeadChip array by comparison with individual samples

Clinical Epigenetics

Methodology

Shinichiro Takiguchi¹  Akiko Yao²  Takashi X. Fujisawa³  Shota Nishitani³  Akemi Tomoda⁴ 

[1] Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, University of Fukui, Osaka, Japan;Life Science Innovation Center, University of Fukui, Fukui, Japan;Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan;Research Center for Child Mental Development, University of Fukui, Fukui, Japan;Research Center for Child Mental Development, University of Fukui, Fukui, Japan;Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, University of Fukui, Osaka, Japan;Life Science Innovation Center, University of Fukui, Fukui, Japan;Research Center for Child Mental Development, University of Fukui, Fukui, Japan;Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, University of Fukui, Osaka, Japan;Life Science Innovation Center, University of Fukui, Fukui, Japan;Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan;

关键词: Blood;    Child;    DNA methylation;    Epigenome;    Illumina EPIC array;    Methodology;    Pooled sample;    Pooling;   

DOI  :  10.1186/s13148-023-01544-3

 received in 2023-05-09, accepted in 2023-07-29,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundThe pooled sample method is used in epigenomic research and expression analysis and is a cost-effective screening approach for small amounts of DNA. Evaluation of the pooled sample method in epigenomic studies is performed using the Illumina Infinium Methylation 450K BeadChip array; however, subsequent reports on the updated 850K array are lacking. A previous study demonstrated that the methylation levels obtained from individual samples were accurately replicated using pooled samples but did not address epigenome-wide association study (EWAS) statistics. The DNA quantification method, which is important for the homogeneous mixing of DNA in the pooled sample method, has since become fluorescence-based, and additional factors need to be considered including the resolution of batch effects of microarray chips and the heterogeneity of the cellular proportions from which the DNA samples are derived. In this study, four pooled samples were created from 44 individual samples, and EWAS statistics for differentially methylated positions (DMPs) and regions (DMRs) were conducted for individual samples and compared with the statistics obtained from the pooled samples.ResultsThe methylation levels could be reproduced fairly well in the pooled samples. This was the case for the entire dataset and when limited to the top 100 CpG sites, consistent with a previous study using the 450K BeadChip array. However, the statistical results of the EWAS for the DMP by individual samples were not replicated in pooled samples. Qualitative analyses highlighting methylation within an arbitrary candidate gene were replicable. Focusing on chr 20, the statistical results of EWAS for DMR from individual samples showed replicability in the pooled samples as long as they were limited to regions with a sufficient effect size.ConclusionsThe pooled sample method replicated the methylation values well and can be used for EWAS in DMR. This method is sample amount-effective and cost-effective and can be utilized for screening by carefully understanding the effective features and disadvantages of the pooled sample method and combining it with candidate gene analyses.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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