Evaluation of the HumanMethylationEPIC v2.0 Bead Chip Using Low Quality and Quantity DNA Samples.

IF 4.3 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Biological Procedures Online Pub Date : 2025-08-21 DOI:10.1186/s12575-025-00292-3

Brando Poggiali, Mikkel Eriksen Dupont, Marie-Louise Kampmann, Athina Vidaki, Vania Pereira, Claus Børsting, Jacob Tfelt-Hansen, Jeppe Dyrberg Andersen

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Abstract

Background: The HumanMethylationEPIC v2.0 BeadChip (EPIC v2.0) microarray is a widely used tool for genome-wide DNA methylation (DNAm) analysis, designed for high-quality human DNA with a recommended input of 250 ng. However, in clinical and forensic settings, DNA samples may be of low quality and/or quantity (highly fragmented and/or available in low amounts). This study assessed the performance of the EPIC v2.0 on DNA samples with various combinations of average DNA fragment size (350, 230, 165, and 95 bp) and DNA input amount (100, 50, 20, and 10 ng), compared to a paired control sample analyzed under optimal conditions (high-quality DNA and 250 ng DNA input).

Results: The best performance was obtained for samples with average DNA fragment size of 350 bp and 100 ng DNA input (~ 90% probe detection rate, r = 0.995, and median absolute beta value differences|Δβ| = 0.012 when compared with the control sample). Samples with lower average DNA fragment sizes and DNA input amount performed worse, with the lowest probe detection rate (~ 43%), r = 0.946, and the highest|Δβ| (0.038). Samples with average DNA fragment sizes of 95 bp and those with 165 bp at 10 ng DNA input failed to pass sample quality control (QC). CpG sites with intermediate DNAm values (β = 0.1-0.9) showed higher|Δβ| than the extreme DNAm values (β = 0-0.1, and β = 0.9-1). Finally, we assessed an application of DNAm by performing epigenetic age analysis, and observed mean absolute errors (MAEs) below 10 years for 350 bp samples across four epigenetic clocks.

Conclusions: Both DNA fragment size and DNA input amounts affect DNAm analysis on the EPIC v2.0, with the investigated DNA fragment size having a greater impact than the investigated DNA input amount. DNAm measurements were achieved with the EPIC v2.0 microarray down to an average DNA fragment size of 165 bp and a 20 ng DNA input. Highly fragmented DNA (95 bp) did not result in usable DNAm analysis as all samples failed QC. Overall, our study demonstrates the potential and limitations of EPIC v2.0 microarray with low quality and quantity DNA samples.

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低质量和低数量DNA样品对HumanMethylationEPIC v2.0芯片的评价

背景：HumanMethylationEPIC v2.0 BeadChip （EPIC v2.0）微阵列是一种广泛用于全基因组DNA甲基化（DNAm）分析的工具，设计用于高质量的人类DNA，推荐输入量为250 ng。然而，在临床和法医环境中，DNA样本的质量和/或数量可能较低（高度碎片化和/或可获得的数量较少）。本研究评估了EPIC v2.0在不同平均DNA片段大小（350、230、165和95 bp）和DNA输入量（100、50、20和10 ng）组合下的DNA样品上的性能，并与在最佳条件下（高质量DNA和250 ng DNA输入）分析的配对对照样品进行了比较。结果：平均DNA片段大小为350 bp、DNA输入为100 ng时，探针检出率为~ 90%，r = 0.995， β绝对值中位数差|Δβ| = 0.012，与对照样品相比，检测效果最佳。平均DNA片段大小和DNA输入量越小的样品表现越差，探针检出率最低（~ 43%），r = 0.946， |Δβ|最高（0.038）。在10 ng DNA输入时，平均DNA片段大小为95 bp和165 bp的样品未能通过样品质量控制（QC）。中间DNAm值（β = 0.1 ~ 0.9）的CpG位点|Δβ|高于极端DNAm值（β = 0 ~ 0.1和β = 0.9 ~ 1）。最后，我们通过进行表观遗传年龄分析来评估DNAm的应用，并观察到在四个表观遗传时钟中350 bp样本的平均绝对误差（MAEs）低于10年。结论：DNA片段大小和DNA输入量都影响EPIC v2.0上的DNA分析，研究的DNA片段大小的影响大于研究的DNA输入量。使用EPIC v2.0微阵列实现DNAm测量，平均DNA片段大小为165 bp， DNA输入为20 ng。高度碎片化的DNA （95bp）没有导致可用的DNA分析，因为所有样品都没有通过QC。总的来说，我们的研究证明了EPIC v2.0微阵列在低质量和低数量DNA样本下的潜力和局限性。

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来源期刊

Biological Procedures Online 生物-生化研究方法

CiteScore

10.50

自引率

0.00%

发文量

审稿时长

>12 weeks

期刊介绍： iological Procedures Online publishes articles that improve access to techniques and methods in the medical and biological sciences. We are also interested in short but important research discoveries, such as new animal disease models. Topics of interest include, but are not limited to: Reports of new research techniques and applications of existing techniques Technical analyses of research techniques and published reports Validity analyses of research methods and approaches to judging the validity of research reports Application of common research methods Reviews of existing techniques Novel/important product information Biological Procedures Online places emphasis on multidisciplinary approaches that integrate methodologies from medicine, biology, chemistry, imaging, engineering, bioinformatics, computer science, and systems analysis.