甲基化捕获测序能否替代450K

生信技能树

发布于 2021-11-23 15:20:54

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发布于 2021-11-23 15:20:54

任何一个新技术，在蓬勃发展的过程中肯定是少不了大量的测评研究，从技术细节，平台，软件工具算法多个维度的对比探索。

发表于 Epigenetics . 2016; 链接 https://pubmed.ncbi.nlm.nih.gov/26786415/，文章标题是：《Comparison of Methyl-capture Sequencing vs. Infinium 450K methylation array for methylome analysis in clinical samples》，随着甲基化技术的深入人心， epigenome-wide association studies (EWAS) 时代到来了，但是临床上的EWAS研究要求成本可控，而且样品DNA起始量低，但是红极一时的450K芯片不尽人意，所以研究者们想试试看Methyl-Capture Sequencing (MC Seq) 能否替代450K。

首先遍历一下其它相似技术的缺点

甲基化技术里面，whole-genome bisulfite conversion (WGBS) 是金标准，但是价格昂贵，数据处理消耗计算资源，而Reduced- representation bisulfite sequencing (RRBS) 和Methylated DNA Immunoprecipitation Sequencing (MeDIP-Seq),都是片面的，只有 MC Seq 克服了它们其它这些技术的缺点：

lower genome coverage (Infinium 450K),
high cost and processing time (WGBS),
overrepre- sentation of repeated (RRBS)
methylated regions (MeDIP- Seq).

设计实验来评估

主要是采用 SureSelect Human Methyl-Seq panel (Agilent Technologies) 这个平台做 Methyl-Capture Sequencing (MC Seq) ，纳入7个样品：

技术指标是都超级好！

首先它自己内部的重复性很好，其次它不同DNA起始量差异也不大。最重要的是它跟最流行的450K基本上也没有差异，如下所示：

可以从以下5个点来比较 (MC Seq vs. Infinium 450K) 是否值得被选用做EWAS研究：

(i) desired genomic coverage (MC Seq has higher density of CpGs, and hence higher coverage of variable sites);
(ii) expected inter-group differences in methylation or sensitivity desired (Infinium 450K has higher sensitivity for subtle variations in methylome);
(iii) cost (Infinium 450K has lower cost)
(iv) coverage of methylation sites in non-CpG context (MC Seq has a higher capacity).
The fifth factor for consideration is whether an investigator wishes to customize and specify methylation sites of interest, which can be only done through bait design in MC Seq.

有意思的是作者并没有公布数据，这样的结论很难让人信服啊！难道不能是两个公司打架：