甲基化DNA免疫沉淀
DNA甲基化
胎儿游离DNA
液体活检
亚硫酸氢盐测序
DNA
计算生物学
生物
表观遗传学
分子生物学
基因
遗传学
基因表达
癌症
胎儿
产前诊断
怀孕
作者
Shu Yi Shen,Justin Burgener,Scott V. Bratman,Daniel D. De Carvalho
出处
期刊:Nature Protocols
[Springer Nature]
日期:2019-08-30
卷期号:14 (10): 2749-2780
被引量:134
标识
DOI:10.1038/s41596-019-0202-2
摘要
Circulating cell-free DNA (cfDNA) comprises small DNA fragments derived from normal and tumor tissue that are released into the bloodstream. Recently, methylation profiling of cfDNA as a liquid biopsy tool has been gaining prominence due to the presence of tissue-specific markers in cfDNA. We have previously reported cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) as a sensitive, low-input, cost-efficient and bisulfite-free approach to profiling DNA methylomes of plasma cfDNA. cfMeDIP-seq is an extension of a previously published MeDIP-seq protocol and is adapted to allow for methylome profiling of samples with low input (ranging from 1 to 10 ng) of DNA, which is enabled by the addition of 'filler DNA' before immunoprecipitation. This protocol is not limited to plasma cfDNA; it can also be applied to other samples that are naturally sheared and at low availability (e.g., urinary cfDNA and cerebrospinal fluid cfDNA), and is potentially applicable to other applications beyond cancer detection, including prenatal diagnostics, cardiology and monitoring of immune response. The protocol presented here should enable any standard molecular laboratory to generate cfMeDIP-seq libraries from plasma cfDNA in ~3-4 d.
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