甲基化DNA免疫沉淀
DNA甲基化
CpG站点
DNA
基因组DNA
计算生物学
差异甲基化区
甲基化
胎儿游离DNA
分子生物学
生物
化学
遗传学
基因
基因表达
胎儿
产前诊断
怀孕
作者
Samantha L. Wilson,Shu Yi Shen,Lauren Harmon,Justin M. Burgener,Tim Triche,Scott V. Bratman,Daniel D. De Carvalho,Michael M. Hoffman
标识
DOI:10.1016/j.crmeth.2022.100294
摘要
Cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) identifies genomic regions with DNA methylation, using a protocol adapted to work with low-input DNA samples and with cell-free DNA (cfDNA). We developed a set of synthetic spike-in DNA controls for cfMeDIP-seq to provide a simple and inexpensive reference for quantitative normalization. We designed 54 DNA fragments with combinations of methylation status (methylated and unmethylated), fragment length (80 bp, 160 bp, 320 bp), G + C content (35%, 50%, 65%), and fraction of CpG dinucleotides within the fragment (1/80 bp, 1/40 bp, 1/20 bp). Using 0.01 ng of spike-in controls enables training a generalized linear model that absolutely quantifies methylated cfDNA in MeDIP-seq experiments. It mitigates batch effects and corrects for biases in enrichment due to known biophysical properties of DNA fragments and other technical biases.
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