cfDNA Methylation

Comparison of cfDNAmet-seq methods

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cfDNAmet-seq Comparison.pdf

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Methods		WGBS	WGBS’	WGBS’’	RRBS	RRBS'	cfMeDIP-seq	cfMeDIP-seq +WGS(shallow)	cfTAPS
Availability as a Kit		illumina	Zymo Research	QIAGEN	illumina	Zymo Research	Diagenode	Diagenode+vazyme	Yeasan
Theory		Bisulfite conversion	Bisulfite conversion	Bisulfite conversion	Enzyme digestion	Enzyme digestion	Affinity enrichment	Affinity enrichment	Enzyme conversion
Resolution		1bp	1bp	1bp	1bp	1bp	100bp	100bp	1bp
Coverage		95% of CpG	95% of CpG	95% of CpG	12% of CpG(~60% of promotors,85 of CGI)	12% of CpG(>70% of promotors,>75 of CGI)	67% of CpG	67% of CpG	95% of CpG
input		50-100ng	10pg-100ng	10pg-500ng	1ug	10-500ng	1-10ng	1-10ng	1-200ng
Feature	Methylation	✔️	✔️	✔️	✔️	✔️	✔️	✔️	✔️
	SNV	✔️	✔️	✔️	✔️	✔️	❌	❌	✔️
	CNV	✔️	✔️	✔️	❌	❌	❌	✔️	✔️
	Fragment size	✔️	✔️	✔️	❌	❌	❌	✔️	✔️
	Nucleosome occupancy	✔️	✔️	✔️	❌	❌	❌	✔️	✔️
	Tissue contribution	✔️	✔️	✔️	✔️	✔️	✔️	✔️	✔️
	End motif	❌	❌	❌	❌	❌	❌	✔️	✔️
Source of Bias	Incomplete bisulfite conversion	⭕	⭕	⭕	⭕	⭕
	Bisulfite PCR bias	⭕	⭕	⭕	⭕	⭕
	GC density bias				⭕	⭕
	GC content bias				⭕	⭕	⭕	⭕
	Crose-hybridization bias						⭕	⭕
Kit Price		¥35,000	¥850	¥365	¥2,100	¥415	¥1,050	¥1,050 +¥280	¥1000？
Sequencing Depth		60-90G	60-90G	60-90G	3-5G	3-5G	5-9G	5-9G+10G	30-90G
Total Cost		￥39000-41000	￥4900-6900	￥4400-6400	¥2,400	¥715	￥1400-1635	￥2330-2565	￥2500-6400
Reference		Shicheng Guo et al.Nature Genetics.2017	--	- -	Widschwendter M et al.Clinical Trial.2017	--	Shu Yi Shen et al.Nature Protocals.2019	- -	Siejka-Zielińska et al.Science Advances.2021.