cfDNA Methylation
Comparison of cfDNAmet-seq methods
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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. |
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