cfDNA Methylation
Last updated
Last updated
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
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Widschwendter M et al.Clinical Trial.2017
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Shu Yi Shen et al.Nature Protocals.2019
- -
Siejka-Zielińska et al.Science Advances.2021.