Table 2.
Clinical applications of ctDNA in HCC.
| Region | Patient | Target site | Methods | Function of the gene | Ref. |
|---|---|---|---|---|---|
| Early detection and prognosis | |||||
| China | 37 HCC 33 healthy | DBX2, THY1 | Targeted bisulfite sequencing | Hypermethylation of DBX2, THY1 may result in HCC development | (73) |
| Hong Kong | 26 HCC 32 healthy | Hypomethylation, CNAs | Massively parallel bisulfite sequencing | / | (74) |
| United States | 66 HCC 43 benign chronic liver diseases | INK4A | Pyrosequencing and MSP | Promoter hypermethylation of INK4A leads to loss of p16 expression | (75) |
| China | 121 HCC 37 chronic hepatitis B 31 healthy | MT1M, MT1G promoter | MSP | Methylation of MT1M and MT1G promoters is associated with vascular invasion or metastasis | (76) |
| China | 100 HCC 29 healthy | HOXA9 | MSP, bisulfite sequencing, and Q-MSP | Hypermethylation of HOXA9 may be present in precancerous lesion during carcinogenesis | (77) |
| China | 1098 HCC 835 healthy | BMPR1A, PSD, ARHGAP25, KLF3, PLAC8, ATXN1, Chr 6:170, Chr 6:3, ATAD2, Chr 8:20 | Targeted bisulfite sequencing | / | (67) |
| Taiwan | 180 HCC | APC, COX2, RASSF1A miRNA | qMSP | Hypermethylation of RASSF1A suggests the early stage of HCC. Hypermethylation of APC and COX2 is associated with liver carcinogenesis | (78) |
| Taiwan | 237 HCC 257 controls | TBX2 | Pyrosequencing assay, Real-time PCR | Hypermethylation of TBX2 is associated with increased HCC risk | (79) |
| France and Germany | 98 HCC 191 cirrhosis | SEPT9 | MSP | Hypermethylation of SEPT9 is associated with liver carcinogenesis | (68) |
| United States | 116 HCC 81cirrhosis 98 healthy | HOXA1, EMX1, AK055957, ECE1, PFKP, CLEC11A | qMSP | / | (69) |
| China | 1204 HCC 392 CH/cirrhosis 958 healthy | 5hmC modifications | 5hmC-Seal technique | Serve as ideal markers for specific gene/locus activation in chromatin | (80) |
| China | 508 HCC 2250 cirrhosis 476 healthy | 5-hmc, NF, 5′end motif, fragmentation | NGS | / | (81) |
| ctDNA mutation | |||||
| United States | 66 HCC 35 cirrhosis 41HCV-related chronic hepatitis | hTERT | real-time PCR | The amount of hTERT gene in plasma served as serves as a surrogate of cfDNA | (82) |
| China | 48 HCC | TP53, CTNNB1, TERT | Droplet digital PCR | Mutation of TP53 and CTNNB1 suggests the occurrence of HCC; TERT promoter mutation is an early event in liver carcinogenesis; | (83) |
| China | 41 HCC | TERT, CTNNB1, TP53 | MiSeq sequencing | Mutation of TP53 and CTNNB1 suggests the occurrence of HCC; TERT promoter mutation is an early event in liver carcinogenesis; | (84) |
| China | 65 HCC 70 non- HCC 331 at risk patients | TP53, CTNNB1, AXIN1, the TERT promoter, HBV insertion site, AFP, DCP | HCCscreen | AXIN1 mutation is associated with HCC | (85) |
| China | 384 HCC | SCNA | WGS | / | (86) |
| Monitoring and guide therapy | |||||
| China | 34 HCC | SNVs, CNVs | Target sequencing Whole exome sequencing | / | (87) |
| United States | 14 HCC | TP53, CTNNB1, PTEN, CDKN2A, ARID1A, MET; CDK6, EGFR, MYC, BRAF, RAF1, FGFR1, CCNE1, PIK3CA, ERBB2/HER2 | NGS | / | (88) |
| United States | 26 HCC | TP53, CTNNB1, ARID1A | NGS | Mutations of TP53, CTNNB1 and ARID1A are associated with treatment response | (89) |
Q-MSP, Quantitative methylation-specific PCR; MSP, methylation-specific PCR; qMSP, real-time quantitative methylation-specific PCR; WGS, whole-genome sequencing; NGS, next-generation sequencing; SNVs, single nucleotide variants; CNVs, copy-number variants; SCNA, somatic copy number aberration.