Table 2.
Summary of cfDNA-based cancer liquid biopsy studies.
| Cancer type | Marker(s) | Technical method | Clinical significance | Sample | References |
|---|---|---|---|---|---|
| Hematological malignancies | Copies of circulating NPM mutation A (NPM mut.A) DNA; TP53 mutations; MYD88 p.L265P mutation | RT-PCR and sequencing analysis; direct sequencing and a PCR-restriction digestion analysis (RFLP); droplet digital PCR (ddPCR) | Diagnosis | Plasma; serum; cerebrospinal fluid (CSF) | Hosny et al., 2009; Quan et al., 2015; Zorofchian et al., 2018 |
| Thyroid cancer | Cell-free DNA quantity and integrity index 180/67 | Quantitative real-time PCR (qPCR) | Diagnosis | Plasma | Salvianti et al., 2017 |
| Colorectal cancer | ALU115; dozens of DNA hypermethylation markers (e.g., SEPT9 and IKZF1, EMBP1, KCNQ5, CHST11, APBB1IP, and TJP2) | qPCR; methylated CpG tandem amplification and sequencing (MCTA-Seq) | Diagnosis | Plasma | Bhangu et al., 2017; Li et al., 2019 |
| High cfDNA and ctDNA levels; methylated circulating DNA biomarkers (EYA4, GRIA4, ITGA4, MAP3K14-AS1, MSC) | ddPCR | Predicting response to therapy | Plasma | Barault et al., 2018; Lyskjaer et al., 2019 | |
| High cfDNA levels; methylation levels of HLTF, HPP1/TPEF, hMLH1, TAC1, and SEPT9 | ddPCR; quantitative methylation-specific PCR | Indicating prognosis | Plasma; serum | Wallner et al., 2006; Tham et al., 2014; Hamfjord et al., 2019 | |
| Gastric cancer | Mutations of cadherin (CDH1), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), ARID1A (AT-rich interactive domain 1A), epidermal growth factor receptor (EGFR), and phosphatase and tensin homolog deleted on chromosome 10 (PTEN); 5-hydroxymethylcytosine (5hmC) | Bidirectional sequencing; 5 hmC quantification | Diagnosis | Plasma | Samuels et al., 2004; Li et al., 2005, 2017; Velho et al., 2005; Kaurah et al., 2007; Heald et al., 2010; Wen et al., 2010; Corso et al., 2011, 2012; Liu et al., 2011; Lee et al., 2012; Zang et al., 2012; Chen et al., 2013 |
| Hepatocellular carcinoma | RASSF1A promoter hypermethylation | Methylation-specific PCR | Diagnosis | Serum | Chan et al., 2008 |
| Post-radiotherapy (RT) cfDNA levels; mutation of BAX, CYP2B6 and HNF1A | RT-PCR; NGS | Predicting response to therapy | Plasma | Park et al., 2018; Alunni-Fabbroni et al., 2019 | |
| Methylation of insulin-like growth factor-binding protein 7 (IGFBP7); higher level of circulating DNA | RT-PCR | Indicating prognosis | Serum; plasma | Ren et al., 2006; Li et al., 2018 | |
| HPV-positive metastatic cervical cancer | HPV cfDNA | Duplex digital droplet PCR (ddPCR) | Diagnosis; predicting response to therapy | Serum | Kang et al., 2017 |
| Nasopharyngeal carcinoma | Epstein–Barr virus (EBV) DNA | PCR | Diagnosis | Plasma | Chan et al., 2017 |
| Lung cancer | act-EGFR mutant allele frequency (MAF) and T790M/act-EGFR MAF ratio; 36 cancer-related genes; TP53, RB1, BRAF, KIT, NOTCH1–4, PIK3CA, PTEN, FGFR1, MYC, MYCL1, and MYCN | ddPCR; NGS | Predicting response to therapy | Plasma | Almodovar et al., 2018; Del Re et al., 2018; Guibert et al., 2019 |
| EGFR19del, L858R, and T790M; cfDNA concentration; KRAS mutation | ddPCR; RFLP-PCR; mutant-enriched PCR | Indicating prognosis | Plasma or serum | Ai et al., 2016; Yanagita et al., 2016 | |
| Prostate cancer | Androgen receptor gene (AR) copy numbers (CN) and mutations; cfDNA concentration and mutations (BRCA2, PALB2); AR amplification, TMPRSS2-ERG fusion, PTEN gene deletion, NOTCH1 locus amplification along with genomic amplifications | dPCR and target sequencing; targeted cfDNA sequencing; whole-genome sequencing (WGS) | Predicting response to therapy | Plasma, urine | Xia et al., 2016; Goodall et al., 2017; Sumiyoshi et al., 2019 |
| Hypermethylation patterns of two genes (GSTP1 and APC) | Methylation-specific PCR | Indicating prognosis | Plasma | Hendriks et al., 2018 | |
| Breast cancer | ESR1 mutation | Digital PCR | Predicting response to therapy | Plasma | Beije et al., 2018 |
| cfDNA concentration and cfDNA integrity (cfDI); ALU-247, ALU-115, and cfDNA Integrity; methylation of KLK10, SOX17, WNT5A, MSH2, GATA3 | RT-qPCR; quantitative methylation-specific PCR | Indicating prognosis | Plasma | Cheng et al., 2018; Hussein et al., 2019; Panagopoulou et al., 2019 | |
| Cervical cancer | Increased cfDNA allele fraction deviation (AFD) | Targeted deep sequencing | Predicting response to therapy | Plasma | Tian et al., 2019 |
| Bladder carcinoma | Presence and dynamics of ctDNA | Ultra-deep multiplex polymerase chain reaction–based next-generation sequencing | Predicting response to therapy | Plasma | Christensen et al., 2019 |
| Pancreatic cancer | ABL1, ATM, DNMT3A, FLT3, HNF1A, NRAS, and SMAD4 | NGS; Library Preparation Kit | Predicting response to therapy | Plasma | Vietsch et al., 2017 |
| Pretreatment cfDNA fragment size of ≤167 bp (mode) and high pre-treatment cfDNA levels | Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA chip | Indicating prognosis | Plasma | Lapin et al., 2018 | |
| Esophageal cancer | Mutations of TP53, PIK3CA, ERBB2 | NGS; ddPCR | Predicting response to therapy | Plasma | Pasternack et al., 2018 |
| Oral squamous cell carcinoma | Higher cfDNA levels | Quantitative spectrometry | Indicating prognosis | Plasma | Lin et al., 2018 |
| Metastatic melanoma | Baseline cfDNA concentration | ddPCR | Indicating prognosis | Plasma | Valpione et al., 2018 |