Table 4.
cfDNA hypermethylation performance as biomarker for lung cancer diagnosis.
| Study | Year | Assay | Methylated genes | Study population | Sample | Diagnostic performance | ||
|---|---|---|---|---|---|---|---|---|
| S | E | AUC | ||||||
| Single-Dual biomarker | ||||||||
| Wang (106) | 2007 | Methylation-Specific RT-PCR | RASSF1A | 15 healthy controls 35 benign pulmonary diseases patients 80 LC patients (40 ADC, 26 SCC, nine adenosquamous carcinoma, five SCLC) Stages: I: 9; II: 18; III: 29; IV: 24 |
Serum | 34% | 100% | – |
| Schmidt (107) | 2010 | Methylation-Specific RT-PCR | SHOX2 | 242 controls 281 LC patients (109 ADC, 103 SCC, 37 NOS NSCLC, 29 SCLC, three others) Stages: I: 59; II: 43; III: 108; IV: 62; unknown: 9 |
Bronchial aspirates | 68% | 95% | 0.860 |
| Kneip (108) | 2011 | Methylation-Specific RT-PCR | SHOX2 | 155 controls 188 LC patients (38 SCC, 31 SCC, 15 SCLC, 104 other) Stages: I:37; II:29; III:53; IV:42; unknown:27 |
Plasma | 60% | 90% | 0.780 |
| Hwang (109) | 2011 | Pyrosequencing | HOXA9 | 51 healthy controls 58 benign lung diseases patients 76 LC patients (42 ADC and 34 SCC). Stages: I: 14; II: 5; III: 28; IV: 29 |
Induced sputum | 71% | 55% | 0.969 |
| Dietrich (110) | 2012 | Epi proLung BL | SHOX2 and PTGER4 | 125 controls 125 LC patients (26 ADC, 28 SCC, 40 SCLC, 9 NSCLC NOS, 32 others) |
Bronchial aspirates | 78% | 96% | 0.940 |
| Ponomaryova (111) | 2013 | Methylation-Specific RT-PCR | RARB2and RASSF1A | 32 healthy donors 60 NSCLC patients (40 SCC and 20 ADC) Stages: I/II: 20; III: 40 |
Plasma and cell-surface-bound circulating DNA | 85% | 75% | – |
| Powrózek 2014 (112) | 2014 | Methylation-specific RT-PCR | Septin 9 | 100 healthy controls 70 LC patients (20 ADC, 20 SCC, 23 SCLC, seven others) Stages: IIA–IIIA: 23; IIIB–IV: 47 |
Plasma | 44% | 92% | |
| Konecny (113) | 2016 | Epi proLung BL | SHOX2 | 69 suspected LC patients; 31 excluded LC (controls) and 38 LC confirmed including 28 NSCLC and one SCLC. Stages: I–II: 5; III–IV: 30; unknown: 3 |
Bronchial lavage | 89% | 85% | 0.890 |
| Plasma | 81% | 79% | 0.870 | |||||
| Powrózek (114) | 2016 | Methylation-specific RT-PCR | DCLK1 | 95 healthy controls 65 LC patients (22 ADC, 20 SCC, 19 SCLC, four others) Stages: IIA–IIB: 7; IIIA: 21; IIIB–IV: 37 |
Plasma | 49% | 92% | – |
| Ren (115) | 2017 | Methylation-specific RT-PCR | SHOX2 and RASSF1A | 130 controls (112 benign lung disease patients and 18 patients with other malignancies) 52 patients with no exact diagnosis 123 LC patients including 82 ADC, 17 SCC, eight SCLC, 16 others Stages: 0: 4; I: 47; II: 13; III: 19; IV: 25; unknown: 15 |
Bronchoalveolar lavage | 72% | 90% | – |
| Nunes (116) | 2019 | Methylation-specific RT-PCR | 4 genes: APC, HOXA9, RARβ2, and RASSF1A | 28 benign lung diseases patients 129 LC cancer patients (65 ADC, 42 SCC, 19 SCLC) Stages: I: 15; II: 11; III: 27; IV: 76 |
Plasma | APC: 25% RASSF1A: 24% APC and RASSF1A: 38% |
APC: 96% RASSF1A: 95% APC and RASSF1A: 93% |
APC: 0.622 RASSF1A: 0.591 |
| Combination biomarker | ||||||||
| Fujiwara (117) | 2005 | Methylation-Specific RT-PCR | RARβ, p16INK4a, DAPK, RASSF1A, and MGMT | 100 non-malignant diseases patients nine other malignancies 91 LC patients (64 ADC, 21 SCC, four SCLC, two carcinoid). Stages: I: 53; II: 7; III: 22; IV: 9 |
Serum | 50% | 85% | – |
| Hsu (118) | 2007 | Methylation-Specific RT-PCR | BLU, CDH13,FHIT, p16, RARβ, and RASSF1A | 36 cancer-free controls 63 NSCLC patients (41 ADCs, 13 SCC) Stages: I–II: 41; III–IV: 21; Not staged: 1 |
Plasma | 73% | 82% | |
| Zhang (119) | 2011 | Methylation-Specific RT-PCR | 9 genes: APC, CDH13, DLEC1, EFEMP1, KLK10, p16INK4A, RARβ, RASSF1A, SFRP1 | 50 cancer-free controls 110 NSCLC patients (Stage I/II) |
Plasma | 90% APC, RASSF1A, CDH13, KLK10 and DLEC1: 84% |
58% APC, RASSF1A, CDH13, KLK10 and DLEC1: 74% |
– |
| Begum (120) | 2011 | Methylation specific RT-PCR | 6 genes: APC, AIM1, CDH1, DCC, MGMT and RASSF1A | 30 controls 76 LC patients (36 ADC, 26 SCC, 14 others) Stages: I: 41; II: 17; III: 11; IV: 5; unknown: 2 |
Serum | 84% | 57% | – |
| Nikolaidis (121) | 2012 | Methylation specific RT-PCR | 4 genes: TERT, WT1, p16 and RASSF1 | 109 controls; 139 LC cases (22 ADC, 31 SCC, 39 SCLC, 16 LCC, 31 others) Stages: T1: 46; T2: 91; T3: 20; T4: 53; N0: 94; N1: 35; N2: 63; N3: 13 |
Bronchial lavage | 82% | 91% | – |
| Diaz-Lagares (122) | 2016 | Pyrosequencing | 4 genes: BCAT1, CDO1, TRIM58, and ZNF177 | Bronchial aspirates cohort: -29 cancer-free controls -51 LC patients (17 ADC, 19 SCC, 11 NSCLC NOS, 4 other) Stages: I: 5; II: 6; III: 21; IV: 18; unknown: 1 BAL cohort: -29 cancer-free controls -82 LC patients (25 ADC, 40 SCC, 12 SCLC, 5 others) Stages: I: 17; II: 8; III: 20; IV: 18; unknown: 19 Sputum cohort: -26 cancer-free controls -72 LC patients (38 ADC, 24 SCC, 5 SCLC, 4 other) Stages: I: 12; II: 13; III: 23; IV: 19; unknown: 5 |
Bronchial aspirates | 84% | 81% | 0.910 |
| Bronchioalveolar lavages | ~80% | ~80% | 0.850 | |||||
| Sputum | ~65% | ~65% | 0.930 | |||||
| Ma (123) | 2016 | Quantum dots combined with FRET | PCDHGB6, HOXA9 and RASSF1A | 50 controls 50 NSCLC patients (24 ADC and 16 SCC) Stages: I: 23; II: 17 |
Bronchial brushing | 80% | 100% | 0.907 |
| Hulbert (124) | 2017 | Methylation-specific RT-PCR | 6 genes: SOX17, TAC1, HOXA7, CDO1, HOXA9, ZFP42 | 60 cancer-free controls 150 LC cases (121 ADC, 26 SCC, 3 others) Stages: IA–IB: 136; IIA: 14 |
Sputum | TAC1, HOXA17 and SOX17: 93% 6 genes, age, PY, COPD and FVC: 91% |
TAC1, HOXA17 and SOX17: 89% | TAC1, HOXA17 and SOX17: 0.890 6 genes, age, PY, COPD and FVC: 0.850 |
| Plasma | CDO1, TAC1 and SOX17: 86% 6 genes, age, PY, COPD and FVC: 85% |
CDO1, TAC1 and SOX17:78% | CDO1, TAC1 and SOX17: 0.770 6 genes, age, PY, COPD and FVC: 0.890 |
|||||
| Ooki (125) | 2017 | Methylation-specific RT-PCR | 6 genes: CDO1, HOXA9,AJAP1, PTGDR, UNCX, and MARCH11 | 42 controls 43 primary NSCLC with matched serum samples from stage IA ADC 40 serum samples from stage IA SCC 70 pleural effusions samples 49 ascites samples |
Serum | ADC: 72%SCC: 60% | 71% | – |
| Pleural effusions | 4-gene panel (CDO1, PTGDR, UNCX, and MARCH11): 70% 5-gene panel (CDO1, AJAP1, PTGDR, UNCX, and MARCH11): 76% |
4-gene panel (CDO1, PTGDR, UNCX, MARCH11): 85% 5-gene panel (CDO1, AJAP1, PTGDR, UNCX, MARCH11): 76% |
– | |||||
| Hubers (126) | 2017 | Methylation-specific RT-PCR | 7 genes: RASSF1A, APC, cytoglobin,3OST2, PRDM14, FAM19A4 and PHACTR3 | 219 controls 56 LC patients (34 ADC,7 SCC, 2 SCLC, 13 others Stages: I:36, II:4, III:6, IV:10 |
Sputum | 17% | 93% | – |
| Liang (127) | 2019 | Methyl-seq | 9 genes | 27 controls 39 LC patients (32 ADC, 6 SCC and 1 other) Stages: IA: 20; IB: 7; IIA: 1; Later stages: 10; unknown: 1 |
Plasma | 80% | 85% | 0.820 |
ADC, adenocarcinoma; AUC, area under the curve; COPD, chronic obstructive pulmonary disease; E, specificity; FRET, fluorescence resonance energy transfer; FVC, forced vital capacity; IS, in situ; LC, lung cancer; LCC, large cell carcinoma; NSCLC, non-small cell lung cancer; NOS-NSCLC, not otherwise specified non-small cell lung cancer; PY, pack-years; S, sensitivity; SCC, squamous cell carcinoma; SCLC, small cell lung cancer.