Table 2.
Prognostic and predictive methylated ctDNA in colorectal cancer patients
| Gene | Country | Type of study | No. of cases | Time of sample collection | Cases characteristics | FU duration | Sample type | Technology used | Hypermethylation reported association with | HR (p-value) | References |
|---|---|---|---|---|---|---|---|---|---|---|---|
| HPP1 | Germany | Prospective | 77 | Pretherapy |
UICC I (10), II (24) III (27), IV (15) |
5 Y | Serum | MethyLight | Higher risk of death | 5.1 (0.001) | [77] |
| HLTF | 3 (0.008) | ||||||||||
| HPP1 and/or HLTF | HR (uni) = 4.2 (< 0.001), HR (multi) = 3.4 (0.007) | ||||||||||
| HLTF | Germany | Prospective | 103 | Pretherapy | UICC IV | 6 Y | Serum | MSP | Worse OS in stage IV | 1.8 (0.0438) | [76] |
| HPP1 | Germany | Prospective | 103 | Pretherapy | UICC IV | 6 Y | Serum | MSP | Worse OS in stage IV | 1.6 (0.0495) | [76] |
| HLTF | Germany | Prospective | 259 | Pretherapy | I (51), II (68), III (51), IV (89) | 10 Y | Serum | MethyLight | Shorter OS (p = 0.0008) esp. in stage IV (p = 0.0081) | [78] | |
| HPP1 | Germany | Prospective | 259 | Pretherapy | I (51), II (68), III (51), IV (89) | 10 Y | Serum | MethyLight | Shorter OS (p < 0.0001) esp. in stage IV (p = 0.0005) | [78] | |
| HPP1 | Germany | Prospective | 467 | Pretherapy and after first cycle | mCRC on combination of a fluoropyrimidine, oxaliplatin and bevacizumab | 24 W | Plasma | MethyLight | At baseline with worse OS, after the first cycle with high risk of progression | HR baseline = 1.86 (0.0001), HR during treatment = 2.13 (0.0001) | [79] |
| HLTF | Germany | 106 | Pretherapy | UICC I–III | 5 Y | Serum | MethyLight | Increased risk of recurrence | HRuni = 2.7 (0.014), HRmulti = 2.5 (0.023) | [80] | |
| SEPT9 | Singapore | Prospective | 150 | Preoprative, 6 M-FU and 1Y-FU | I–III; 1 neoadjuvant treatment and 45 adjuvant chemo and radiotherapy | 7 Y | Serum | MSP | 1Y-FU with poor DFS and CSS; dynamic change from 6 M to 1Y and from baseline and 1Y with recurrence | HR (1Y-FU; CSS) = 2.69 (< 0.05); HR (1Y-FU;DFS) = 3.50 (0.001); HR (6 M-FU to 1Y-FU;DFS) = 2.58 (0.05), HR (baseline to 1Y-FU;DFS) = 3.35 (0.01) | [81] |
| SEPT9 | China | Prospective | 98 | Preoperative and at 3 M intervals | Performed surgery | 28 M | Plasma | MSP | Postoperative with higher mortality rate (p = 0.024) and presence of mets (p = 0.013) and lower OS (p = 0.014) | [18] | |
| SEPT9 | China | Retrospective | 300 from china, 330 from TCGA | Preoperative | Absent | 30 M for Chinese people, 125 M for TCGA | Plasma | MSP | Shorter PFS (p = 0.019) and OS (p = 0.008) | [83] | |
| SEPT9 | China | Prospective | 82 | Preoperative and 1 and 7 days postoperative | I (14), II (40), III (45) | 21 M | Plasma | MSP | Higher risk of death post-surgery | HR (OS) = 2.51 (0.036) | [82] |
| SEPT9 (10 subregions) | China | Prospective | 82 | Postoperative (within 2 W) | 3Y | Plasma | MSP | Poor RFS | HR (RFS) = 4.20 (0.0005) | [29] | |
| SEPT9 (10 subregions) | China | Prospective | 19 | Serial postoperative | 3Y | Plasma | MSP | Poor RFS; better in recurrence prediction than single detection | HR (RFS) = 7.49 (0.01) | [29] | |
| NPY | Denmark | Prospective | 97 | Pretherapy, 2 W of treatment and before every new cycle | mCRC receiving regorafenib as last-line treatment | Every second week for 2 months and then monthly if stable | Plasma | MSP ddPCR | Baseline with shorter OS (p < 0.001) | [86] | |
| NPY | Denmark and Canada | Prospective | 146 | Pretherapy | Locally advanced rectal cancer taking Neoadjuvant Chemoradiotherapy | 5 Y | Serum | MSP ddPCR | Higher risk of death and distant disease progression | HR (OS) = 2.08 (0.007), HR (distant mets) = 2.20 (0.01) | [88] |
| NPY | Denmark | Prospective | 123 | Pretherapy | mCRC taking 5-FU, oxaliplatin, and bevacizumab | 7.5 Y | Plasma | MSP ddPCR | Shorter PFS and OS | HR (PFS) = 0.48 (0.0005), HR (OS) = 0.50 (0.0001) | [89] |
| RASSF1A | Greece | Prospective | 155 | Preoperative | Early operable (88), mets (67) | 8 Y | Serum | MSP | Worse survival in early and mets; more pronounced in mets | HR (early; OS) = 3.06 (0.038), HR (mets; OS) = 5.76 (0.001) | [93] |
| RASSF1A | China | Prospective | 108 CRC, 78 healthy | Pretherapy and after two cycles | II–III receiving oxaliplatin-based chemo | 3 Y | Blood | MSP | Shorter PFS and OS | HR = 2.471 (0.02) | [92] |
| BCAT1 and IKZF1 | Australia and New Zealand | Prospective | 172 | 12 M post-surgery | Invasive CRC requiring surgery | 12 M | Plasma | MSP | Increased risk of residual disease and recurrence | HR = 3.8 (0.004) | [94] |
| BCAT1 and IKZF1 | USA | Prospective | 322 | Within 6 M post-therapy | Stage II or III CRC | Plasma | MSP (COLVERA) | Increased recurrence | [97] | ||
| BCAT1 and IKZF2 | Australia and New Zealand | Prospective | 144 | Within 12 M in remission | I (21), II (50), III (62), IV (11) | Plasma | MSP (COLVERA) | Increased recurrence | [96] | ||
| BCAT1 and IKZF3 | Australia and New Zealand | Prospective | 122 | 3, 6, or 12 M in remission | I (28), II (40), III (47), IV (4) | Plasma | MSP | Increased recurrence | [95] | ||
| SST | Singapore | Prospective | 165 | Preoperative | Done surgery without neoadjuvent chemo | 7 Y | Serum | MSP | Higher risk of cancer-specific death esp stage III and risk of recurrence | HR (OS) = 1.96 (0.031), HR (DFS) = 2.60 (0.003) | [99] |
| TAC1 | Singapore | Prospective | 150 | Preoperative, 6 M-FU and 1Y-FU | I–III; 1 neoadjuvant treatment and 45 adjuvant chemo- and radiotherapy | 7 Y | Serum | MSP | 6 M-FU with poor DFS and CSS; dynamic change from baseline to 6 M with recurrence | HR (6 M-FU; CSS) = 4.12 (< 0.001), HR (6 M-FU, DFS) = 5.72 (< 0.001), HR (from baseline to 6 M-FU; DFS) = 4.71 (< 0.001) | [81] |
| APC | Greece | Prospective | 155 | Preoperative | Early operable (88), mets (67) | 8 Y | serum | MSP | Worse survival in early and mets; more pronounced in early operable | HR (early; OS) = 7.88 (< 0.001), HR (mets; OS) = 3.47 (0.017) | [93] |
| 13 markers *** | Minnesota, USA | Prospective | 40 recurrent, 60 healthy | Post-surgery | I (11), II (26), III (24), IV (23) | Plasma | TELQAS | detect recurrent/metastatic CRC with 90% sensitivity, 90% specificity, AUC = 0.96 | [59] | ||
| MYO1G, CALML4, GCET2, KLF3, ATXN1 | China | Prospective | 528 | Pretherapy | Training cohort | 26.6 M | Plasma | Deep sequencing of bis-DNA | High cp-score associated with poor prognosis (OS) | 2.24 (< 0.001) | [57] |
| 273 | Validation cohort | 26.6 M | 2.21 (< 0.001) | ||||||||
| EYA4, GRIA4, ITGA4, MAP3K14-AS1, MSC | Italy | Retrospective | 60 before and 62 during treatment | Pretherapy and biweekly during regorafenib treatment | mCRC patients who received regorafenib | 5.5 M (1.25–56.5 M) | Plasma | Methyl-BEAMing | Baseline with worse OS and shorter PFS, during treatment with shorter PFS | HR baseline (OS) = 3.471 (0.0001), HR baseline (PFS) = 2.196 (0.0015), HR during treatment (PFS) = 2.985 (< 0.0001), HR dynamic (PFS) = 1.78 (0.028) | [101] |
***(FER1L4, VAV3, CHST2, DTX1, PDGFD, SFMBT2, QKI, ZNF568, ANKRD13B, ZNF671, CNNM1, GRIN2D, JAM3)
CECT, contrast enhanced computed tomography; Chemo, Chemotherapy; CSS, Cancer-specific survival; ddPCR, digital droplet PCR; DFS, Disease-free survival; FU, fluorouracil; MethyLight, fluorescence-based real time PCR; Mets, Mestastasis; M, month; MS-HRM, methylation‐sensitive high‐resolution melting assay; Multi, Multivariate; OS, Overall Survival; PFS, Progression-free survival; RFS, recurrence-free survival; TELQAS, target enrichment long-probe quantitative-amplified signal TA, tubular adenoma; 1FU, 1-year follow-up; 6MFU, 6-month follow-up; Uni, univariate; Y, year