1. State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China 2. Genetron Health (Beijing) Co. Ltd., Beijing 102206, China
Minimal residual disease (MRD) is termed as the small numbers of remnant tumor cells in a subset of patients with tumors. Liquid biopsy is increasingly used for the detection of MRD, illustrating the potential of MRD detection to provide more accurate management for cancer patients. As new techniques and algorithms have enhanced the performance of MRD detection, the approach is becoming more widely and routinely used to predict the prognosis and monitor the relapse of cancer patients. In fact, MRD detection has been shown to achieve better performance than imaging methods. On this basis, rigorous investigation of MRD detection as an integral method for guiding clinical treatment has made important advances. This review summarizes the development of MRD biomarkers, techniques, and strategies for the detection of cancer, and emphasizes the application of MRD detection in solid tumors, particularly for the guidance of clinical treatment.
High sensitivity; decreased error rates associated with sequencing process
Dependent on the efficiency of amplification; the desired sequence needs to be previously characterized
Tam-Seq
Forshew et al. [49]
PCR amplicon-based NGS
Using primers to tag
High sensitivity and specificity; high efficiency; detection of abundant and rare mutations
The desired sequence needs to be previously characterized
CAPP-Seq
Newman et al. [96]
Hybrid capture-based NGS
Covering multiple classes of somatic alterations that identified mutations in > 95% of tumors
High sensitivity and specificity; wide application; reduced the impact of stochastic noise and biological variability
Sufficient cfDNA input; inefficient capture of fusions
PhasED-seq
Kurtz et al. [102]
Hybrid capture-based NGS
Identification of phased variants
Super sensitivity; decreased technical and biological error rates
Need more studies to validate, particularly in solid tumors
MAESTRO
Gydush et al. [103]
Hybrid capture-based NGS
Converted low-abundance mutations into high-abundance mutations
Improved breadth, depth, accuracy and efficiency
Costly; limited sensitivity with error-prone loci discarded
WGS
Zviran et al. [58]
WGS
Identification of genome-wide mutational signals
Comprehensive mutation profiling
High cost; low sensitivity; limited sequencing depth
WGBS
Lissa et al. [109]
WGBS
Bisulfite conversion-based
Comprehensive methylation profiling
Costly; low depth sequencing
cfMeDIP-seq
Shen et al. [112]
Immunoprecipitation based NGS
Antibody enrichment-based; antibody specific to 5mC
Sensitive; reduced the required DNA input amount to 1–10 ng
Limited sensitivity; dependent on the quality of antibody
Tab.1
Fig.2
Fig.3
Application
Cancer
Study & year
Patient
Stage
Biomarker
Technique & strategy
Main conclusions
Prognosis prediction
Colorectal cancer
Diehl et al., 2008 [46]
20
CRC II–IV
Mutation
BEAMing; tumor-informed
1. Postoperative ctDNA was associated with RFS: 15 of the 16 ctDNA+ patients relapsed while 4 ctDNA– patients did not relapse (P = 0.006)
Liu et al., 2022 [71]
60
CRC II–III
Mutation/CNV
Target NGS/sWGS; tumor-informed and tumor-naïve
Three approaches were used to detect post-NAT ctDNA and all showed the association of post-NAT ctDNA and relapse: 1. Personalized mutation detection (N = 60): HR = 23.4, P≤ 0.0001; Sen = 76.5%, Spe = 97.7% 2. Universal panel (N = 57): HR = 5.18, P = 0.0086; Sen = 66.7%, Spe = 78.4% 3. Baseline specific CNV (N = 22): HR = 9.24, P = 0.00017 4. The combination of personalized assay and baseline-specific CNV had a better prediction of RFS: HR = 35.89; P < 0.0001; Sen = 82.35%, Spe = 97.67%
Breast cancer
Radovich et al., 2020 [75]
196
TNBC I–III
cfDNA/CTC
Target NGS/CellResearch system; tumor-informed
1. Post-NAT ctDNA was associated with prognosis (ctDNA+ vs. ctDNA–):DDFS: 32.5 months vs. not reached; HR = 2.99; P = 0.006DFS: HR = 2.67; P = 0.009OS: HR = 4.16; P = 0.002 2. Post-NAT increasing of CTC count was significantly associated with inferior prognosis:DDFS: HR = 1.07; P = 0.02DFS: HR = 1.11; P = 0.004OS: HR = 1.09; P = 0.01 3. The combination of ctDNA and CTC improved the sensitivity of DDFS, DFS and OS prediction (ctDNA+/CTC+ vs. ctDNA–/CTC–):DDFS: 32.5 months vs. not reached; HR = 5.29; P = 0.009DFS: HR = 3.15; P = 0.04OS: HR = 8.60; P = 0.007
Hrebien et al., 2019 [145]
58
ER + mBC
Mutation
ddPCR; tumor-informed
The dynamics of ctDNA ratio from the start to the cycle 2 (CDR28) of treatment predict the PFS of patients 1. Part A (n = 16): CDR28 suppressed vs. CDR28 high: P = 0.0003 2. Part B (n = 42): CDR28 suppressed vs. CDR28 high: HR = 0.2, P < 0.0001
Lung cancer
Yue et al., 2022 [132]
22
NSCLC IB–IIIA
Mutation
Target NGS; tumor-naïve
1. MRD detection after NAT predicts the treatment outcome 2. The sensitivity of MRD detection to predict recurrence at 1 week and 3 months after operation was 62.5% and 83.3%, and the specificity was 85.7% and 90%
Chaudhuri et al., 2017 [128]
40
LC IB–III
Mutation
CAPP-seq; tumor- naïve
1. An MRD detection was performed within 4 months after treatment, 100% of MRD-positive patients relapsed, which was significantly higher than that of MRD-negative relapsed patients
Chen et al., 2019 [182]
205
LC I–IIIA
Mutation
cSMART assay; tumor-naïve
1. ctDNA detection at 3 days or 1 month after surgery both predicts recurrence
Pancreatic cancer
Lee et al., 2022 [184]
53
PDAC resectable
Mutation
iDES-CAPP-Seq; tumor-informed
1. Patients with postoperative ctDNA > 1 hGE/mL had shorter RFS at 1 year than patients with postoperative ctDNA ≤ 1 hGE/mL (P = 0.06)
Patel et al., 2019 [150]
94
PDAC advanced
Mutation
Target NGS; tumor-naïve
Patients with lower levels of total %ctDNA (< 0.6%) had better survival: 1. OS: higher %ctDNA vs. lower %ctDNA: 11.7 vs. 6.3 months, P = 0.001
Wang et al., 2021 [153]
97
PDAC resectable
CNV
qPCR; tumor-naïve
Postoperative copy number of cfDNA was significantly correlated with OS (P = 0.022): 1. 1-year OS: ≥ 7724 vs. < 7724 copies/mL: 70.2% vs. 93.9% 2. 5-year OS: ≥ 7724 vs. < 7724 copies/mL: 21.2% vs. 23.7%
Bernard et al., 2019 [154]
194
PDAC local and advanced
Mutation
ddPCR; tumor-naïve
Postoperative ctDNA was associated with poorer prognosis: 1. RFS: ctDNA+ vs. ctDNA–: 118 vs. 321 days, HR = 1.93, P = 0.012 2. OS: ctDNA+ vs. ctDNA–: 258 vs. 440 days; HR = 2.36, P = 0.018
Other tumors
Cai et al., 2019 [33]
34
HCC I–III
Mutation/CNV
PCR-NGS/lcWGS; tumor-informed
1. MRD detection after radical treatment effectively predicts OS and PFS 2. The predictive effect of ctDNA combined with cancer protein is better than ctDNA or protein alone
Szabados et al., 2022 [155]
94
MIUC
Mutation
mPCR-NGS; tumor-informed
1. Patients who turned to MRD– after neoadjuvant therapy achieved pCR 2. The relapse probability of MRD– patients after radical operation was significantly lower than MRD+ patients
Recurrence monitoring
Colorectal cancer
Wang et al., 2019 [166]
58
CRC I–III
Mutation
SafeSeqS; tumor-informed
1. Postoperative ctDNA was associated with RFS: 10 (77%) of the 13 ctDNA+ patients relapsed while 45 ctDNA– patients did not relapse 2. ctDNA preceded radiologic and clinical evidence of relapse by a median of 3 months
Øgaard et al., 2022 [167]
96
CRC IV
Mutation
ddPCR; tumor-naïve
1. Postoperative was associated with RFS: n = 60, HR = 7.0, P < 0.0001 2. Post-ACT ctDNA was associated with RFS: n = 36, HR = 8.4, P < 0.0001 3. ctDNA monitoring detected relapse 3.1 months (median time) earlier than CT
Mo et al., 2023 [185]
299
CRC I–III
Methylation
qPCR; tumor-naïve
1. ctDNA detection at 1 month after surgery was associated with RFS: HR = 17.5, P < 0.0001; Sen = 78%, Spe = 90.2% 2. ctDNA detection after all therapy was associated with RFS: HR = 20.6, P < 0.0001 3. ctDNA preceded radiologically confirmed relapse by a median of 3.3 months
Henriksen et al., 2022 [164]
160
CRC III
Mutation
mPCR-NGS; tumor-informed
1. Postoperative was associated with RFS: n = 140, HR = 4.5, P < 0.001 2. Post-ACT ctDNA was associated with RFS: n = 93, HR = 50.76, P < 0.001 3. The ctDNA growth rate was prognostic of survival: HR = 2.7, P = 0.039 4. ctDNA preceded radiologic evidence of relapse by a median of 9.8 months
Breast cancer
Coombes et al., 2019 [125]
49
BC I–III
Mutation
mPCR-NGS; tumor-informed
1. Predict RFS according to the detection of ctDNA in the first postoperative plasma sample: HR = 11.8, P < 0.001 2. Predict RFS according to the detection of ctDNA in any follow-up plasma sample after surgery: HR = 35.8, P < 0.001 3. Metastasis was predicted with a lead time of median 8.9 months
Lipsyc-Sharf et al., 2022 [171]
83
HR + BC
Mutation
mPCR-NGS; tumor-informed
1. Detection of ctDNA after treatment was associated with RFS (n = 101): HR = 5.8; P = 0.01 2. ctDNA detection had a median lead time of 12.4 months than clinical relapse
Garcia-Murillas et al., 2019 [146]
144
BC I–III
Mutation
ddPCR; tumor-informed
1. Detection of ctDNA before any treatment was associated with RFS (n = 101): HR = 5.8; P = 0.01 2. Detection of ctDNA during follow-up was associated with RFS (n = 101): HR = 25.2; P < 0.001 3. In all patients, ctDNA detection had a median lead time of 10.7 months than clinical relapse
Lung cancer
Yue et al., 2022 [132]
22
LC IB–IIIA
Mutation
Target NGS; tumor-naïve
1. Plasmas were taken 2–3 months after surgery, and relapse was found 145 days earlier than imaging
Chaudhuri et al., 2017 [128]
40
LC IB–III
Mutation
CAPP-seq; tumor-naïve
1. 72% of the patients underwent MRD detection every 3–6 months after treatment, which indicated relapse 5.2 months earlier than imaging detection on average
Pancreatic cancer
Pietrasz et al., 2016 [149]
135
PDAC local and advanced
Mutation
Target NGS & ddPCR; tumor-informed
Advanced PDAC: 50/104 patients were ctDNA+ 1. OS: ctDNA+ vs. ctDNA–: 6.5 vs. 19.0 months; P < 0.001 Local PDAC: 6/31 patients were ctDNA+ 1. DFS: ctDNA+ vs. ctDNA–: 4.6 vs. 17.6 months; P = 0.03 2. OS: ctDNA+ vs. ctDNA–: 19.3 vs. 32.3 months; P = 0.027 3. 4/6 patients with ctDNA+ relapsed ctDNA preceded CT detection of progression (median 2.4 months vs. 4.0 months)
Groot et al., 2019 [152]
59
PDAC resectable
Mutation
ddPCR; tumor-informed
Postoperative ctDNA was associated with poorer prognosis: 1. RFS: ctDNA+ vs. ctDNA–: 5 vs. 15 months, P < 0.001 2. OS: ctDNA+ vs. ctDNA–: 17 months vs. not reached, P = 0.011 3. ctDNA+ at any time point: predict recurrence at a sensitivity of 90% and a specificity of 88%, mean lead time of 84 days prior to imaging method
Sausen et al., 2015 [173]
20
PDAC II
Mutation
ddPCR; tumor-informed
10/20 patients were postoperative ctDNA+ 1. Patients with ctDNA+ were more likely to relapse: 9.9 months vs. not reached; P = 0.02 2. Time of ctDNA detected relapse earlier than CT imaging: median 6.5 months, n = 9, P = 0.0004
Other tumors
Cai et al., 2019 [33]
34
HCC I–III
Mutation/CNV
PCR-NGS/lcWGS; tumor-informed
1. MRD detection detected relapse 4.6 months earlier than imaging during the follow-up
Zhao et al., 2022 [76]
66
HCC I–IV
ctDNA/CTC
Target NGS; tumor-informed and tumor-naïve
1. Compared the performance of several MRD detection methods in predicting relapse 2. CTC and PPWES detected relapse 3 months earlier than imaging
Azad et al., 2020 [97]
45
ESCA IA–IIIB
Mutation
CAPP-seq; tumor-naïve
1. Progression detected by MRD detection 2.8 months earlier than imaging method
Therapy guidance
Colorectal cancer
Wang et al., 2021 [178]
119
CRC II–III
Mutation
Target NGS; tumor-naïve
1. ctDNA clearance during nCRT predicts pCR: AUC = 0.818 2. ctDNA clearance combined with mrTRG after nCRT predict pCR more accurately: AUC = 0.886 3. The detection of potential CRC driver genes in ctDNA after nCRT indicated worse RFS: HR = 9.29, P < 0.001
Tie et al., 2022 [186]
455
CRC II
Mutation
SafeSeqS; tumor-informed
Demonstrated that de-escalation treatment of ctDNA– patients does not affect the survival of patients 1. The 2-year RFS of the ctDNA-guided group and the standard treatment group were 93.5% and 92.4%, respectively 2. The 3-year RFS rates of ctDNA-guided group and the standard treatment group were 91.7% and 92.4%, respectively
Breast cancer
Li et al., 2020 [144]
44
Early BC
Mutation
Target NGS; tumor-informed
1. Positive baseline ctDNA is significantly associated with worse disease-free survival (P = 0.011) and overall survival (P = 0.004) 2. The ctDNA level after 2 cycles of NAC was predictive of local tumor response after all cycles of NAC, with AUC = 0.81
Magbanua et al., 2020 [141]
84
Early BC
Mutation
mPCR-NGS; tumor-informed
Blood was collected at 4 time point: pretreatment (T0), 3 weeks after initiation of paclitaxel (T1), between paclitaxel and anthracycline regimens (T2), and prior to surgery (T3): 1. At T1, ctDNA status was associated with pCR: ctDNA+ vs. ctDNA–: 83% vs. 52% non-pCR, OR = 4.33, P = 0.012 2. After NAC, all patients who achieved pCR were ctDNA negative (n = 17, 100%) 3. For 43 patients who did not achieve pCR, ctDNA+ was associated with DRFS: ctDNA+ vs. ctDNA–: HR = 10.4 4. Patients who were non-pCR/ctDNA– (n = 37) had similar outcome to those who achieved pCR (n = 17): HR = 1.4
Lung cancer
Moding et al., 2020 [185]
65
LC II–III
Mutation
CAPP-seq; tumor-naïve
1. Patients with MRD-negative after CRT have a good prognosis and may not benefit from immune checkpoint inhibitors (ICI) consolidation 2. After CRT, the survival of MRD-positive patients who received ICI treatment was significantly better than that of patients who did not receive it 3. Early ctDNA changes in ICI treatment identify patients who may benefit from ICI: patients with decreased ctDNA levels have a better prognosis
Pancreatic cancer
Du et al., 2023 [187]
29
PADC resectable
Mutation
Target NGS; tumor-informed
Patients with a > 50% decline in ctDNA maxVAF between 2-cycle therapy and pre-therapy had better prognosis and higher response rate: 1. PFS: decline vs. non-decline: 20.0 vs. 10.3 months; HR = 0.33; P = 0.024 2. OS: decline vs. non-decline: not reached vs. 13.5 months; HR = 0.21; P = 0.024 3. ORR: decline vs. non-decline: 90% vs. 35.7%; P = 0.013
Cheng et al., 2017 [188]
188
PDAC advanced
Mutation
ddPCR; tumor-naïve
1. In 188 metastatic PDAC patients, ERBB2 exon17 mutation and K-ras G12V mutation were significantly correlated with OS (P = 0.016 and 0.015) 2. In the 13 patients under longitudinal surveillance, ctDNA changes in 10 patients were coincident with CT detection under the ACT treatment
Lee et al., 2019 [148]
42
PDAC local
Mutation
SafeSeqS; tumor-informed
13/35 patients were postoperative ctDNA+ 1. DFS: ctDNA+ vs. ctDNA–: 5.4 vs. 17.1 months, HR 5.4, P < 0.0001 2. OS: ctDNA+ vs. ctDNA–: 10.6 vs. not reached, HR 4.5, P < 0.0001 3. Recurrence occurred in 13/13 patients with ctDNA detected despite the fact that 7 patients received chemotherapy
Other tumors
Powles et al., 2021 [176]
581
MIUC
Mutation
mPCR-NGS; tumor-informed
1. ctDNA+ patients benefits from adjuvant immunotherapy 2. Whether ctDNA-patients receive adjuvant immunotherapy does not affect the prognosis
Tab.2
Fig.4
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