Table 2 Methodology.
Author, Year | Timing of post-op liquid biopsy | Limit of detection (VAF) | Cut-off level | Method of detection | Gene panel | Number of genes |
|---|---|---|---|---|---|---|
Allegretti, 2020 | 3 months | ā„0.2% | Any mutations detected | NextSeq Digital PCR plus validation with dPCR | TruSight Tumour panel | 15 |
Beagan, 2020 | 2 weeksā3 months | Not stated | Not stated | ddPCR | Variants in metastases VAFāā„ā3% | (48) |
BeneÅ”ovĆ”, 2019 | 1 week | 0.03ā1% | Not stated | PCR and DCE | KRAS, TP53, APC, PIK3CA, BRAF, CTNNB1 | 6 |
Boysen, 2020 | 2 weeks | 0.10% | Any mutations detected | ddPCR and MassARRAY | UltraSEEK MA Colon Panel | 5 |
Carpinetti, 2015 | Not stated | 1 amplifiable copy/mL plasma | 3 positive droplets from 10 to 15,000 droplets | Taqman assays | Chromosomal rearrangements from WGS of tumour | (WGS) |
Chen, 2021 | 3ā7 days | Not stated | >5% of total tracking variants | Geneseeq Prime | Geneseeq Primeā¢ 425-gene panel | 425 |
Diehl, 2008 | 1 day | Not stated | Fraction of beads bound to mutant fragments higher than the negative control, mean mutant DNA fragments plus one standard deviation >1.0 | BEAMing | Mutations detected in tumour FFPE sequencing | (4) |
He, 2020 | Within 7 days | Not stated | Not stated | Capture-based targeted deep sequencing | ColonCore panel NextSeq 500 system (Illumina, Inc.) | 41 |
Huang, 2019 | 1 month | Not stated | >4 mutant reads in plasma with >1 read on each strand | Illumina NextSeq 500 | 85 genes | 85 |
Ji, 2021 | 1 day | Not stated | TMBā>ā10/ctDNAāany mutations/change in TMB | Illumina HiSeq X-Ten | 30 mutation signatures | 30 |
Jin, 2021 | 1ā14 days | 0.05% tumour DNA | mqMSP assay: ĪCq valueā>āā1. SEPT9 assay: at least one out of three qPCR replicates had a Ct value <45 | Methylation-specific quantitative PCR assay (mqMSP) | Septin 9 (SEPT9) gene hypermethylated | NA |
Khakoo, 2020 | 4ā12 weeks | not stated | Two mutant-positive droplets present for at least one variant | ddPCR | 1ā3 variants with highest VAF in tumour | 1ā3 (6) |
Lee, 2021 | 3ā4 weeks | 1% | VAFāā„ā1% | Ultra-deep targeted sequencing | Somatic variants identified from primary and metastatic tumour | (50) |
Leon Arellano, 2020 | 3 months | Valid when the ACTB Ct was ā¤32.1 | SEPT9 Ct <45 cycles | Duplex quantitative PCR, Fast Real-Time PCR | Septin 9 (SEPT9) hypermethylated | 1* |
Levy, 2012 | <1 week | Not stated | 5% of mutated alleles | Fluorescently labelled PCR and DCE | Somatic mutations previously found in tumour | (5) |
Lindforss, 2005 | 3 days | Not stated | Not stated | PCR | KRAS | 1 |
LĆ³pez-Rojo, 2020 | 48āh | Not stated | Concentration compared between samples and wild-type controls using a Z test, pā<ā0.05 used for positivity | ddPCR | KRAS | 1 |
Mason, 2021 | Median 13 months (range 1ā45 months) | 0.30% | Any mutations detected | Guardant360 CDx | 70 genes | 70 |
Murahashi, 2020 | 12 weeks | Not stated | VAF 0.15% | Amplicon-based deep sequencing | 14 genes | 14 |
Murray, 2018 | Within 12 months | Not stated | At least one PCR replicate positive for methylation | Triplex real-time qPCR assay | BCAT1 and IKZF1 methylation | 2* |
Ng, 2017 | Within 5 days | 0.05% | Positive on a one-tailed exact conditional test of the ratio of two Poisson rates to distinguish from negative controls | Multiplex-PCR amplicon sequencing | Somatic variants identified from the primary tumour | 1ā14 (799) |
Parikh, 2021 | 11ā148 days | Not stated | Any mutations detected | Guardant Reveal test | Not stated | Not stated |
Reinert, 2019 | 30 days | Not stated | At least 2 variants detected | HiSeq 2500 system | 16 somatic single-nucleotide variants and short indels based on WES of tumour | 16 (WES) |
Ryan, 2003 | 1 week | Not stated | Not stated | PCR | KRAS | 1 |
ScĆøhler, 2017 | 8 days | 0.50% | Any mutations detected | ddPCR | Mutations identified on WES of tumour | Mean 4.2 (WES) |
Schou, 2018 | 3 months | 170āng/mL | Above 75th quartile | Direct fluorescent assay | Not applicable | not applicable |
Suzuki, 2020 | At the end of hospitalisation | 0.02% | NGS: at least one mutated ctDNA PCR: one copy of mutated ctDNA | Pre op: Oncomine Pan Cancer Cell Free Assay. Post op: ddPCR | Mutations identified pre-surgery in plasma by NGS | ((52)) |
Taieb, 2021 | After surgery, before adjuvant chemotherapy | Above limit of blank | Above limit of blank | Multiplex droplet-based digital PCR (ddPCR) and NGS | WIF1 and NPY gene hypermethylation (AmpliSeq Colon and Lung Cancer Panel V2 performed in a subset of patients) | 2*+22 |
Tanaka, 2021 | 1 day | 0.10% | VAF 0.15% | dPCR Taqman assays | BRAF | 1 |
Tarazona, 2019 | 6ā8 weeks | Not stated | VAF 5% | Orthogonal droplet digital PCR | Two mutations with the highest VAF on NGS of tumour | 2 (29) |
Tie, 2016 | 4ā10 weeks | Not stated | Permutation test comparing mutation frequency between samples and controls | Illumina MiSeq | Somatic mutation with highest VAF in tumour FFPE | 1 (15) |
Tie, 2019 (1) | 4ā10 weeks | Not stated | Permutation test comparing mutation frequency between samples and controls | Illumina MiSeq | Mutation with the highest VAF in tissue from surgery | 1 (15) |
Tie, 2019 (2) | 4ā10 weeks | Not stated | Permutation test comparing mutation frequency between samples and controls | Safe-SeqS and Illumina MiSeq | Somatic mutation with the highest VAF in tumour tissue | 1 (15) |
Tie, 2021 | 4ā10 weeks | Not stated | Permutation test comparing mutation frequency between samples and controls | Safe-SeqS | Mutation with the highest VAF in tumour tissue | 1 (15) |
Yamada, 2016 | Within 1 month | <1.00%. | Ratio of 0.1% mutant to 99.9% wild type | Invader Plus assay with peptide nucleic acid clamping method and digital PCR | KRAS | 1 |
Zhou, 2016 | 1 month | Not stated | VAFā>ā0 | Illumina HiSeq 2500 | 545 genes | 545 |
Zhou, 2021 | Within 1 month | Not stated | At least one mutation in ctDNA also detected in tissue | HiSeq 3000 Sequencing System (Illumina) | 1021 genes | 1021 |
Zou, 2020 | 12 weeks | Not stated | VAF 1% | ddPCR | Somatic mutations from targeted sequencing of FFPE slides | 2 (71) |
