|
| Methods | Application | Advantages | Limitations |
|
| SeqCap EZ HGSC VCRome® | Differential presence of exons (DPE) detection and tumor mutation load of plasma cfDNA by WES [57, 58] | High-throughput screening alternative of target regions up to 7 Mb, cost effective, limiting the risk for incidental findings, and increasing sensitivity and specificity rates [59] | Require certain equipment such as the hybridization station [59] |
|
| QX200 Droplet Digital PCR System® | Quantified detection of low-frequency alleles within a limited cfDNA pool [58] | Absolute count of target nucleic acid copies per sample volume, most commonly copies per microliter. Superior accuracy and partitioning [60] | Droplet variability in size and shape adversely affect robustness and reproducibility [61] |
|
| Guardant360® assay | Tumor profiling by liquid biopsy for monitoring and aftercare of a cancer therapy [62] | Comprehensive genomic profiling in patients with advanced solid tumors [63] | Detecting somatic cfDNA mutations that simultaneously exist in the blood lineage [64] |
|
| ProFlex PCR system® | The method of KRAS mutations analysis using loading dPCR reaction admixture over a QuantStudio 3D Digital PCR 20K Chip v2 [65] | Partitioning of a reaction into nanoliter reaction chambers by a microfluidic device, more sensitive for strain’s specific detection with less variability than qPCR [66] | Not declared |
|
| Commercial KRAS Screening Multiplex® | The sensitive and quantitative QX100 droplet digital PCR for multiplex ready-to-use KRAS somatic mutation detection [67] | Good sensitivity and specificity and good concordance with conventional clinical mutation testing of archival specimens [68] | High cost and high DNA input requirements [69] |
|
| Onco BEAM-TM-RAS-CRC™® | Highly sensitive and quantitative digital PCR platform for screening somatic KRAS and NRAS mutations by flow cytometry [67] | Reliable detection of mutations from cell-free DNA that occur at mutant allele frequencies (MAF) as low as 0.01% [70] | Not declared |
|
| 56GOncology Panel® | The multiple targeted next-generation sequencing library preparation [73] | Comprehensive and hotspot coverage of 56 clinically relevant, oncology related genes [71] | Not declared |
|
| Quant Studio 3D Digital PCR 20K chip® | The detection of the mutational spectrum of cfDNA [72] | Less pipetting steps and to reduce PCR contamination accuracy and precision to quantification of cfDNA [73] | Performing only one sample per chip, and two probes per chip in multiplex fluorescence [73] |
|
| Ion AmpliSeq Library and IonAmpliSeq ®LibraryIon 318 Chip® | To detect cancer-specific mutations of ccfDNA using the Ion Chef System [72] | Targeted gene sequencing with 4–5.5 million reads per run, easy handling and loading of templated products for sequencing, compatibility with current library preparation methods [74] | Not declared |
|
| Illumina HiSeq 2500 ® | The ultra-deep targeted sequencing [75] | Low instrument costs and a small instrument footprint, all while maintaining the high data accuracy of SBS [76] | No long lengths of DNA sequences can be obtained using these methods [77] |
|
| BD Accuri C6® | The interrogation of harvested beads by fluorescent probes that specifically hybridize to either methylated or nonmethylated derived sequences within the queried sequence [78] | Reliable instrument performance with automated QC, volumetric counting and continuous sampling [79] | Not declared |
|
| Invader Plus assay® | Invader Plus assay with peptide nucleic acid clamping for KRAS mutations status [80] | Significantly more sensitive as more than 107 reporter molecules were generated per target molecule in a 4 hr reaction. No longer requires the synthesis of allele-specific labeled oligonucleotides [81] | Less-abundant targets mostly require PCR-driven preamplification [82] |
|
Biocartis Idylla™,
Roche COBAS z480®
Sysmex Inostics BEAMing® | Three commercially available PCR-based platforms for detection of hotspot mutations in KRAS [83] | Fast and accurate detection of KRAS mutations by a sensitive and specific standardized cost-effective method, easy to implement in settings with limited expertise in molecular diagnostics [87] | They are single-gene tests and therefore only a few genes can be analyzed [84] |
|
| QX1000 Droplet Generator DG8 Cartridge System® | To analyze the hyper methylated genes in plasma cfDNA based on the droplet digital quantitative methylation-specific PCR (dd-QMSP) [85] | Partitions each sample into 20,000 uniform nanoliter-sized droplets in which nucleic acid molecules are distributed in a random fashion [85] | Not declared |
|
| ColoDefense assay® | New blood-based methylation assay for disease screening [86] | Excellent sensitivity and specificity for combined detection of multiple biomarkers in the same run and avoidance of repeated blood draws [87] | Not declared |
|
