Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
Copyright © 2023 by the Korean Cancer Association
This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Author Contributions
Conceived and designed the analysis: Kim H, Park KU.
Collected the data: Kim H, Park KU.
Wrote the paper: Kim H.
Conflicts of Interest
Conflict of interest relevant to this article was not reported.
Epi ProColona) | Cobas EGFR mutation test V2a) | Terascreen PIK3CA RCQ PCR Kita) | Guardant360 CDxa) | FoundationOne Liquid CDx (F1 Liquid CDx)a) | |
---|---|---|---|---|---|
Type | IVD | IVD | IVD | Laboratory service | Laboratory service |
Applicant | Epigenomics AG | Roche | Qiagen | Guardant Health | Foundation Medicine |
Method | RT-PCR with bisulfite-treated DNA | AS-PCR | RT-PCR | NGS | NGS |
Accuracy | |||||
Comparison against NGS | - | 491 | 542 | 772 | 691 |
Comparison against microarray-based test | - | - | - | - | - |
Concordance between Guardant360 CDx and Guardant360 LDT | - | - | - | 258 | - |
FoundationOne Liquid LDT to FoundationOne Liquid CDx concordance | - | - | - | - | 927 |
Orthogonal concordance | - | - | - | - | 556 |
Contrived sample comparison | - | 640 | 744 | Total 48 samples with cell line cfDNA sample pools: 13–20 replicates; clinical cfDNA sample; 14 replicates | 23,959 |
Comparision between type of specimen | - | 128 | - | - | - |
Clinical specimen confirmation | - | 264 | - | - | 825 |
Robustness | 29 | - | - | - | - |
Analytical sensitivity | |||||
DNA input | - | - | 176 | - | - |
LoB | - | 198 | 180 | 240 | 2,212 |
LoD | 420 | 807 | 120 | 5 Concentrations with 14/20 replicates | 8,770 |
Combined LoD and precision study | - | - | - | 300 | - |
Precision | 201 | - | - | 11,546 | 54,987 |
Analytical specificity | |||||
Cross reactivity | 394 | - | 239 | - | - |
Interference | 66 | 45 | 468 | 146 | 3,024 |
Cross contamination | - | - | 195 | 352 | 1,880 |
Molecular index barcode performance | - | - | - | - | 7,637 |
Hybrid capture bait specificity | - | - | - | - | 3,546 |
Reproducibility | - | 756 | 5,736 | - | - |
Intra-run repeatability | - | - | - | - | - |
Sample handling | - | - | 216 | - | - |
Guardbanding; temperature | 50 Items | 162 | 120 | - | 3,750 |
Guardbanding; injection time | - | - | - | - | - |
Blood collection tube validation | - | - | 256 | 177 | 11,520 |
Reagent lot interchangeability | - | - | - | 70 | 1,536 |
Methylation testing; Sanger sequencing | 48 | - | - | - | - |
Stability | 1,144 | 517 | 312 | 984 | 35,610 |
Interpretation and reporting | - | - | - | - | - |
Cutoff determination | 203 | - | - | - | - |
General lab equipment and reagent evaluation | - | - | - | 11,357 | 1,496 |
Variant report curation | - | - | - | 11,097 | 19,868 |
Clinical validation and utility | |||||
Pan cancer analysis | - | - | - | - | 376 |
Clinical validation | - | - | - | - | 1,083 |
AS-PCR, allele-specific PCR; cfDNA, cell-free DNA; ctDNA, circulating tumor DNA; EGFR, epidermal growth factor receptor; FDA, Food and Drug Administration; IVD, in vitro diagnostics device; LDT, laboratory-developed tests; LoB, limit of blank; LoD, limit of detection; NGS, next-generation sequencing; RT-PCR, real-time reverse transcription polymerase chain reaction.
a) See FDA approval documentation (https://www.accessdata.fda.gov/scripts/cdrh/devicesatfda/index.cfm).
Type applicant | Guardant360 CDxa) Laboratory service Guardant Health | FoundationOne Liquid CDx (F1 Liquid CDx)a) Laboratory service Foundation Medicine |
---|---|---|
Bioinformatics pipeline |
Custom-developed analysis bioinformatics pipeline software module Alteration calling metrics |
Sequence Analysis software developed by Foundation Medicine External tools used include |
CNA, copy number alterations; ctDNA, circulating tumor DNA; FDA, Food and Drug Administration; Indel, small insertion/deletions; MAF, mutant allele frequency; NGS, next-generation sequencing; SNV, single nucleotide variants.
a) See FDA approval documentation (https://www.accessdata.fda.gov/scripts/cdrh/devicesatfda/index.cfm).
Assay (Corporation) | Method | Biomarker | Aprroval |
---|---|---|---|
EGFR Mutations Detection Kit (AmoyDx) | Real-time PCR | EGFR | CE-IVDa) |
Epi ProColon (Epigenomics) | PCR for the qualitative detection of methylation | Methylation of Septin 9 DNA | FDAb)/CE-IVDa) |
Cobas EGFR Mutation Test v2 (Roche) | Real-time PCR | EGFR | FDAb)/CE-IVDa) |
Super-ARMS EGFR Mutation Test (AmoyDx) | Real-time PCR | EGFR | CE-IVDa) |
BRCA Complete kit (EntroGen) | NGS | BRCA1, BRCA2 | CE-IVDa) |
ctEGFR Mutation Detection Kit (EntroGen) | Real-time PCR | EGFR | CE-IVDa) |
Therascreen PIK3CA RGQ PCR Kit (QIAGEN) | Real-time PCR | PIK3CA | FDAb) |
Guardant360 CDx (Guardant Health) | NGS | Among designed 74 genes, 55 FDA-approved genes | FDAb)/CE-IVDa) |
FoundationOne Liquid CDx (Foundation Medicine) | NGS | 311 Genes, 3 CNA, 3 rearrangements | FDAb)/CE-IVDa) |
Archer LIQUIDPlex ctDNA 28 (Diagnostica Longwood) | NGS | 28 Genes | CE-IVDa) |
CE, Conformité Européenne; CNA, copy number alterations; ctDNA, circulating tumor DNA; EGFR, epidermal growth factor receptor; FDA, Food and Drug Administration; IVD, in vitro diagnostic; NGS, next-generation sequencing; PCR, polymerase chain reaction.
a) The CE-IVD list is an excerpt from the literature search results and may be missing tests,
b) The list of assays is an excerpt from the FDA database and includes all FDA-approved tests.
Epi ProColon |
Cobas EGFR mutation test V2 |
Terascreen PIK3CA RCQ PCR Kit |
Guardant360 CDx |
FoundationOne Liquid CDx (F1 Liquid CDx) | |
---|---|---|---|---|---|
Type | IVD | IVD | IVD | Laboratory service | Laboratory service |
Applicant | Epigenomics AG | Roche | Qiagen | Guardant Health | Foundation Medicine |
Method | RT-PCR with bisulfite-treated DNA | AS-PCR | RT-PCR | NGS | NGS |
Accuracy | |||||
Comparison against NGS | - | 491 | 542 | 772 | 691 |
Comparison against microarray-based test | - | - | - | - | - |
Concordance between Guardant360 CDx and Guardant360 LDT | - | - | - | 258 | - |
FoundationOne Liquid LDT to FoundationOne Liquid CDx concordance | - | - | - | - | 927 |
Orthogonal concordance | - | - | - | - | 556 |
Contrived sample comparison | - | 640 | 744 | Total 48 samples with cell line cfDNA sample pools: 13–20 replicates; clinical cfDNA sample; 14 replicates | 23,959 |
Comparision between type of specimen | - | 128 | - | - | - |
Clinical specimen confirmation | - | 264 | - | - | 825 |
Robustness | 29 | - | - | - | - |
Analytical sensitivity | |||||
DNA input | - | - | 176 | - | - |
LoB | - | 198 | 180 | 240 | 2,212 |
LoD | 420 | 807 | 120 | 5 Concentrations with 14/20 replicates | 8,770 |
Combined LoD and precision study | - | - | - | 300 | - |
Precision | 201 | - | - | 11,546 | 54,987 |
Analytical specificity | |||||
Cross reactivity | 394 | - | 239 | - | - |
Interference | 66 | 45 | 468 | 146 | 3,024 |
Cross contamination | - | - | 195 | 352 | 1,880 |
Molecular index barcode performance | - | - | - | - | 7,637 |
Hybrid capture bait specificity | - | - | - | - | 3,546 |
Reproducibility | - | 756 | 5,736 | - | - |
Intra-run repeatability | - | - | - | - | - |
Sample handling | - | - | 216 | - | - |
Guardbanding; temperature | 50 Items | 162 | 120 | - | 3,750 |
Guardbanding; injection time | - | - | - | - | - |
Blood collection tube validation | - | - | 256 | 177 | 11,520 |
Reagent lot interchangeability | - | - | - | 70 | 1,536 |
Methylation testing; Sanger sequencing | 48 | - | - | - | - |
Stability | 1,144 | 517 | 312 | 984 | 35,610 |
Interpretation and reporting | - | - | - | - | - |
Cutoff determination | 203 | - | - | - | - |
General lab equipment and reagent evaluation | - | - | - | 11,357 | 1,496 |
Variant report curation | - | - | - | 11,097 | 19,868 |
Clinical validation and utility | |||||
Pan cancer analysis | - | - | - | - | 376 |
Clinical validation | - | - | - | - | 1,083 |
AS-PCR, allele-specific PCR; cfDNA, cell-free DNA; ctDNA, circulating tumor DNA; EGFR, epidermal growth factor receptor; FDA, Food and Drug Administration; IVD, in vitro diagnostics device; LDT, laboratory-developed tests; LoB, limit of blank; LoD, limit of detection; NGS, next-generation sequencing; RT-PCR, real-time reverse transcription polymerase chain reaction.
a)See FDA approval documentation (
Type applicant | Guardant360 CDx |
FoundationOne Liquid CDx (F1 Liquid CDx) |
---|---|---|
Bioinformatics pipeline | Custom-developed analysis bioinformatics pipeline software module Alteration calling metrics - SNV Calling Property DNA molecule support ≥ 2 MAF estimate ≥ 0.001% Log likelihood ratio ≥ 0 - Indel Calling Property DNA molecule support ≥ 2 Log likelihood ratio ≥ 10 MAF estimate ≥ 0.01% - CNA Calling Property ERBB2 copy number ≥ 2.18 ERBB2 Z-score ≥ 10 ERBB2 amplification is not associated with chromosome-arm aneuploidy: TRUE MET copy number ≥ 2.16 MET Z-score ≥ 10 MET amplification is not associated with chromosome-arm aneuploidy: TRUE - Fusion Calling Property MAPQ score of supporting molecule to fusion sequence > 30 Number of unique fusion molecules ≥ 2 Number of unique fusion reads > 2 |
Sequence Analysis software developed by Foundation Medicine External tools used include BWA (Burrows-Wheeler Aligner) v0.7.17, for aligning sequence reads to the genomic reference Samtools v1.6 for utility operations Picard tools v1.56 for metrics calculations Biopython for the pairwise2 sequence alignment module |
CNA, copy number alterations; ctDNA, circulating tumor DNA; FDA, Food and Drug Administration; Indel, small insertion/deletions; MAF, mutant allele frequency; NGS, next-generation sequencing; SNV, single nucleotide variants.
a)See FDA approval documentation (
Assay (Corporation) | Method | Biomarker | Aprroval |
---|---|---|---|
EGFR Mutations Detection Kit (AmoyDx) | Real-time PCR | EGFR | CE-IVD |
Epi ProColon (Epigenomics) | PCR for the qualitative detection of methylation | Methylation of Septin 9 DNA | FDA |
Cobas EGFR Mutation Test v2 (Roche) | Real-time PCR | EGFR | FDA |
Super-ARMS EGFR Mutation Test (AmoyDx) | Real-time PCR | EGFR | CE-IVD |
BRCA Complete kit (EntroGen) | NGS | BRCA1, BRCA2 | CE-IVD |
ctEGFR Mutation Detection Kit (EntroGen) | Real-time PCR | EGFR | CE-IVD |
Therascreen PIK3CA RGQ PCR Kit (QIAGEN) | Real-time PCR | PIK3CA | FDA |
Guardant360 CDx (Guardant Health) | NGS | Among designed 74 genes, 55 FDA-approved genes | FDA |
FoundationOne Liquid CDx (Foundation Medicine) | NGS | 311 Genes, 3 CNA, 3 rearrangements | FDA |
Archer LIQUIDPlex ctDNA 28 (Diagnostica Longwood) | NGS | 28 Genes | CE-IVD |
CE, Conformité Européenne; CNA, copy number alterations; ctDNA, circulating tumor DNA; EGFR, epidermal growth factor receptor; FDA, Food and Drug Administration; IVD, in vitro diagnostic; NGS, next-generation sequencing; PCR, polymerase chain reaction.
a)The CE-IVD list is an excerpt from the literature search results and may be missing tests,
b)The list of assays is an excerpt from the FDA database and includes all FDA-approved tests.
AS-PCR, allele-specific PCR; cfDNA, cell-free DNA; ctDNA, circulating tumor DNA; EGFR, epidermal growth factor receptor; FDA, Food and Drug Administration; IVD, See FDA approval documentation (
CNA, copy number alterations; ctDNA, circulating tumor DNA; FDA, Food and Drug Administration; Indel, small insertion/deletions; MAF, mutant allele frequency; NGS, next-generation sequencing; SNV, single nucleotide variants. See FDA approval documentation (
CE, Conformité Européenne; CNA, copy number alterations; ctDNA, circulating tumor DNA; EGFR, epidermal growth factor receptor; FDA, Food and Drug Administration; IVD, The CE-IVD list is an excerpt from the literature search results and may be missing tests, The list of assays is an excerpt from the FDA database and includes all FDA-approved tests.