Table 2.
Cell-free DNA (cfDNA) workflow details.
| Worflow I: NGS & dPCR—TP53 only |
Worflow II: NGS only—Multigene Hotspot Panels Including TP53 |
|||
|---|---|---|---|---|
| Samples | Tissue DNA | Longitudinal cfDNA | Tissue DNA | Baseline cfDNA only |
| NGS panel names & details | Ampliseq TP53 community panel | Ampliseq TP53 community panel | Ampliseq Customized Diagnostic panel |
Oncomine breast cfDNA assay with molecular barcoding |
| Panel details | 24 amplicons, 2550 bp | 328 amplicons, 35793 bp, 41 genes | 26 amplicons, 4420 bp, 10 genes | |
| Input amount | 10 ng | 1.5–3.3 ng | 10 ng | 15–20 ng |
| Mean reads depth coverage (range) | 1725 reads/amplicon (943–3584 reads) | 1851 reads/amplicon (843–3776 reads) | 1166 reads/amplicon (430–1796 reads) | 32902 reads/amplicon (5786–59976 reads) |
| Estimated costs per sample for: | ||||
| NGS | €150–€250 | €150–€250 | €250–€350 | €350–€450 |
| dPCR (€400 per mutation assay) |
€20–€30 | €20–€30 | NA | NA |
| Workflow cfDNA NGS vs. dPCR total costs for: | ||||
| Baseline cfDNA only | €150–€250 vs. €420–€430 | €350–€450 vs. €420–€430 | ||
| cfDNA at baseline & progression | €300–€500 vs. €440–€460 | €700–€900 vs. €440–€460 | ||
| 3 longitudinal cfDNAs | €450–€750 vs. €460–€490 | €1050–€1350 vs. €460–€490 | ||
| 5 longitudinal cfDNAs | €750–€1250 vs. €500–€550 | €1750–€2250 vs. €500–€550 | ||