Table 8. Concordance of FoundationOne Liquid CDx and an externally validated cfDNA NGS assay for platform-wide variants (n = 912 positive variants; n = 157,008 negative variants as determined by the comparator assay).
| Variant Type | CDx(+) Ref(+) | CDx(-) Ref(+) | CDx(+) Ref(-) | CDx(-) Ref(-) | PPA (95% CI) | NPA (95% CI) | OPA (95% CI) |
|---|---|---|---|---|---|---|---|
| All Short Variants (Substitutions and Indels) | 871 | 34 | 8 | 155315 | 96.2% (94.8%, 97.4%) | >99.9% (99.9%, 100.0%) | >99.9% (99.9%, 100.0%) |
| Substitutions | 848 | 34 | 8 | 151954 | 96.2% (94.7%, 97.3%) | >99.9% (99.9%, 100.0%) | >99.9% (99.9%, 100.0%) |
| Indels | 23 | 0 | 0 | 3361 | 100.0% (85.18%, 100.0%) | 100.0% (99.89%, 100.0%) | 100.0% (99.89%, 100.0%) |
| Rearrangements | 7 | 0 | 3 | 1682 | 100.0% (59.04%, 100.0%) | 99.8% (99.5%, 100.0%) | 99.8% (99.5%, 100.0%) |
CDx = FoundationOne Liquid CDx; cfDNA = cell-free DNA; CI = confidence interval; NPA = negative percent agreement; PPA = positive percent agreement; Ref = reference assay.