Measurement of ctDNA Tumor Fraction Identifies Informative Negative Liquid Biopsy Results and Informs Value of Tissue Confirmation

Abstract

Purpose: Liquid biopsy (LBx) for tumor profiling is increasingly used, but concerns remain regarding negative results. A lack of results may truly reflect tumor genomics, or it may be a false negative that would be clarified by tissue testing. A method of distinguishing between these scenarios could help clarify when follow-on tissue testing is valuable.

Experimental design: Here we evaluate circulating tumor DNA (ctDNA) tumor fraction (TF), a quantification of ctDNA in LBx samples, for utility in identifying true negative results. We assessed concordance between LBx and tissue-based results, stratified by ctDNA TF, in a real-world genomic dataset of paired samples across multiple disease types. We also evaluated the frequency of tissue results identifying driver alterations in patients with lung cancer after negative LBx in a real-world clinicogenomic database.

Results: The positive percent agreement and negative predictive value between liquid and tissue samples for driver alterations increased from 63% and 66% for all samples to 98% and 97% in samples with ctDNA TF ≥1%. Among 505 patients with lung cancer with no targetable driver alterations found by LBx who had subsequent tissue-based profiling, 37% had a driver, all of which had ctDNA TF <1%.

Conclusions: Patients with lung cancer with negative LBx and ctDNA TF ≥1% are unlikely to have a driver detected on confirmatory tissue testing; such informative negative results may benefit instead from prompt treatment initiation. Conversely, negative LBx with ctDNA TF <1% will commonly have a driver identified by follow-up tissue testing and should be prioritized for reflex testing.

Figure 1.

ctDNA tumor fraction identifies liquid biopsy samples with high concordance to tissue. PPA and NPV of liquid biopsy with results at any ctDNA TF (A), results with ctDNA TF≥1% (B), and results with ctDNA TF <1% (C).

Figure 2.

Data from a real-world CGDB was analyzed to understand the value of reflex tissue testing. Patients with liquid biopsy prior to 1L therapy were analyzed for rates of driver detection. Patients who were driver negative by liquid biopsy who subsequently received tissue biopsy CGP were further analyzed to understand their treatment patterns and outcomes.

Figure 3.

Negative liquid biopsy results are frequently false negatives when confirmed by tissue-based testing. A, Among patients tested prior to initiation of 1L therapy, liquid biopsy–based CGP identifies targetable drivers in approximately 40% of patients with NSCLC. B, Patients with no drivers identified by liquid biopsy had a driver mutation newly identified upon subsequent tissue-based CGP.

Figure 4.

ctDNA tumor fraction informs the relative benefit of confirmatory tissue-based testing. Left: Patients with low ctDNA TF (<1%, n = 56) and no driver alterations detected have underlying driver alterations in 51.8% of cases when assessed by subsequent tissue CGP. Right: Zero patients with high ctDNA TF (≥1%) and subsequent tissue CGP (0/24) had driver alterations identified by confirmatory testing.

Figure 5.

Timely confirmatory testing of TBx following negative LBx results leads to more frequent use of targeted therapies and prolonged clinical benefit. A, Among patients with negative LBx receiving confirmatory TBx CGP before initiation of 1L therapy, 41 (17%) received a matched targeted therapy, while only 9 (4%) of those with TBx CGP after 1L did so. B, When excluding patients with KRAS driver alterations due to the relatively recent approval of therapies for KRAS alterations, 63% of patients with confirmatory TBx CGP prior to 1L received a matched targeted therapy, compared with 27% of those with TBx CGP after 1L. C, The rwPFS among patients with TBx CGP before 1L is 24.2 months. D, The rwOS among these patients is 45.8 months.

Figure 6.

A clinical paradigm distinguishing actionable liquid biopsy results. For patients with liquid biopsy results, actionable drivers can guide targeted therapy use. Results that are negative for driver alterations can be distinguished by tumor fraction: a result with a low ctDNA TF (<1%) is an indeterminate negative where confirmatory tissue may likely reveal a driver alteration, whereas a result with high ctDNA TF (≥1%) is an informative negative that provides confidence in the true absence of driver alterations in the tumor.