Detection rate of actionable mutations in diverse cancers using a biopsy-free (blood) circulating tumor cell DNA assay

Abstract

Analysis of cell-free DNA using next-generation sequencing (NGS) is a powerful tool for the detection/monitoring of alterations present in circulating tumor DNA (ctDNA). Plasma extracted from 171 patients with a variety of cancers was analyzed for ctDNA (54 genes and copy number variants (CNVs) in three genes (EGFR, ERBB2 and MET)). The most represented cancers were lung (23%), breast (23%), and glioblastoma (19%). Ninety-nine patients (58%) had at least one detectable alteration. The most frequent alterations were TP53 (29.8%), followed by EGFR (17.5%), MET (10.5%), PIK3CA (7%), and NOTCH1 (5.8%). In contrast, of 222 healthy volunteers, only one had an aberration (TP53). Ninety patients with non-brain tumors had a discernible aberration (65% of 138 patients; in 70% of non-brain tumor patients with an alteration, the anomaly was potentially actionable). Interestingly, nine of 33 patients (27%) with glioblastoma had an alteration (6/33 (18%) potentially actionable). Overall, sixty-nine patients had potentially actionable alterations (40% of total; 69.7% of patients (69/99) with alterations); 68 patients (40% of total; 69% of patients with alterations), by a Food and Drug Administration (FDA) approved drug. In summary, 65% of diverse cancers (as well as 27% of glioblastomas) had detectable ctDNA aberration(s), with the majority theoretically actionable by an approved agent.

Keywords: actionable alteration; cancer; ctDNA; liquid biopsy; personalized therapy.

Figure 1. List of altered genes

Overall, 211/238 (89%) alterations were mutations and 27/238 (11%) were amplifications. Of 29 patients with EGFR alterations, 11 (38%) had an EGFR amplification only; two (7%), both an EGFR amplification and EGFR mutation(s); and 16 (55%) had EGFR mutation(s) only. Of eight patients with ERBB2 anomalies, two (25%) had an ERBB2 amplification only; two (25%), both an ERBB2 amplification and ERBB2 mutation(s); and four (50%), only an ERBB2 mutation. Of 18 patients with a MET aberration, 10 (56%) had a MET amplification only (10/18=56%) and eight (44%), a MET mutation only.

Figure 2. Description of the number of alterations identified in 171 patients

Panel A. displays the number of patients per designated number of alterations (total=238 alterations; median 1 alteration per patient, range 0-19). A total of 99 patients (58%) had alterations(s). Panel B. describes the percentage of patients with the designated number of alterations, by histology. As an example, for patients with lung cancer: 20% had no alterations, 20% had 1 alteration, and 60% had ≥2 alterations reported. Other included: unknown primary, n=39; melanoma, n=1; sarcoma, n=1; thymic sarcoma, n=1.

Figure 3. Most frequent alterations detected in breast and lung cancers

Bar graphs representing frequencies of the most frequent alterations for breast cancer cases Panel A. and lung cancer cases Panel B. Alterations harbored by ≥ 2 patients have been included. Numbers into brackets indicate the number of patients with the designated alteration.

Figure 4. Analysis of actionability in 171 patients with diverse cancers

Panel A. there is some overlapping as some patients might have approved agents on and off-label, as well as experimental drugs options for their disease - patients described in box A (on label use) all also have “off label use” options and are included in box B (Off-label use). Similarly, patients described in boxes A and B all also have clinical trial options and are included in box C. All patients with actionable alterations had at least one clinical trial suggested. Panel B. displays the percentages of actionability data by tumor sites. Other included: unknown primary, n=39; melanoma, n=1; sarcoma, n=1; thymic sarcoma, n=1.