Dual tissue and plasma testing to improve detection of actionable variants in patients with solid cancers.
Authors: Mackay Matthew , Mitsiades Nicholas , Chae Young Kwang , Davis Andrew A. , Lammers Philip Edward , Maher James F. , Theodorescu Dan , Rubin Peter , Pluard Timothy J. , Langer Lee , Manghnani Kabir , Ben-Shachar Rotem , Blackwell Kimberly L. , Chen James Lin , Dudley Joel , Guinney Justin , Iams Wade Thomas 
Published: June 2022

3017

Background: Next generation sequencing (NGS) of tumor tissue and plasma (circulating tumor DNA [ctDNA]) are used clinically to identify actionable genomic alterations, with implications for treatment selection and disease surveillance. Early studies have observed that solid tumor tissue and ctDNA testing may capture both overlapping and complementary alterations. Using the Tempus database, we examined whether dual tissue and ctDNA testing, “dual testing”, improved identification of actionable variants compared with either modality alone. Methods: We used Tempus Lens to retrospectively analyze 3153 de-identified stage 4 patients (breast [N = 644], colorectal [N = 841], non-small cell lung cancer (NSCLC) [N = 1232], and prostate [N = 436]). Each patient had dual testing—Tempus xF (ctDNA, 105 panel genes) and Tempus xT (tumor tissue, 595-648 panel genes), representing 6306 total samples. Samples were defined as concurrent if biopsied ≤30 days apart and longitudinal if plasma was collected between 31–365 days after tissue biopsy. All analyses were limited to single nucleotide variants and insertions/deletions that met the limit of detection criteria for both assays (104 genes). Indication matched actionable variants were defined by OncoKB Level 1 and 2 evidence, or R1 within both xF and xT (13 genes). Results: Of the 3153 patients with dual testing, 37% (1168) had actionable variants identified by at least one test. 94% (1100/1168) of these patients had variants identified via solid tumor profiling alone, 73% (856) had variants identified via ctDNA profiling alone, and 64% (745) had perfectly concordant variants. Thus, dual testing identified additional variants in 36% (423/1168) of these patients compared to any singular test. Of the 423 patients who had additional actionable alterations discovered through dual testing, ctDNA revealed unique alterations—which were not found in solid tissue testing—in 22% (95/423) of patients. Of these patients, 72% (68/95) had all actionable variants identified solely from ctDNA. Of the 251 patients with additional alterations identified by concurrent dual testing, 24% (61/251) had unique alterations identified in plasma. Similarly, of the 172 patients with additional alterations identified by longitudinal dual testing, 20% (34/172) had unique alterations identified in ctDNA alone. Conclusions: In the largest study of its kind, we show that dual tumor tissue and ctDNA testing—with samples collected either concurrently or longitudinally—identified more patients with actionable alterations than single modality testing alone and therefore should be considered as part of routine NGS testing. Additional studies to explore the genetic and intra-patient tumor heterogeneity of these variants as well as the impact of time between tissue and plasma sampling assessments and implications for timing of therapeutic recommendations are underway.