Concurrent Tissue and Circulating Tumor DNA Molecular Profiling to Detect Guideline-Based Targeted Mutations in a Multicancer Cohort

Abstract

Importance: Tissue-based next-generation sequencing (NGS) of solid tumors is the criterion standard for identifying somatic mutations that can be treated with National Comprehensive Cancer Network guideline-recommended targeted therapies. Sequencing of circulating tumor DNA (ctDNA) can also identify tumor-derived mutations, and there is increasing clinical evidence supporting ctDNA testing as a diagnostic tool. The clinical value of concurrent tissue and ctDNA profiling has not been formally assessed in a large, multicancer cohort from heterogeneous clinical settings.

Objective: To evaluate whether patients concurrently tested with both tissue and ctDNA NGS testing have a higher rate of detection of guideline-based targeted mutations compared with tissue testing alone.

Design, setting, and participants: This cohort study comprised 3209 patients who underwent sequencing between May 2020, and December 2022, within the deidentified, Tempus multimodal database, consisting of linked molecular and clinical data. Included patients had stage IV disease (non-small cell lung cancer, breast cancer, prostate cancer, or colorectal cancer) with sufficient tissue and blood sample quantities for analysis.

Exposures: Received results from tissue and plasma ctDNA genomic profiling, with biopsies and blood draws occurring within 30 days of one another.

Main outcomes and measures: Detection rates of guideline-based variants found uniquely by ctDNA and tissue profiling.

Results: The cohort of 3209 patients (median age at diagnosis of stage IV disease, 65.3 years [2.5%-97.5% range, 43.3-83.3 years]) who underwent concurrent tissue and ctDNA testing included 1693 women (52.8%). Overall, 1448 patients (45.1%) had a guideline-based variant detected. Of these patients, 9.3% (135 of 1448) had variants uniquely detected by ctDNA profiling, and 24.2% (351 of 1448) had variants uniquely detected by solid-tissue testing. Although largely concordant with one another, differences in the identification of actionable variants by either assay varied according to cancer type, gene, variant, and ctDNA burden. Of 352 patients with breast cancer, 20.2% (71 of 352) with actionable variants had unique findings in ctDNA profiling results. Most of these unique, actionable variants (55.0% [55 of 100]) were found in ESR1, resulting in a 24.7% increase (23 of 93) in the identification of patients harboring an ESR1 mutation relative to tissue testing alone.

Conclusions and relevance: This study suggests that unique actionable biomarkers are detected by both concurrent tissue and ctDNA testing, with higher ctDNA identification among patients with breast cancer. Integration of concurrent NGS testing into the routine management of advanced solid cancers may expand the delivery of molecularly guided therapy and improve patient outcomes.

Figure 1.. Percentage of Patients With Actionable Variants

A, Percentage of patients with at least 1 actionable variant detected by 1 or both assays across individual cancer types as well as in the combined cohort. B, Patient-level findings by type: concordant refers to patients with identical findings in both assays, solid unique references patients who were not perfectly concordant across assays but where solid-tissue testing detected all unique variants, and ctDNA unique refers to all patients who had a unique actionable finding detected via ctDNA testing. CRC indicates colorectal cancer; ctDNA, circulating tumor DNA; and NSCLC, non–small cell lung cancer.

Figure 2.. Positive Percentage Agreement (PPA) for Thresholds of Circulating Tumor DNA (ctDNA) Burden

A, Using solid-tissue results as the comparator, PPA is shown for different thresholds of ctDNA burden, where “n” is the number of variants in the cohort greater than or above the sample’s ctDNA burden threshold (ctDNA burden is maximum somatic variant allele frequency). B, Distributions of ctDNA burdens for concordant, ctDNA unique, and solid unique variants. The horizontal lines represent medians, while the boxes represent IQRs; whiskers represent 1.5 × IQRs. The dots represent outliers outside of these distributions. C, Proportion of concordant variants (n = 1124) at varying ctDNA burden thresholds. D, Proportion of ctDNA unique variants (n = 175) at varying ctDNA burden thresholds. E, Proportion of solid-unique variants (n = 388) at varying ctDNA burden thresholds. ^aP < .01. ^bP < .001.

Figure 3.. Actionable Variants Detected in Non–Small Cell Lung Cancer (NSCLC) Cohort

A, Distribution of actionable variants in NSCLC by assay concordance: concordant (gray), circulating tumor DNA (ctDNA) unique (dark blue), and solid unique (light blue). B, Proportion of all ctDNA unique variants detected in the indicated genes (top) and proportion of all solid unique variants detected in the indicated genes (bottom). C, At the individual gene level, variants detected in the NSCLC cohort are classified as either concordant or assay-unique (top), with concordance varying across genes. Assay-unique variants are separately categorized according to whether they were uniquely detected by ctDNA or tissue testing (bottom). D, Per gene, the percentage increase in the number of patients with an actionable finding identified by concurrent testing compared with solid-tissue testing alone.

Figure 4.. Actionable Variants Detected in Breast Cancer Cohort

A, Distribution of actionable variants in breast cancer by assay concordance: concordant (gray), circulating tumor DNA (ctDNA) unique (dark blue), and solid unique (light blue). B, Proportion of all ctDNA unique variants detected in the indicated genes (top) and proportion of all solid unique variants detected in the indicated genes (bottom). C, At the individual gene level, variants detected in the breast cancer cohort are classified as either concordant or assay-unique (top), with concordance varying across genes. Assay-unique variants are separately categorized according to whether they were uniquely detected by ctDNA or solid-tissue testing (bottom). D, Per gene, the percentage increase in the number of patients with an actionable finding identified by concurrent testing compared with solid-tissue testing alone.

Figure 5.. Breast Cancer Variant Subtypes

A, The distribution of breast cancer subtypes among patients in the actionable cohort. B, Distribution of circulating tumor DNA (ctDNA) burden values by ESR1 variant assay concordance among patients with hormone receptor–positive breast cancer. The horizontal lines represent medians, while the boxes represent IQRs; whiskers represent 1.5 × IQRs. The dots represent outliers outside of these distributions. C, At the individual ESR1 variant level, variants detected in the breast cancer cohort are classified as either concordant or assay-unique (top), with concordance varying across genes. Assay-unique variants are separately categorized according to whether they were uniquely detected by ctDNA or solid-tissue testing (bottom). D, Sequential ctDNA monitoring of ESR1 variants in an individual patient with metastatic breast cancer. The variant allele frequencies (VAFs) of the 3 ESR1 variants plotted show distinct trajectories over time, with indicated therapies and outcomes shown below. AI indicates aromatase inhibitor. ^aP < .001.