A large prospective analysis, published by Bayle et al in Annals of Oncology, evaluated differences between tissue and circulating tumor DNA (ctDNA) next-generation sequencing (NGS) with a large cancer gene panel. The investigators compared the impacts of both methods in terms of molecular tumor board recommendation and treatment guidance based on actionable alterations classified according to the ESMO Scale for Clinical Actionability of Molecular Targets for patients with advanced solid tumors.
Researchers analyzed data from December 2020 to November 2021 among 1,021 patients who were enrolled in two ongoing, precision-medicine studies: BIP and STING. The findings provide sufficient evidence of the clinical utility of the ctDNA NGS approach for capturing actionable alterations in patients with advanced cancer as a complementary—or even an alternative—approach to a tissue-based strategy when tissue is not available.
In a letter to the editor, the authors of the study wrote that tissue-based genomic profiling is still considered the gold standard to assist decision-making for genomics-driven treatment in patients with advanced cancer. However, it has several limitations, including screening failures as a result of limited tissue availability, and inability to capture intratumor spatial and temporal heterogeneity, which may impair accurate treatment selection. Furthermore, a tumor biopsy can be challenging.
The authors explained that NGS of ctDNA is increasingly becoming the preferred method for the genomic profiling of cancer and has several advantages in comparison with NGS of tissue biopsies: namely, it is a noninvasive method, easily achievable and repeatable, and representative of the whole molecular landscape of the patient’s tumor. Several studies have demonstrated the potential of ctDNA NGS to detect genomic alterations with greater accuracy than tissue analysis. However, no study has comprehensively evaluated the differences between tissue and ctDNA NGS results with a large cancer gene panel and compared their respective impact in terms of molecular tumor board recommendation.
ctDNA vs Tissue NGS From BIP and STING
Among the enrolled patients in two ongoing, precision medicine studies—BIP and STING—the most frequent tumor types were colorectal cancer (13%), non–small cell lung cancer (13%), breast cancer (12%), prostate cancer (8%), and pancreatic adenocarcinoma (6%). Genomic analysis was performed by using the FoundationOne Liquid CDx assay and the FoundationOne CDx assay, covering an analysis of 324 genes, including calculations for the tumor mutational burden (TMB) and microsatellite instability (MSI). The results were discussed during a weekly molecular tumor board, and actionable alterations were classified according to ESCAT classification.
Median time difference between archival tumor acquisition and ctDNA collection for NGS testing was 15 months. The median time that elapsed between request and assay results was 12 days for ctDNA NGS and 28 days for tissue NGS. Testing failure with no results was 15% for tissue sequencing and 3.9% for ctDNA NGS (P < .001). Overall, 824 patients (81%) had evaluable results for both tissue and ctDNA sequencing.
After exclusion of genes univocally associated with clonal hematopoiesis of indeterminate potential (CHIP), the five most frequent cancer-related alterations identified through ctDNA sequencing were: TP53 (16.8%), ATM (7.8%), APC (6.1%), KRAS (4.3%), and PIK3CA (3.9%) mutations. The most frequently detected cancer-related alterations through tissue sequencing were: TP53 mutation (11.5%), APC mutation (5%), KRAS mutation (4.3%), CDKN2A copy number variation (CNV) (3.9%), and PIK3CA mutation (3.81%).
The proportion of patients with a higher number of cancer alterations identified in ctDNA, compared with tissue, increased in parallel with the time elapsed between the tissue and ctDNA sampling. Among patients whose results could be evaluated for both tissue and ctDNA sequencing, the proportion of genes with CNVs was higher in tissue than in liquid (47% vs 22%). In contrast, the proportion of mutations and rearrangements was higher in liquid (17% vs 13% and 36% vs 21%, respectively). In total, 58 patients (7%) had nondetectable ctDNA alterations despite cancer-related alterations identified in tissue.
Regarding CHIP, the study team found 409 patients (42%) with at least one alteration in the genes known to be associated univocally with CHIP, and 52 patients (5%) had only genes associated with CHIP in their liquid biopsy. DNA repair genes such as ATM and CHEK2 have also been described as genes associated with CHIP. Their potential actionability was assessed on a case-by-case basis centered on allele frequency, the presence or absence of other concomitant CHIP variants, and the presence or absence of other variants associated with tumorigenesis.
MSI status and TMB were evaluable for 97% and 95% of patients through ctDNA NGS vs 90% and 92% through tissue sequencing. A total of 9% of patients had high blood–TMB through ctDNA NGS with a cutoff of 16 mutations/Mb, vs 14% in tissue sequencing with a cutoff of 10 mutations/Mb. MSI and TMB status were concordant for 71% and 64% of patients. A patient with a blood–TMB ≥ 10 mutations/Mb through ctDNA sequencing had a probability of having a TMB ≥ 10 mutations/Mb through tissue sequencing of 51.9%. This probability was 43% when considering a cutoff of 16 mutations/Mb.
The number of actionable alterations was identical in 42% of cases; it was higher in tissue sequencing than in ctDNA NGS. A ctDNA profiling allowed the identification of an ESCAT I/II, III, or IV alteration not observed in tissue for 9%, 14%, and 6% of patients, respectively. Overall, the molecular tumor board recommended a matched therapy for 52% of patients. Such a recommendation would not have been made for 17% of patients without the results of tissue sequencing and for 15% of the patients without the results of ctDNA NGS.
In this study, only 10% of all alterations found in ctDNA NGS were CNVs; they represented 38% of all alterations in tissue, which is in line with previous studies showing a lower sensitivity of ctDNA NGS for CNV detection. The authors commented that further developments will be key to better differentiate true from false negative results and improve sensitivity for CNVs.
Disclosure: For full disclosures of the study authors, visit annalsofoncology.org.
