Implementation of circulating tumor DNA (ctDNA) testing in precision oncology: A four-year experience from a tertiary cancer center in India.

Abstract

Introduction: Liquid biopsy testing has emerged as a pivotal tool in molecular characterization of solid malignancies. Circulating tumor DNA (ctDNA) analysis is quintessential in precision oncology for early detection, disease monitoring, prognosis, and theranostic purposes. This study summarizes ctDNA analysis performed on patients with advanced or metastatic solid tumors at tertiary cancer centers in India (2021-2024).

Methods: ctDNA was isolated following standard pre-analytical protocols and quality control measures. Sequencing was performed using the Oncomine Precision Assay on Thermo Fisher platform and Custom Solid Tumor Panel (SOPHiA Genetics) on Illumina platforms. Variant annotation and clinical interpretation were performed as per ACMG and AMP Guidelines.

Results: Out of 236 ctDNA samples, majority were lung malignancies (47 %), gastric cancers (43 %), head & neck cancers (2 %), other malignancies (8 %). A total of 250 clinically relevant genomic alterations were reported. On Illumina, 19.8 % of variants were classified as Tier I, 18.3 % Tier II, and 11.7 % as Tier III. Thermofisher platform identified Tier I alterations in 33 %, Tier II in 54 %, and Tier III in 11 % cases. In the GI cohort, TP53 was most frequently mutated (51 %), followed by KRAS (25 %), BRAF (13 %), PIK3CA (13 %), and CHEK2 (9 %). Among lung cancer patients, EGFR mutations (44 %), followed by TP53 (43 %), CDKN2A (9 %), PIK3CA (9 %), and BRAF (6 %).Tissue-liquid biopsy concordance was observed in 36 of 96 cases for which baseline tissue NGS data was available. The mutational landscape derived from this cohort was compared with the MSKCC dataset for Asian and Western populations. The comparison revealed high concordance, clinical relevance, and reliability of liquid biopsy-based genomic profiling in diverse oncologic settings.

Conclusion: Study underscores substantial increase in the adoption of liquid biopsy and the real-world utility of ctDNA-based NGS testing in solid tumors contributing to improved patient care management.