Non-invasive profiling of KRAS mutations in lung cancer using droplet digital polymerase chain reaction

With rising cases of lung cancer worldwide, liquid biopsies are becoming increasingly popular as clinically relevant potential non-invasive alternatives to tissue-based biopsies. The principle of partitioning utilized by the droplet digital polymerase chain reaction (ddPCR) makes it a highly sensitive technique for detecting rare tumor-derived mutations in blood. The presence of KRAS mutations is a negative prognostic marker for tyrosine kinase inhibitor (TKI) therapy in lung cancer; hence, profiling of major KRAS mutations before treatment is very crucial for the success of TKI therapy. This study was aimed at profiling 3 major KRAS mutations, namely G12D (GGT→GAT), G12V (GGT→GTT), and G13D (GGC→GAC) in lung cancer patients using ddPCR. ddPCR assays that rely on probe-based chemistry were standardized for KRAS G12D, KRAS G12V, and KRAS G13D mutations using cfDNA extracted from the patient's blood. To determine the concordance, blood-derived cfDNA and tumor DNA were compared using ddPCR. A positivity rate of 81.67% for KRAS mutations was observed in the cohort analyzed. KRAS mutations in the cfDNA from blood were effectively detected by ddPCR even at low fractional abundance. Moreover, a comparison of blood-derived cfDNA and tumor-derived genomic DNA-based analysis revealed a concordance of 66.67%, suggesting tumor heterogeneity as the probable reason for the lack of total concordance between the data. This study highlights the usefulness of ddPCR as a prospective clinical tool in oncology and liquid biopsy using blood cfDNA. It can be considered a better alternative to tissue biopsies and mutation profiling of candidate genes, particularly those that are linked to therapeutic response to TKIs.