Detection of mutated KRAS, TP53, CDKN2A, and SMAD4 in tumor cell-free DNA of Brazilian pancreatic adenocarcinoma patients using next-generation sequencing

Pancreatic adenocarcinoma (PDAC) is one of the most lethal cancer types worldwide, with early diagnosis being challenging due to nonspecific symptoms that are often noticed only when the tumor reaches a large size. Liquid biopsy has emerged as a promising technology in oncology, where the identification of tumoral cell-free DNA (cfDNA) using sensitive methodologies can identify genetic mutations, allowing for tumor diagnosis, prognosis, and therapeutic approaches. However, the cfDNA extracted yields represent the first challenge, highlighting the need for cfDNA concentration. Here, using the NGS approach, we detected mutations in KRAS, TP53, CDKN2A, and SMAD4 in the cfDNA of 55 PDAC patients, using a total of 133 blood samples. After that, we identified 11 pathogenic variants across 13 cfDNA samples from 11 patients: 9 in KRAS, 4 in TP53, and 4 in SMAD4. Additionally, we discovered a SMAD4 variant not previously associated with PDAC, and significantly correlated survival. Our data describes and discusses the properties of cfDNA extraction and yield for NGS and its clinical application. We demonstrate that liquid biopsy using NGS for cfDNA targeting KRAS, TP53, CDKN2A, and SMAD4 represents a promising alternative for the early diagnosis and genetic profiling of PDAC, with implications for prognosis and targeted therapy.