Clinical Utility of Next-generation Sequencing in Real-world Cases: A Single-institution Study of Nine Cases

Abstract

Background/Aim: Targeted next-generation sequencing (NGS) is a well-established technique to detect pathogenic alterations in tumors. Indeed, it is the cornerstone of targeted therapy in precision medicine. We investigated the clinical utility of next-generation sequencing in real-world cases. Patients and Methods: We retrospectively selected six representative cancer cases, wherein targeted NGS played a pivotal role in the diagnosis and treatment of patients. Additionally, we analyzed three cases with rare, unusual pathogenic alterations. Results: Our NGS analysis revealed that four patients had TPR-ROS1, EGFR-RAD51, and NCOA4-RET fusions and MET exon 14 skipping mutation, respectively, which can be treated with targeted therapy. Furthermore, we used NGS as a diagnostic tool to confirm the origin of unknown primary malignant tumors in two cases. Interestingly, NGS also helped us identify the following cases: patients exhibiting BRCA1 and TP53 mutations that exhibited histological and immunohistochemical characteristics consistent with endometrioid carcinoma, patients with high-grade serous carcinoma not possessing a TP53 mutation, and patients with small cell lung cancer with a ERBB2 mutation and displaying no loss of RB1. Conclusion: We recommend targeted NGS for the diagnoses and targeted therapy of cancer patients.Cancer is a genetic disease that is caused by mutations in genes involved in the cell cycle and in cell signaling, cell growth, proliferation, survival, cancer invasion, and immunity (1, 2). In the era of precision oncology, molecular analysis of patient samples is essential for tumor classification, treatment planning, and prognostic stratification (3). Currently, several pathology labs follow the "one-gene one-test" approach, wherein they perform techniques such as polymerase chain reaction (PCR), Sanger sequencing, and pyrosequencing to detect targetable gene alterations, such as those in EGFR, BRAF, KRAS, ALK, ROS, MET, and PIK3CA. However, all these tests require a substantial amount of template DNA and are only applicable to the hotspot regions of targetable genes (4-7).Remarkably, next-generation sequencing (NGS), massive parallel sequencing, simultaneously detect hundreds of genes (8, 9). Although whole exome sequencing and whole genome sequencing are widely used for research purposes, they have limited clinical applications owing to their low coverage depth and high cost (10). Thus, targeted NGS is the most widely employed sequencing approach for molecular analysis in clinical practice (11,12).Conventionally, cancer is diagnosed by histological evaluation. Indeed, a direct visual inspection of the patient's sample by light microscopy provides considerable information regarding diagnosis, prognosis, and a treatment plan (13-15). Despite determining the overall pathological landscape of a patient sample, this approach does not reveal the underlying genetic alterations in cancer. Additionally, interobserver discrepancy and "gray zone" are some other limitations of histologically classifying ca...

NovelTPR::ROS1Fusion Gene Activates MAPK, PI3K and JAK/STAT Signaling in an Infant-type Pediatric Glioma

“…TPR fusions has previously been reported in a few pediatric cancers including TPR::NTRK1 in a high-grade undifferentiated sarcoma (44), a mesenchymal tumor of the small intestine (45), and in a mesenchymal tumor of the neck region (36), a TPR::RET fusion detected in a papillary thyroid carcinoma (46), a TPR::ROS1 fusion detected in lipofibromatosis (37). Also, a TPR::ROS1 fusion was recently reported in an adult lung adenocarcinoma case (47).…”

“…ROS fusions are emerging as clinically important since they can be targeted by small inhibitors. Hence, it is becoming crucial to identify ROS-driven tumors by genetic screening so that the patients may benefit from these treatments (5,14,47,(60)(61)(62)(63). Several ROS inhibitors that have been developed are mainly tested for adult patients with NSCLC (64).…”