Targeted RNA sequencing-based fusion gene analysis as a tool for diagnostics and therapeutic planning in pediatric cancer patients with solid tumors

Czech version

Authors: P. Pokorná ¹; D. Al Tukmachi ¹; K. Trachtová ¹; H. Pálová ¹; S. Adamcová ¹; K. Koželková ¹; P. Múdrý ²; Z. Pavelka ²; J. Štěrba ²; O. Slabý ^1,3
Authors‘ workplace: CEITEC – Středoevropský technologický institut, MU Brno ¹; Klinika dětské onkologie LF MU a FN Brno ²; Biologický ústav, LF MU Brno ³
Published in: Klin Onkol 2022; 35(Supplementum 1): 142-144
Category: Article

Overview

Background: Pediatric cancer genome significantly differs from the genome of adult malignancies and is characterized by low tumor mutational burden, the great importance of epigenetic changes, and also the frequent occurrence of fusion genes. Fusion genes arise as a result of several types of chromosomal rearrangements, such as translocations, deletions, insertions, or inversions, and can have a variety of functional impacts. In the past, they were studied mainly in the context of hematological malignancies; however, their importance in the diagnostics and therapy of solid tumors is increasing. Materials and methods: In 250 patients with solid tumors from the Department of Pediatric Oncology of University Hospital Brno, an analysis of fusion genes was performed using targeted RNA sequencing. Sequencing libraries were prepared using the TruSight RNA Pan-Cancer Panel (Illumina), which covers 1 385 clinically relevant genes, and sequenced using the NextSeq Mid Output Kit (150 cycles) on the NextSeq 500 platform (Illumina). Sequencing reads were mapped to hg38 using the STAR aligner with parameters set to allow fusion genes detection. Arriba and STARfusion tools were used to search for fusion genes, which were subsequently manually verified in the IGV software. Results: Clinically relevant fusion genes were identified in 25% of patients. The largest proportion of fusions identified were fusions associated with sarcomas, such as EWSR1-FLI1, PAX3-FOXO1, or SS18-SSX1/ 2. The second-largest group was represented by CNS tumor fusions, especially KIAA1549-BRAF or other Ras/ MAPK-associated fusions. A previously undescribed DVL3-TFE3 fusion was identified in a renal carcinoma patient. 33% of the identified fusion genes were therapeutically targetable, and 2/ 3 of patients received corresponding treatment. Conclusion: The analysis of fusion genes is of great benefit in the diagnostics, prognostic stratification, and therapeutic planning of pediatric cancer patients. The use of high-throughput approaches such as RNA sequencing enables the identification of novel fusion genes as well as a deeper understanding of the complex changes that are involved in the development of the disease.

Keywords:

precision medicine – Next-generation sequencing – Pediatric oncology – gene fusion

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