Abstract 1203P
Background
IHC- and FISH-based methods of ALK testing do not identify variants of ALK fusions. NGS analysis is expensive, hence its use is still limited. ALK translocations result in increased transcription of the kinase portion of the gene, therefore PCR analysis for unbalanced 5’/3’-end expression is a cost-efficient tool for a comprehensive detection of all variants of ALK rearrangements.
Methods
This study included 4991 EGFR/MET mutation-negative NSCLCs, which were referred for diagnostic purposes to the N.N. Petrov Institute of Oncology (St-Petersburg) between April, 2018 and October, 2020.
Results
744/4991 (14.9%) NSCLCs showed evidences for ALK unbalanced 5’/3’-end expression, although only 427 of them demonstrated a disbalance between the border of the rearrangement (exon 19) and the 3’-portion of the gene. Variant-specific PCR assay, which was designed to detect 20 the most common ALK fusions, revealed translocation in 291/4991 (5.9%) NSCLCs; 266/291 (91.4%) and 278/291 (95.5%) of these ALK-rearranged tumors demonstrated 5’/3’ and ex19/3’unbalanced expression, respectively. We further considered 47 tumors, which appeared the most promising by the test for unbalanced expression and did not carry KRAS mutation. NGS revealed 16 instances of ALK translocations (4 novel (UBCex1-ALKex18, EML4ex13-ALKex3-ALKex20, EML4ex6-ins18bp-ALKex20 and EML4ex5del10-del44ALKex20) variants; 10 tumors with known rare ALK translocations; 2 common variants present in a low fraction of tumor cells). In addition, we subjected to QIAseq RNAscan NGS analysis 32 young-onset NSCLCs, which were negative by PCR ALK/ROS1/RET translocation assays; no NSCLCs with ALK translocations were revealed, although a novel ACTB-ROS1 fusion was observed in a single case.
Conclusions
This study provides a framework for non-expensive and efficient detection of ALK fusions.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
The authors.
Funding
Russian Science Foundation (grant 17-75-30027).
Disclosure
All authors have declared no conflicts of interest.