Intergenic breakpoints identified by DNA sequencing confound targetable kinase fusion detection in non-small cell lung cancer

Authors：Weihua Li; Yutao Liu; Wenbin Li; Li Chen; Jianming Ying

Source：Journal of Thoracic Oncology, 2020.

DOI：10.1016/j.jtho.2020.02.023

• intergenic breakpoint
• kinase fusion
• next-generation sequencing
• non-small cell lung cancer
• targeted therapy

Introduction
Next-generation sequencing (NGS) based on genomic DNA has been widely applied for gene rearrangement detection in patients with non-small cell lung cancer (NSCLC). However, intergenic-breakpoint fusions, in which one or both genomic breakpoints localize to intergenic regions, confound kinase fusion detection. We evaluated the function of intergenic-breakpoint fusions with multiplex molecular testing approaches.
Methods
NSCLCs with intergenic-breakpoint fusion identified by DNA-based NGS were analyzed by RNA-based NGS, immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH).
Results
Twenty-six cases with single intergenic-breakpoint fusion were identified from a large cohort of NSCLCs using DNA-based NGS. Of the 26 cases, RNA-based NGS detected expressed fusion transcripts in 11 cases, and the genomic breakpoint position did not logically predict breakpoint of the fusion transcript in these cases, possibly due to complex rearrangements (n=5), alternative splicing (n=2) and reciprocal rearrangement (n=4). Nonetheless, no expressed fusion transcript was detected in 5 cases. Moreover, positive ALK IHC was observed in 3 of the remaining 10 cases without RNA-based NGS results. Three intergenic-breakpoint ALK fusion cases with or without RNA-based NGS/IHC confirmation receiving crizotinib treatment showed partial responses. However, one intergenic-breakpoint ROS1 case, given the positive FISH result, received crizotinib but developed progressive disease within one month, possibly owing to no functional fusion transcript detected by RNA-based NGS.
Conclusions
Intergenic-breakpoint fusions detected by DNA sequencing confound kinase fusion detection in NSCLC, as functional fusion transcripts may be generated or not. Additional validation testing using RNA/protein assay should be performed in intergenic-breakpoint fusion cases to guide optimal treatment.

• Institution
  中国医学科学院