A Method for Extending Target Regions of Genomic Profiling by Combining a Custom Probe Pool with a Commercial Targeted Panel

Abstract

Background: Next-generation sequencing (NGS)-based genomic profiling is becoming widespread in determining treatment policies for patients with tumors. Commercially available gene panels for pan-tumor targets comprise hundreds of tumor-related genes but frequently lack genes of interest in specific tumor types. In this study, we demonstrate a method for extending target regions of genomic profiling by combining a custom probe pool with a commercial targeted panel.

Methods: We used TruSight Oncology 500 (TSO500) as a commercial targeted panel and a custom probe pool designed for all exons of the SMARCA2 gene. Sequencing libraries of custom targets were constructed using a portion of the TSO500 library solution before the hybridization-capture process. After hybridization capture, both libraries were combined and sequenced using a next-generation sequencer.

Results: Sequencing results showed that >96.8% and 100% of the target exons were covered at a depth of over 100× using the TSO500 and custom panels, respectively. The custom panels had slightly better median exon coverage than the TSO500. The combined libraries of the custom and TSO500 panels showed a mapped read ratio close to the mixing ratio. Analysis of mutation-free regions showed similar accuracies between the TSO500 and custom panels regarding variant calling.

Conclusions: Our devised method easily and affordably extends the targets beyond a ready-made panel. This method provides a valuable solution until the widespread adoption of whole-exome sequencing, which is costly for large target sizes.