Paired Comparison of Whole Genome Sequencing and Comprehensive Targeted Sequencing of Pancreatic Cancer Tissue

Background/Aim: As an increasing number of drugs are approved for targeted cancer therapy, comprehensive genomic profiling of cancer patients is frequently conducted to identify potentially relevant genetic variants. Different sequencing technologies are used for this purpose; targeted gene panels cover a selected set of biomarker genes and hotspot regions, while whole genome sequencing (WGS) delivers genome-wide data. This comparison study aimed at evaluating whether one method performs superiorly to the other regarding the detection of targetable variants. Patients and Methods: To evaluate the performance of the two sequencing technologies, we compared the results of targeted sequencing using the Ion Torrent Oncomine Comprehensive Assay Plus (OCA-Plus) panel to Illumina WGS reports in 11 patients diagnosed with pancreatic cancer (PC). All pathogenic and likely pathogenic variants, including those relevant for targeted therapy, reported by WGS and OCA-Plus, were included in the final comparison. Results: Both techniques identified common driver mutations implicated in PC with high concordance (81%) across all variants. For variants relevant to targeted therapy, a 100% concordance between the technologies was observed. Conclusion: A comparable number of variants were reported by WGS and OCA-Plus, and all genetic variants relevant for targeted therapy were identified by both technologies. Thus, WGS does not provide substantial additional information in this patient group.