Comparison of Comprehensive Genomic Profiling Testing “Ion Torrent Genexus Sequencer” with FoundationOne

Abstract

Abstract Background Molecular diagnostic tests are becoming increasingly routine, and the use of tissue- and blood-based next-generation sequencing (NGS) is integral to the delivery of personalized medicine for targeted cancer therapy. This study aimed to evaluate the variant concordance for somatic variants using two clinical NGS systems for conducting both tissue- and blood-based analyses: Genexus-OCA v3 (OCA) vs. FoundationOne CDx (F1) for tissues and Genexus OPA (OPA) vs. FoundationOne CDx Liquid (F1L) for blood. Methods The concordance of genomic alterations between the two NGS analyses was compared in six patients with breast, head, and neck cancers using tissue and circulating tumor DNA biopsies. Results A total of 130 genes were common between F1 and OCA, and 41 between F1L and OPA. When comparing FoundationOne to Genexus for common genes, the sensitivity and specificity of OCA and OPA were 55% and 99%, respectively. Nine single-nucleotide variants (SNVs), one copy number alteration (CNA), and one fusion were detected by both Genexus and FoundationOne. However, one SNV (MAP2K1 F53V), two CNAs (AKT3 and MYC), and one fusion (ESR-CCDC170) were detected only in Genexus, whereas two SNVs (TP53 Q331* and KRAS G12V) were detected only in FoundationOne. Conclusion The two cancer genome panels were equivalent but not perfect in terms of the detection of variants using tissue and blood, indicating that different assays and analytical methods may have influenced the results. When performing comprehensive genomic profilings (CGPs), it is important to consider the characteristics of each NGS-based CGP test and the genetic variants associated with each disease.