Leveraging a real-world clinicogenomic database for post-sequencing quality assessment in solid tumor comprehensive genomic profiling (CGP)

The quantity and integrity of DNA and RNA extracted from formalin-fixed paraffin-embedded (FFPE) tumor specimens can vary significantly due to factors such as block age, fixation conditions, protein crosslinking, and the presence of chemical inhibitors. Over a decade of research has demonstrated that, with optimized pre- and post-analytical workflows, FFPE samples can serve as reliable input material for both clinical and research-based next-generation sequencing (NGS) applications. Certain tumor types present additional challenges for nucleic acid extraction due to their biological characteristics, such as high metabolic activity and elevated nuclease levels. To evaluate sequencing quality across diverse tumor tissue types, we analyzed post-sequencing metrics from clinical tests performed over a 12-month period using the OmniSeq INSIGHT test for CGP. The cohort included 8,645 solid tumor samples representing 19 distinct cancer types. The most frequently profiled tumors were lung (N=3,984), colorectal (N=1,211), breast (N=578), pancreatic (N=398), prostate (N=331), uterine (N=252), esophageal (N=232), and head and neck (N=221). Key post-sequencing quality metrics that assess sequencing coverage and on target mapping were evaluated. Across all indications, high-quality data metrics were consistently achieved for both DNA and RNA, underscoring the robustness of the workflow regardless of tumor type. These findings support the scalability and reliability of CGP using FFPE tissue across a broad spectrum of solid tumors, reinforcing its utility in clinical oncology and research applications for high-quality genomic reporting.