Comparative evaluation of HTG and TempO Seq targeted transcriptome profiling methods

Transcriptomic profiling is a cornerstone of molecular biology and plays a central role in translational and molecular oncology, where reliable gene expression measurements are essential. Targeted RNA sequencing approaches offer several advantages over whole-transcriptome methods, including high sensitivity, reproducibility, and reduced turnaround time, particularly when working with formalin-fixed paraffin-embedded (FFPE) samples. HTG EdgeSeq HTP has previously addressed these needs; however, the recent discontinuation of this platform has created a technical gap for targeted transcriptome analysis in FFPE specimens. In this study, we perform a systematic technical comparison between HTG EdgeSeq HTP and an analogous targeted platform, TempO-Seq, to assess its suitability as an alternative for research applications in molecular oncology. We analyzed 21 FFPE endometrial cancer samples together with three RNA reference controls derived from cell lines and evaluated concordance across multiple levels of biomarkers, ranging from individual transcripts to complex multi-gene signatures comprising tens to thousands of genes. While single-gene measurements showed limited concordance between platforms, multi-gene biomarkers exhibited substantially higher agreement, indicating that aggregation across multiple probes mitigates platform-specific effects. Overall, our results demonstrate that TempO-Seq provides comparable performance to HTG EdgeSeq HTP at the level of multi-gene biomarkers, supporting its use as a robust alternative for targeted transcriptomic profiling of FFPE samples in molecular oncology research.