Optimizing Tissue Preparation for Molecular Testing in Thyroid Tumors: A Retrospective Analysis of 177 Cases from a High-Volume Japanese Center

Background/Objectives: Reliable molecular testing is essential for selecting targeted therapies for thyroid tumors; however, assay performance can be affected by pre-analytical tissue conditions. This retrospective, single-center study evaluated real-world formalin-fixed, paraffin-embedded (FFPE) specimens to identify pathology practices associated with successful companion diagnostic testing using the next-generation sequencing (NGS)-based Oncomine Dx assay and the polymerase chain reaction (PCR)-based BRAF3 assay widely used in routine clinical care in Japan. Methods: We retrospectively analyzed 177 cases with thyroid tumors tested at a high-volume thyroid center in Japan between 2022 and 2026. Results: All 79 specimens analyzed using the BRAF3 assay yielded successful test results, including specimens fixed in unbuffered formalin and archival blocks stored for up to 27 years. In contrast, the Oncomine Dx assay was successful in 93 of 98 specimens (94.9%), with all five failures occurring in specimens fixed in unbuffered formalin. DNA failure was more common than RNA failure. All five Oncomine Dx failures occurred in archived tissue blocks stored for 3–9 years, all of which had been fixed in unbuffered formalin. The BRAF3 test had a shorter turnaround time and was more frequently used in rapidly progressive tumors, such as anaplastic thyroid carcinoma. Conclusions: The NGS-based Oncomine Dx assay showed reduced success in samples stored long-term or in unbuffered specimens, whereas RNA preservation was high. In contrast, the PCR-based BRAF3 assay remained highly reliable even in long-stored archival blocks. Because fixative type and storage duration were confounded in this cohort, the independent effects of these variables could not be determined. The study’s findings provide practical real-world insights into how specimen handling, fixation, and storage conditions may influence the reliability of genomic diagnostics in routine practice.