HER2-targeted therapies have transformed the management of advanced or recurrent serous endometrial cancer (EC), leading to an increased clinical demand for HER2 testing. Despite its adoption in select academic centers, the global extent of such tumor testing is unclear. In this study, we report on the initial two-year experience of HER2 testing at a major academic center with a reference gynecologic oncology service and biomarker reference laboratory. All patients who underwent HER2 testing based on physician discretion, reflex HER2 testing, and reference laboratory requests were included. From February 2021 to October 2023, HER2 testing was performed on 192 tumor tissue samples from 180 EC patients. Serous carcinoma constituted 52% of samples, reflecting diagnostic challenges and limited therapeutic options for advanced EC. HER2 positivity was found in 28% of all cases and 30% of p53-aberrant cases. An immunohistochemistry (IHC) score of 3+ was found in 15% of samples, while IHC 2+ was found in 45% (13% IHC 2+/ISH+ and 32% IHC 2+/ISH−). The newly identified ‘HER2-low’ category comprised 46% of the samples. Heterogeneity was noted in 42% of HER2-positive cases, with complex patterns in 3%. NGS and HER2 IHC-FISH showed a 24% discordance, attributed to intratumoral heterogeneity, tumor cellularity, a small number of amplified cells, and the HER2/CEP17 ratio near the cut-off. This study offers real-world insights into HER2 testing in EC, highlighting the challenges and underscoring the need for standardized guidelines in specimen handling, proficiency testing, and scoring criteria to enhance patient management and therapeutic decision-making.

The detection of gene fusions by RNA-based next-generation sequencing (NGS) is an emerging method in clinical genetic laboratories for oncology biomarker testing to direct targeted therapy selections. A recent Canadian study (CANTRK study) comparing the detection of NTRK gene fusions on different NGS assays to determine subjects’ eligibility for tyrosine kinase TRK inhibitor therapy identified the need for recommendations for best practices for laboratory testing to optimize RNA-based NGS gene fusion detection. To develop consensus recommendations, representatives from 17 Canadian genetic laboratories participated in working group discussions and the completion of survey questions about RNA-based NGS. Consensus recommendations are presented for pre-analytic, analytic and reporting aspects of gene fusion detection by RNA-based NGS.

Genomic profiling of pancreatic cancer using small core biopsies has taken an increasingly prominent role in precision medicine. However, if not appropriately preserved, nucleic acids (NA) from pancreatic tissues are known to be susceptible to degradation due to high intrinsic levels of nucleases. PAXgene fixation (PreAnalytix, Switzerland) represents a novel formalin-free tissue preservation method. We sought to compare the NA and histomorphological preservation of pancreatic cancer tissues preserved with PAXgene-fixed paraffin-embedding (PFPE) and formalin-fixed paraffin-embedding (FFPE). Tissues from 19 patients were obtained prospectively from pancreaticoduodenectomy specimens and evaluated by four gastrointestinal pathologists. The extracted NA were quantified by Nanodrop and Qubit and assessed for quality by qPCR, targeted next-generation sequencing (NGS) assay, and RNA-sequencing. Our results demonstrated that, when assessed blindly for morphological quality, the four pathologists deemed the PFPE slides adequate for diagnostic purposes. PFPE tissues enable greater yields of less fragmented and more amplifiable DNA. PFPE tissues demonstrated significantly improved quality control (QC) metrics in a targeted NGS assay including Median Absolute Pair-wise Difference (MAPD) scores. Our results support the use of PAXgene fixative for the processing of specimens from pancreatic cancers with the potential benefits of improved yields for more amplifiable DNA in low-yield biopsy specimens and its ideal use for amplicon-based NGS assays.

Background: Targeted next-generation sequencing (NGS) panels are increasingly being utilized to identify actionable gene amplifications (copy number > 4) among solid tumors. Methods: This study validated the analytical performance of two amplicon-based NGS assays, the Oncomine Comprehensive Panel (OCAv3) and the Oncomine Focus Assay (OFA), for detecting gene amplification in formalin-fixed paraffin-embedded (FFPE) tumors of varying cellularity. OCAv3 was assessed for amplification detection in 756 FFPE samples comprising various tumor types. Results: We demonstrated that with standardized quality control metrics, including median absolute pairwise difference score, these assays can achieve a near-perfect positive predictive value, although their sensitivity for detecting amplifications significantly decreased in tumors with cellularity below 30%. Stratifying tumor cellularity into 10–30%, 31–60%, and 61–95% groups revealed significantly higher gene amplification detection rates in the 31–60% and 61–95% groups versus the 10–30% group (20.6% and 26.7% vs. 9.2%, p < 0.0001). When considering all detected gene amplifications, the average amplification calling per sample was nearly five-fold lower in the 10–30% group versus the 61–95% group (0.11 vs. 0.52; p < 0.0001). To further investigate the analytic performance of OCAv3 in detecting ERBB2 amplification, we analyzed a cohort of 121 uterine carcinomas with confirmed ERBB2 status by HER2 IHC or FISH, in which a threshold incorporating amplifications and tumor cellularity achieved 79% sensitivity and 100% specificity, potentially eliminating the need for FISH analysis in 34% of equivocal cases. In a separate validation cohort, similar analytical performance was observed, with the threshold demonstrating consistent sensitivity and specificity. Conclusions: This study highlights the strengths and limitations of amplicon-based NGS assays in detecting amplifications using real-world data.

Background/Objectives: HER2 overexpression and/or amplification defines a molecularly distinct subset of endometrial carcinomas (ECs) that may benefit from HER2-targeted therapies. However, HER2 testing algorithms remain non-standardized and vary across institutions. This study is a large single-institution audit of EC HER2 testing practices, using both gynecologic (ISGyP) and gastric cancer-specific scoring algorithms at a major academic center with a reference gynecologic oncology service and biomarker laboratory. Methods: HER2 immunohistochemistry (IHC) and whole-slide fluorescence in situ hybridization (FISH) were interpreted by subspecialty breast and gynecologic pathologists, with HER2 IHC performed on 494 tumor samples (2021–2025) and reflex FISH for equivocal cases. Results: Using ISGyP criteria, 15.0% (74/494) of tumors were HER2 IHC 3+, 44.5% (220/494) equivocal (2+), and 40.5% (200/494) were negative (0/1+). Among equivocal cases, 28.2% (58/205) demonstrated ERBB2 amplification, yielding an overall HER2-positive rate of 27.5% (132/480). Re-assessment with gastric scoring criteria demonstrated variability in HER2 classification, with high concordance in cytology specimens (100%) and resections (90.8%; K = 0.842, p < 0.001) but substantially lower concordance in biopsies (60.6%; K = 0.401, p < 0.001), mainly due to reclassification of equivocal cases. Notably, 47.9% (n = 34) of ISGyP-equivocal biopsy specimens were reclassified as HER2 IHC 3+ using gastric biopsy criteria, potentially expanding eligibility for T-DXd therapy. Conclusions: These findings highlight the evolving nature of HER2 testing in EC and demonstrate the significant impact of scoring methodology on HER2 interpretation. Our results support the development of EC-specific HER2 testing guidelines and a dual-reporting approach incorporating both ISGyP and gastric scoring criteria, with selective confirmatory FISH testing, to optimize patient selection for HER2-targeted therapies.

Next-generation sequencing (NGS) is integral to colorectal cancer (CRC) care, but its value depends on results being available when treatment decisions are made. We conducted a qualitative study to identify quality gaps in CRC NGS pathways and assess perspectives on digital and artificial intelligence (AI)-enabled workflow support. Semi-structured interviews were conducted with 22 medical oncologists and pathologists from 14 Ontario hospitals, and transcripts were analyzed thematically. Five themes emerged: (1) clinical indications and test ordering, where initiation was inconsistent because of unclear reflex-testing criteria, reliance on upstream clinicians, staging uncertainty, evolving indications, and funding constraints; (2) tissue, pathology, and laboratory workflow, where participants attributed bottlenecks and turnaround variability to send-out testing, staffing, infrastructure, and capacity; (3) interdisciplinary communication and tracking, where informal communication, unclear ownership, and manual tracking highlighted the need for closed-loop confirmation and alerts; (4) reporting and clinical integration, where report clarity, interpretability, and timing affected use; and (5) electronic health record integration and AI integration, where fragmented systems and limited interoperability delayed result access. Participants supported clinician-supervised digital or AI-enabled tools for case identification, triage, tracking, and overdue-result alerts. CRC NGS optimization requires standardized reflex criteria, clearer ownership, closed-loop tracking, reliable routing, structured reporting, and interoperable infrastructure.