Pujari, Ganesh P.

Abstract Introduction Accurate detection of gene fusions is critical for the diagnosis and management of sarcomas. However, occasional false-negative results may occur due to factors such as low tumor cellularity, limited assay coverage of relevant genomic regions, or mis-annotation by bioinformatic pipelines. We recently encountered a case in which our clinical SARCP fusion detection assay failed to identify an HMGA2::NCOR2 (exon 3–exon 16) fusion. Method The SARCP assay is a targeted, amplicon-based RNA-seq next-generation sequencing (NGS) assay designed to detect gene fusions across 138 genes, including HMGA2. Although NCOR2 is not among the targeted genes, the assay is capable of detecting fusions when only one gene partner is represented. Results Suspicion of a false-negative result arose when the pathologist noted that the tumor’s histologic features—keratin-positive, giant cell-rich soft tissue—were consistent with a subtype previously associated with the HMGA2::NCOR2 fusion. This prompted a review of the bioinformatic output, which had erroneously reported an HMGA2::MAML2 fusion. The misannotation was traced to sequence homology involving a CAA/CAG repeat at the 5′ end of NCOR2 exon 16, likely resulting from DNA polymerase slippage and misalignment in low-complexity, partially complementary repetitive regions. This erroneously lead to the target genomic sequence getting mapped to MAML2 exon 2 as opposed to the NCOR2 exon 16. Discussion This case highlights how bioinformatic mis-annotation can lead to occasional false-negative fusion calls. It underscores the importance of manual review in cases with strong clinical or pathologic suspicion and calls attention to the need for fusion-calling algorithms that better handle repetitive and homopolymeric sequences. Citation Format: Ganesh P. Pujari, Mitch L. Klebig, Kurt S. Willkom, Montha Chhunn, Stefan W. Nelson, Neiladri Saha, Kevin C. Halling. Mis-Annotation of an HMGA2::NCOR2 Fusion in FFPE Sarcoma Samples: A Case Illustrating Bioinformatic Limitations in Fusion Detection [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Fusion-Positive Cancer: From Discovery to Therapy; 2026 Jan 13-15; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86(1_Suppl):Abstract nr A012.

Key Points Increased protein expression of tissue inhibitor of metalloproteinase-3, glypican 6, synuclein γ , apolipoprotein A-4, and Ecto-5′-nucleotidase was observed in old adults compared with young adults. In old adults, overexpressed proteins were enriched in mitochondrial processes while under expressed proteins enriched in RNA metabolism. Validated differentially expressed proteins were not significantly correlated with kidney pathology after adjusting for age. Background Kidney aging is characterized by a loss of glomeruli, predominantly in the superficial cortex, with a resultant decline in GFR and an increased risk of various kidney-related diseases. The early molecular alterations in glomeruli associated with the aging process are not well studied. Methods We combined laser capture microdissection and mass spectrometry–based unbiased proteomic analysis of nonsclerosed, nonischemic glomeruli in the superficial cortex from young and old adults who underwent a radical nephrectomy for a tumor to understand the age-related molecular changes in glomeruli. Twenty-four young and 30 old adults were used for the discovery dataset, and the significant differentially expressed proteins were further validated using an independent set comprising six young and eight old adults. Results Kidneys from old adults had lower eGFR, less kidney parenchyma on computed tomography imaging, and more glomerulosclerosis and arteriosclerosis on histology. Quantitative proteomic analysis of nonsclerosed, nonischemic glomeruli identified increased expression of tissue inhibitor of metalloproteinase-3, glypican 6, synuclein γ , apolipoprotein A-4, and Ecto-5′-nucleotidase in old adults that were further validated in an independent set. Pathway analysis indicated that proteins with increased expression in old adults were enriched in mitochondrial translational processes, aerobic respiration, and TCA cycle, whereas proteins with decreased expression in old adults were enriched in mRNA splicing, mRNA processing, and nonsense mediated decay. Furthermore, validated differentially expressed proteins did not show any significant correlation with the kidney pathology independent of age group. Conclusions Overall, this study identified proteins that are specifically associated with the aging process in otherwise normal-appearing glomeruli.