Halling, Kevin C.

Abstract Introduction: Clinical staging of multifocal non-small cell lung cancer (NSCLC) is facilitated by comparative genomic analysis of separate tumor nodules, but the role of genome-wide copy number profiling for this purpose is uncertain. Methods: We analyzed single nucleotide variants (SNVs), gene fusions, small copy number variants (gene amplifications and homozygous deletions) (sCNVs), and large-scale copy number variants (lCNVs) in a retrospective cohort of 34 patients with >1 lung cancer nodule tested on a previously validated tumor-only 515-gene next generation sequencing (NGS) panel (MayoComplete Solid Tumor Panel). For patients with <2 shared SNVs, a Bayesian approach was formulated to calculate the probability of shared versus independent events occurring in different tumor nodules in the same patient. The prevalence of specific lCNVs in NSCLC was derived from an independent dataset of 100 NSCLC peers tested by the same panel, and the prevalence of SNVs, fusions, and sCNVs in NSCLC was derived from publicly available data. Alterations unique to different tumor nodules and suspected germline alterations were excluded from the Bayesian analysis. Results: There were 54 total comparisons for 34 patients. Eleven of the patients (32.4%) had >=2 shared SNVs along with one or more shared lCNVs also identified in each patient. Eight patients (23.5%) had no shared SNVs, gene fusions, sCNVs, or lCNVs. Using the Bayesian approach for the remaining fifteen (44.1%) patients with at least one shared alteration (SNVs, sCNVs, and lCNVs), the probability of clonal relatedness ranged from 73% for a shared whole arm or whole chromosome lCNV to >99% for tumors with two or more shared alterations including multiple or complex lCNVs and SNVs. Whole chromosome or whole arm lCNVs were sometimes shared between tumor nodules with different driver SNVs. Conclusions: Incorporating lCNVs into comparative genomic analysis provides additional evidence of clonal relatedness in a subset of multifocal NSCLCs. However, differences in bioinformatics pipelines for calling lCNVs, concerns over the imprecision of genome-wide copy number profiling, and uncertainty regarding the temporal relationship between lCNVs and carcinogenesis (including somatic events possibly related to “field cancerization”) create challenges for integrating lCNVs into comparative genomic analysis with standard clinical workflows for tumor-only NGS on paraffin embedded tissue sections. Our simplified approach mitigates some of the uncertainty introduced by incorporating lCNVs into clonality determination. Citation Format: Claire Teigen, Ying-Chun Lo, Sounak Gupta, Stephanie Smoley, Beth Pitel, Hussam Al Kateb, Gopi Sivasankaran, Benjamin Kipp, Ande Rumilla, Gang Zheng, Kevin Halling, Katherine Geiersbach, . A Bayesian framework for evaluating somatic copy number variants into comparative genomic analysis of multifocal non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 5423.

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.

Abstract Introduction/Objective Mutations in KIT and PDGFRA drive the majority of gastrointestinal stromal tumors (GIST) and inform targeted therapy selection. While single-driver mutations are typical, a subset of cases harbors multiple KIT mutations, complicating clinical interpretation. This study investigated the frequency, distribution, and inferred hierarchy of primary and secondary KIT mutations using DNA-based sequencing in a large GIST cohort. Methods/Case Report We retrospectively reviewed 579 GIST cases that underwent DNA-based next-generation sequencing using a custom panel targeting all coding exons of KIT and PDGFRA. Tumor-rich formalin-fixed paraffin-embedded (FFPE) tissue was required. In double-mutant cases, the mutation with higher variant allele frequency (VAF) was presumed to be primary. Results Mutations in KIT or PDGFRA were detected in 482/579 cases (83.2%). Among KIT-mutant cases, 28 had two mutations and one had three. Secondary mutations frequently occurred in exons 13, 14, and 17 and were significantly more common in non-gastric tumors (p < 0.0001). Primary mutations most often involved exon 11. Conclusion VAF analysis enabled classification of mutation hierarchy in cases with multiple KIT mutations. The distinct anatomical and exon-specific distribution of primary vs. secondary mutations highlights their potential therapeutic implications and warrants further study.

ABSTRACT Myxoid liposarcoma (MLS) accounts for 20%–30% of all liposarcomas, with most cases harboring the fusion gene FUS::DDIT3 , while approximately 5% exhibit the EWSR1::DDIT3 fusion. We report the case of a 26‐year‐old male patient with a right upper arm mass. The tumor displayed the classic histological features of MLS, including small spindle/ovoid cells, variable univacuolated lipoblasts, and a prominent myxoid stroma with delicate arborizing vasculature. Despite these characteristic features, fluorescence in situ hybridization (FISH) revealed no apparent rearrangement of the DDIT3 locus. Next‐generation sequencing (NGS) identified a novel fusion transcript in which SMARCA2 exon 4 was fused in‐frame with DDIT3 exon 2. Chromosomal microarray analysis demonstrated the unbalanced nature of the rearrangement, with partial deletions of 0.243 and 0.176 Mb flanking the centromeric end of the DDIT3 locus on 12q13.3 (which also included GLI ) and disrupting the SMARCA2 locus on 9p24, respectively. The resultant chimeric fusion protein is predicted to lack the SMARCA2 DNA‐binding domains while retaining the DDIT3 leucine zipper dimerization domain. These findings indicate an unusual and complex rearrangement, leading to the recruitment of a novel DDIT3 partner gene. Moreover, they emphasize that the functional aspects of myxoid liposarcoma fusion genes depend on the retention of the key DDIT3 domain. Finally, this case illustrates how classic morphology can appropriately trigger reflex molecular analyses, which may, in turn, uncover novel fusion genes or other molecular alterations.

ABSTRACTVarious cutaneous adnexal neoplasms have been associated with gene fusions as the main driver of their histogenesis, most of which showed poroid or hidradenomatous differentiation or represented other tumors of sweat glands. Recently, we encountered two cases of primitive basaloid neoplasms of predominantly folliculogenic/pilosebaceous origin, both surprisingly harboring recurrent EWSR1 rearrangements. Both tumors presented in young patients of either sex (1 F; 17 years; 1 M; 37 years) and involved the dermis and subcutaneous tissue of the abdominal wall (case 1) and the buttock (case 2). Histologically, the tumors were composed of primitive, basaloid cells with areas of keratinization (case 1) or foci of sebaceous differentiation (case 2) and stained strongly with keratins, p40 (case 1) or p63 (case 2), while lacking significant CD99 expression in both cases. Case 1 harbored an EWSR1::FLI1 fusion while case 2 harbored an EWSR1::PBX3 fusion. Clinical follow‐up was available for case 2 and showed no evidence of disease at 15 months of follow‐up. Methylation profiling showed case 1 to cluster with cutaneous squamous cell carcinoma, while case 2 was independent but positioned close to salivary gland epithelial‐myoepithelial carcinoma. These findings expand on the histopathologic and molecular genetic features of basaloid tumors with apparent adnexal differentiation and raise awareness to carefully interpret and correlate molecular findings with morphology and immunophenotype to avoid misinterpretation as a mesenchymal neoplasm.

Myoepithelial tumors are typically characterized by distinct molecular profiles that have been shown to correlate with their anatomical locations. EWSR1 or FUS rearrangements are common in cutaneous, soft tissue and bone tumors, whereas salivary gland myoepithelial tumors are frequently associated with PLAG1 and HMGA2 alterations. This apparent molecular divergence led some previous studies to doubt a common pathogenetic relationship between myoepithelial tumors of soft tissue and bone with their salivary gland counterparts. Herein, we present primary intraosseous myoepithelioma harboring HMGA2::WIF1 fusion. This fusion has been previously identified in a range of salivary gland myoepithelial tumors including myoepitheliomas, myoepithelial carcinomas arising from pleomorphic adenomas, and pleomorphic adenomas themselves. Primary myoepithelial tumors of the bone are exceedingly rare, and to our knowledge, HMGA2 rearrangements have not been previously reported in soft tissue or bone myoepithelial neoplasms. Through this report, we aim to enhance the existing literature on myoepithelial neoplasms, while highlighting the importance of recognizing primary bone myoepitheliomas and contributing to a broader understanding of the pathogenetic landscape of myoepithelial tumors across diverse tissue types.

ABSTRACTXanthogranulomatous epithelial tumor (XGET)/Keratin‐positive giant cell tumor (KP‐GCT) represents a spectrum of recently described neoplasms characterized by a proliferation of distinctive mononuclear cells expressing keratin within a background of osteoclast‐like giant cells, mixed inflammatory cells, and a variably prominent xanthogranulomatous component. Recent studies demonstrated a recurrent HMGA2::NCOR2 fusion in many cases. We herein describe a case of XGET/KP‐GCT arising in the right femoral head of a 19‐year‐old male harboring a rare novel HMGA2::COL14A1 fusion.

AbstractBackgroundWhile the list of fusion‐driven soft tissue neoplasms is expanding rapidly, their importance among cutaneous and superficial mesenchymal and adnexal neoplasms remains poorly understood. This challenge is especially evident in cases with ambiguous histopathology that are difficult to classify based on morphology.AimsOur goal was to investigate the benefits of next‐generation sequencing in diagnosing complex cutaneous neoplasms.Materials & MethodsDepartmental archives were searched for fusion‐driven cutaneous neoplasms. Slides were retrieved and clinical information including follow‐up was obtained.ResultsFifteen cases occurred in eight female and seven male patients, with a median age of 26 years (range: 1–83) at diagnosis. Tumors involved the extremities (9), scalp (5), and head and neck (1). Predominant features included myoepithelial (5), nested spindled with clear cytoplasm (2), atypical adnexal/squamoid (2), small round blue cell (2), cellular spindled (3), and fibrohistiocytic morphology (1). Most frequently encountered fusions involved EWSR1 (6) fused to ERG (1), FLI1 (1), CREB1 (2), CREM (1), PBX3 (1), followed by PLAG1 (4) with LIFR (2), TRPS1 (1) and CHCHD7. Additional fusions encountered were YAP1::NUTM1, EML4::ALK, SS18::SSX1 (2), and a novel fusion: ACTB::ZMIZ2. Integration of histologic features and molecular findings led to final diagnoses of primary cutaneous Ewing sarcoma (2), soft tissue myoepithelioma (4), cutaneous syncytial myoepithelioma (1), cutaneous adnexal carcinoma (1), porocarcinoma (1), inflammatory myofibroblastic tumor (1), synovial sarcoma (2), clear cell sarcoma (2), and angiomatoid fibrous histiocytoma (1).Discussion and conclusionOur results show that fusion testing can be a helpful diagnostic tool, especially in cases with unusual or uncommon morphology in superficial sites. Furthermore, it can allow for the identification of potential therapeutic targets in some instances.