NanoString nCounter-Based Assay for Detection of Fusion-Associated Salivary Gland Tumors.

IF 3.2 Q2 PATHOLOGY Head & Neck Pathology Pub Date : 2024-10-28 DOI:10.1007/s12105-024-01710-w
Angela Goytain, Tony L Ng
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Abstract

Purpose: Salivary gland tumors include numerous subtypes that vary from benign to highly aggressive, with many showing overlapping histopathological features that can make diagnosis challenging. Most subtypes express driver fusion genes that are tumor specific, and detection of such fusions is useful for differentiating amongst specific diagnoses, determining appropriate tumor grading, and guiding effective treatment. Currently, fusions can be detected by FISH, RT-PCR or through next-generation sequencing approaches, all of which are highly effective methodologies but can be costly or time consuming.

Methods: We developed a rapid NanoString nCounter platform-based assay to detect salivary gland tumor fusions using a combination of fusion junction-specific probes and an approach through differential exon expression analysis. The assay includes 68 junction-specific probes and analysis of exon expression across 9 fusion-associated genes in a single multiplex assay.

Results: Out of 55 retrospective and 171 prospective cases assayed, we accurately detected the majority of cases of pleomorphic adenoma, adenoid cystic carcinoma, cribriform adenocarcinoma, clear cell carcinoma, secretory carcinoma and NUT-rearranged carcinoma, including cases of these tumor types arising in non-salivary gland sites, with the major drawback being an inability to detect MAML2-containing mucoepidermoid samples. With mucoepidermoid carcinoma excluded, the assay shows an overall sensitivity of 96.1% and specificity of 100%.

Conclusion: We show that the majority of salivary gland tumor fusions can be effectively detected with a single rapid NanoString based assay, which can serve as a useful adjunctive tool for routine diagnostic head and neck pathology. The assay is low cost with a rapid turnaround time (30 h total assay time per sample batch, with minimal technician input required) compared to alternate detection methods.

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基于 NanoString nCounter 的融合相关唾液腺肿瘤检测试剂盒。
目的:唾液腺肿瘤包括从良性到高度侵袭性的众多亚型,其中许多亚型的组织病理学特征相互重叠,这给诊断带来了挑战。大多数亚型表达的驱动融合基因具有肿瘤特异性,检测此类融合基因有助于区分特定诊断、确定适当的肿瘤分级和指导有效治疗。目前,可通过 FISH、RT-PCR 或新一代测序方法检测融合基因,所有这些方法都非常有效,但可能成本高昂或耗时较长:方法:我们开发了一种基于 NanoString nCounter 平台的快速检测方法,利用融合结特异性探针和差异外显子表达分析相结合的方法检测唾液腺肿瘤融合。该检测方法包括 68 个接合点特异性探针和 9 个融合相关基因的外显子表达分析:结果:在55个回顾性病例和171个前瞻性病例中,我们准确检测出了大多数多形性腺瘤、腺样囊性癌、楔形腺癌、透明细胞癌、分泌性癌和NUT排列癌病例,包括这些肿瘤类型发生在非唾液腺部位的病例,主要缺点是无法检测出含有MAML2的粘液表皮样癌样本。在排除粘液表皮样癌的情况下,该检测方法的总体灵敏度为 96.1%,特异性为 100%:我们的研究表明,大多数唾液腺肿瘤融合都能通过基于 NanoString 的单一快速检测方法有效检测出来,该检测方法可作为常规头颈部病理诊断的有用辅助工具。与其他检测方法相比,该检测方法成本低、周转时间短(每批样本的总检测时间为 30 小时,所需技术人员最少)。
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来源期刊
CiteScore
5.70
自引率
9.50%
发文量
99
期刊介绍: Head & Neck Pathology presents scholarly papers, reviews and symposia that cover the spectrum of human surgical pathology within the anatomic zones of the oral cavity, sinonasal tract, larynx, hypopharynx, salivary gland, ear and temporal bone, and neck. The journal publishes rapid developments in new diagnostic criteria, intraoperative consultation, immunohistochemical studies, molecular techniques, genetic analyses, diagnostic aids, experimental pathology, cytology, radiographic imaging, and application of uniform terminology to allow practitioners to continue to maintain and expand their knowledge in the subspecialty of head and neck pathology. Coverage of practical application to daily clinical practice is supported with proceedings and symposia from international societies and academies devoted to this field. Single-blind peer review The journal follows a single-blind review procedure, where the reviewers are aware of the names and affiliations of the authors, but the reviewer reports provided to authors are anonymous. Single-blind peer review is the traditional model of peer review that many reviewers are comfortable with, and it facilitates a dispassionate critique of a manuscript.
期刊最新文献
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