Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
J Mol Diagn. 2021 Oct;23(10):1343-1358. doi: 10.1016/j.jmoldx.2021.07.015. Epub 2021 Aug 4.
Somatic gene fusions are common in leukemias/lymphomas and solid tumors. The detection of gene fusions is crucial for diagnosis. NanoString fusion technology is a multiplexed hybridization method that interrogates hundreds of gene fusions in a single reaction. This study's objective was to determine the performance characteristics and diagnostic utility of NanoString fusion assays in a clinical diagnostics laboratory. Validation using 100 positive specimens and 15 negative specimens by a combined reference standard of fluorescence in situ hybridization (FISH)/RT-PCR/next-generation sequencing (NGS) assays achieved 100% sensitivity in leukemias/lymphomas and 95.0% sensitivity and 100% specificity in solid tumors. Subsequently, 214 consecutive clinical cases, including 73 leukemia/lymphoma specimens and 141 formalin-fixed, paraffin-embedded solid tumor specimens, were analyzed by gene fusion panels across 638 unique gene fusion transcripts. A variety of comparator tests, including FISH panels, conventional karyotyping, a DNA-based targeted NGS assay, and custom RT-PCR testing, were performed in parallel. The gene fusion assay detected 31 gene fusions, including 16 in leukemia/lymphoma specimens and 15 in solid tumor specimens. The overall sensitivity, specificity, and accuracy of gene fusions detected by the gene fusion panel in all 329 specimens (validation and consecutive clinical specimens) tested in this study were 94.8%, 100%, and 97.9%, respectively, compared with FISH/RT-PCR/NGS assays. The gene fusion panel is a reliable approach that maximizes molecular detection of fusions among both fresh and formalin-fixed, paraffin-embedded cancer specimens.
体细胞基因融合在白血病/淋巴瘤和实体瘤中很常见。融合基因的检测对诊断至关重要。NanoString 融合技术是一种多重杂交方法，可以在单个反应中检测数百种融合基因。本研究的目的是确定 NanoString 融合检测在临床诊断实验室中的性能特征和诊断效用。通过荧光原位杂交（FISH）/逆转录聚合酶链反应（RT-PCR）/下一代测序（NGS）检测的联合参考标准，对 100 个阳性标本和 15 个阴性标本进行验证，白血病/淋巴瘤的检测灵敏度达到 100%，实体瘤的检测灵敏度为 95.0%，特异性为 100%。随后，通过 638 个独特的融合基因转录本，对包括 73 个白血病/淋巴瘤标本和 141 个福尔马林固定、石蜡包埋的实体瘤标本在内的 214 例连续临床病例进行了基因融合panel 分析。同时平行进行了各种比较器检测，包括 FISH 面板、常规核型分析、基于 DNA 的靶向 NGS 检测和定制 RT-PCR 检测。基因融合检测在所有 329 例标本（验证和连续临床标本）中检测到 31 个基因融合，包括白血病/淋巴瘤标本中的 16 个和实体瘤标本中的 15 个。与 FISH/RT-PCR/NGS 检测相比，基因融合panel 在所有 329 例标本（验证和连续临床标本）中检测到的基因融合的总体灵敏度、特异性和准确性分别为 94.8%、100%和 97.9%。基因融合 panel 是一种可靠的方法，可以最大限度地提高新鲜和福尔马林固定、石蜡包埋的癌症标本中融合基因的分子检测。
