Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario.
Division of Genome Diagnostics, Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
J Mol Diagn. 2020 Apr;22(4):467-475. doi: 10.1016/j.jmoldx.2019.12.008. Epub 2020 Feb 6.
A common rationale in molecular diagnostic laboratories is that implementation of next-generation sequencing (NGS) enables simultaneous multigene testing, allowing increased information benefit compared with non-NGS assays. However, minimal published data exist to support this justification. The current study compared clinical diagnostic yield of TruSight Tumor 26 Sequencing Panel (TST26) in melanoma, colorectal (CRC), and gastrointestinal stromal (GIST) tumors with non-NGS assays. A total of 1041 formalin-fixed, paraffin-embedded tumors, of melanoma, CRC, and GIST, were profiled. NGS results were compared with non-NGS single-gene or single-variant assays with respect to variant output and diagnostic yield. A total of 79% melanoma and 94% CRC tumors were variant positive by panel testing. TST26 panel improved serine/threonine-protein kinase B-raf (BRAF) variant detection in melanoma compared with single-variant BRAF Val600Glu/Lys (V600E/K) routine tests by 24% and detected variants in genes other than BRAF, NRAS, and KIT, which could impact patient management in 20% additional cases. NGS enhanced diagnostic yield in CRC by 36% when compared with routine single-gene assays. In contrast, no added benefit of NGS-based testing for GIST tumors was observed. TST26 panel either missed or inaccurately called complex insertion/deletion variants in KIT exon 11, which were accurately identified by non-NGS methods. Findings of this study demonstrate the differential impact of cancer site and variant type on diagnostic test information yield from NGS assays.
在分子诊断实验室中，一个常见的原理是下一代测序（NGS）的实施能够实现多基因同时检测，与非 NGS 检测相比，能够提供更多的信息收益。然而，支持这一说法的已发表数据很少。本研究比较了 TruSight Tumor 26 测序Panel（TST26）在黑色素瘤、结直肠癌（CRC）和胃肠道间质瘤（GIST）肿瘤中的临床诊断收益与非 NGS 检测。共对 1041 例福尔马林固定、石蜡包埋的黑色素瘤、CRC 和 GIST 肿瘤进行了分析。将 NGS 结果与非 NGS 单基因或单变体检测进行了比较，比较了变异输出和诊断收益。通过面板检测，79%的黑色素瘤和 94%的 CRC 肿瘤存在变异。与常规的 BRAF Val600Glu/Lys（V600E/K）单变体检测相比，TST26 面板检测提高了黑色素瘤中丝氨酸/苏氨酸蛋白激酶 B-raf（BRAF）变体检测的灵敏度，提高了 24%，并检测到了 BRAF、NRAS 和 KIT 以外的基因中的变体，这可能会影响 20%的额外病例的患者管理。与常规的单基因检测相比，NGS 提高了 CRC 的诊断收益，提高了 36%。相比之下，对于 GIST 肿瘤，NGS 检测并没有带来额外的益处。TST26 面板要么错过了，要么不准确地报告了 KIT 外显子 11 中的复杂插入/缺失变体，而非 NGS 方法则准确地识别了这些变体。本研究的结果表明，癌症部位和变体类型对 NGS 检测信息收益有不同的影响。
