Detection of Gene Rearrangements in Targeted Clinical Next-Generation Sequencing
Detection of Gene Rearrangements in Targeted Clinical Next-Generation Sequencing
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DOI：
10.1016/j.jmoldx.2014.03.006
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发表时间：
2014-07-01
影响因子：
4.1
通讯作者：
Duncavage, Eric J.
中科院分区：
文献类型：
--
作者：
Abel, Haley J.;Al-Kateb, Hussam;Duncavage, Eric J.
在临床实验室中识别复发性基因重排是许多恶性肿瘤风险分层和治疗决策的基石。研究报告称，靶向的下一代测序检测有可能识别这种重排;然而，它们在临床实验室中的效用尚不清楚。我们在临床实验室通过下一代测序检查ALK和KMT 2A（MLL）重排检测的灵敏度和特异性。我们分析了一系列的7个ALK重排的癌症，6个KMT 2A重排的白血病，和77个ALK/KMT 2A重排阴性的癌症，以前通过荧光原位杂交（FISH）测试。重排检测使用公开可用的软件工具进行测试，包括Breakdancer、FasterFAST、CREST和Hydra。使用Breakdancer和Faster，我们在7例FISH阳性病例中检测到7例ALK重排，在6例FISH阳性病例中检测到6例KMT 2A重排。在77例ALK/KMT 2A FISH阴性病例中，Breakdancer或ClusterFAST均未做出假阳性鉴定。此外，我们还发现了一例ALK重排病例，其内含子16断裂点为非典型断裂点，这可能影响其对靶向抑制剂的反应。我们报告说，临床相关的染色体重排可以从靶向基因组为基础的下一代测序检测的灵敏度和特异性相当于FISH，同时提供更精细的规模信息和提高效率的分子肿瘤学检测。
The identification of recurrent gene rearrangements in the clinical Laboratory is the cornerstone for risk stratification and treatment decisions in many malignant tumors. Studies have reported that targeted next-generation sequencing assays have the potential to identify such rearrangements; however, their utility in the clinical laboratory is unknown. We examine the sensitivity and specificity of ALK and KMT2A (MLL) rearrangement detection by next-generation sequencing in the clinical laboratory. We analyzed a series of seven ALK rearranged cancers, six KMT2A rearranged Leukemias, and 77 ALK/KMT2A rearrangement-negative cancers, previously tested by fluorescence in situ hybridization (FISH). Rearrangement detection was tested using publicly available software tools, including Breakdancer, ClusterFAST, CREST, and Hydra. Using Breakdancer and ClusterFAST, we detected ALK rearrangements in seven of seven FISH-positive cases and KMT2A rearrangements in six of six FISH-positive cases. Among the 77 ALK/KMT2A FISH-negative cases, no false-positive identifications were made by Breakdancer or ClusterFAST. Further, we identified one ALK rearranged case with a noncanonical intron 16 breakpoint, which is Likely to affect its response to targeted inhibitors. We report that clinically relevant chromosomal rearrangements can be detected from targeted gene panel-based next-generation sequencing with sensitivity and specificity equivalent to that of FISH while providing finer-scale information and increased efficiency for molecular oncology testing.