Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement in Clinical Cancer Specimens
Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement in Clinical Cancer Specimens
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DOI：
10.1016/j.jmoldx.2013.08.004
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发表时间：
2014-01-01
影响因子：
4.1
通讯作者：
Walsh, Tom
中科院分区：
文献类型：
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作者：
Pritchard, Colin C.;Salipante, Stephen J.;Walsh, Tom
近年来，针对特定基因突变的抗癌疗法得到了发展和实施，但以综合方式测定临床癌症标本中关键突变的方法仍不发达。我们已经开发了UW-Oncotoxin，这是一种临床分子诊断检测方法，可基于> 500 x平均覆盖率为194个临床相关基因中的所有类型的突变提供同步深度测序信息。为了验证UW-Oncoblastin，我们测试了来自10种不同癌症类型的98个先前表征的临床肿瘤标本，包括41个福尔马林固定的石蜡包埋组织样本。混合研究表明在具有>10%肿瘤细胞的样品中可靠的突变检测。在肿瘤细胞>= 10%的临床样本中，UW-Oncocaine正确识别了130个已知突变中的129个[灵敏度99.2%，（95% CI，95.8%-99.9%）]，包括单核苷酸变异、小插入和缺失、内部串联重复、基因拷贝数增加和扩增、基因拷贝丢失、染色体增加和丢失以及可操作的基因组重排，在相同的样品中，该测定还鉴定了先前未分析的基因中的可操作的点突变，以及黑素瘤中MLL和GRIK 4的新基因重排，以及急性髓性白血病中ASXL 1、PIK 3R 1和SGCZ的新基因重排。为了更好地指导现有和新兴的治疗方案，并促进基因组检测与患者护理的整合，我们开发了一个数据分析、决策支持和报告临床可行结果的框架。
Recent years have seen development and implementation of anticancer therapies targeted to particular gene mutations, but methods to assay clinical cancer specimens in a comprehensive way for the critical mutations remain underdeveloped. We have developed UW-OncoPlex, a clinical molecular diagnostic assay to provide simultaneous deep-sequencing information, based on >500x average coverage, for all classes of mutations in 194 clinically relevant genes. To validate UW-OncoPlex, we tested 98 previously characterized clinical tumor specimens from 10 different cancer types, including 41 formalin-fixed paraffin-embedded tissue samples. Mixing studies indicated reliable mutation detection in samples with >10% tumor cells. In clinical samples with >= 10% tumor cells, UW-OncoPlex correctly identified 129 of 130 known mutations [sensitivity 99.2%, (95% CI, 95.8%-99.9%)], including single nucleotide variants, small insertions and deletions, internal tandem duplications, gene copy number gains and amplifications, gene copy losses, chromosomal gains and losses, and actionable genomic rearrangements, including ALK-EML4, ROS1, PML-RARA, and BCR-ABL. In the same samples, the assay also identified actionable point mutations in genes not previously analyzed and novel gene rearrangements of MLL and GRIK4 in melanoma, and of ASXL1, PIK3R1, and SGCZ in acute myeloid Leukemia. To best guide existing and emerging treatment regimens and facilitate integration of genomic testing with patient care, we developed a framework for data analysis, decision support, and reporting clinically actionable results.