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A newly developed capture-based sequencing panel for genomic assay of lung cancer.
Genes & Genomics ( IF 2.1 ) Pub Date : 2020-05-24 , DOI: 10.1007/s13258-020-00949-1
Sun-Wha Im 1 , Jeesoo Chae 2 , Se Song Jang 2 , Jaeyong Choi 2 , Jihui Yun 2 , Soojin Cha 1, 3 , Nak-Jung Kwon 4 , Yoon Kyung Jeon 5, 6 , Yoohwa Hwang 7, 8 , Miso Kim 6, 9 , Tae Min Kim 6, 9 , Dong-Wan Kim 6, 9 , Jong-Il Kim 1, 2, 6 , Young Tae Kim 1, 6, 7
Affiliation  

BACKGROUND The increase in genetic alterations targeted by specific chemotherapy in lung cancer has led to the need for universal use of more comprehensive genetic testing, which has highlighted the development of a lung cancer diagnostic panel using next-generation sequencing. OBJECTIVE We developed a hybridization capture-based massively parallel sequencing assay named Friendly, Integrated, Research-based, Smart and Trustworthy (FIRST)-lung cancer panel (LCP), and evaluated its performance. METHODS FIRST-LCP comprises 64 lung cancer-related genes to test for various kinds of genetic alterations including single nucleotide variations (SNVs), insertions and deletions (indels), copy number variations (CNVs), and structural variations. To assess the performance of FIRST-LCP, we compiled test sets using HapMap samples or tumor cell lines with disclosed genetic information, and also tested our clinical lung cancer samples whose genetic alterations were known by conventional methods. RESULTS FIRST-LCP accomplished high sensitivity (99.4%) and specificity (100%) of the detection of SNVs. High precision was also achieved, with intra- or inter-run concordance rate of 0.99, respectively. FIRST-LCP detected indels and CNVs close to the expected allele frequency and magnitude, respectively. Tests with samples from lung cancer patients also identified all SNVs, indels and fusions. CONCLUSION Based on the current state of the art, continuous application of the panel design and analysis pipeline following up-to-date knowledge could ensure precision medicine for lung cancer patients.

中文翻译:

一种新开发的基于捕获的测序组,用于肺癌的基因组测定。

背景技术肺癌中通过特异性化学疗法靶向的基因改变的增加导致需要普遍使用更全面的基因测试,这突出了使用下一代测序的肺癌诊断小组的发展。目的我们开发了一种基于杂交捕获的大规模平行测序测定法,称为友好,整合,基于研究,智能和可信赖(FIRST)的肺癌小组(LCP),并对其性能进行了评估。方法FIRST-LCP包含64个与肺癌相关的基因,以测试各种遗传改变,包括单核苷酸变异(SNV),插入和缺失(indels),拷贝数变异(CNV)和结构变异。为了评估FIRST-LCP的性能,我们使用已公开的遗传信息的HapMap样本或肿瘤细胞系编制了测试集,还测试了我们的临床肺癌样本,这些样本的遗传变异已通过传统方法得知。结果FIRST-LCP实现了SNV检测的高灵敏度(99.4%)和特异性(100%)。还实现了高精度,运行内或运行间一致性比率分别为0.99。FIRST-LCP检测到的插入缺失和CNV分别接近预期的等位基因频率和大小。对来自肺癌患者的样本进行的测试还确定了所有SNV,插入缺失和融合。结论基于当前的最新技术,根据最新知识不断应用面板设计和分析流程可以确保为肺癌患者提供精准的医疗服务。并测试了我们的临床肺癌样本,这些样本的遗传变异已通过常规方法得知。结果FIRST-LCP实现了SNV检测的高灵敏度(99.4%)和特异性(100%)。还实现了高精度,运行内或运行间一致性比率分别为0.99。FIRST-LCP检测到的插入缺失和CNV分别接近预期的等位基因频率和大小。对来自肺癌患者的样本进行的测试还确定了所有SNV,插入缺失和融合。结论基于当前的最新技术,根据最新知识不断应用面板设计和分析流程可以确保为肺癌患者提供精准的医疗服务。并测试了我们的临床肺癌样本,这些样本的遗传变异已通过常规方法得知。结果FIRST-LCP实现了SNV检测的高灵敏度(99.4%)和特异性(100%)。还实现了高精度,运行内或运行间一致性比率分别为0.99。FIRST-LCP检测到的插入缺失和CNV分别接近预期的等位基因频率和大小。对来自肺癌患者的样本进行的测试还确定了所有SNV,插入缺失和融合。结论基于当前的最新技术,根据最新知识不断应用面板设计和分析流程可以确保为肺癌患者提供精准的医疗服务。SNV的检测率为4%)和特异性(100%)。还实现了高精度,运行内或运行间一致性比率分别为0.99。FIRST-LCP检测到的插入缺失和CNV分别接近预期的等位基因频率和大小。对来自肺癌患者的样本进行的测试还确定了所有SNV,插入缺失和融合。结论基于当前的最新技术,根据最新知识不断应用面板设计和分析流程可确保为肺癌患者提供精准的医疗服务。SNV的检测率为4%)和特异性(100%)。还实现了高精度,运行内或运行间一致性比率分别为0.99。FIRST-LCP检测到的插入缺失和CNV分别接近预期的等位基因频率和大小。对来自肺癌患者的样本进行的测试还确定了所有SNV,插入缺失和融合。结论基于当前的最新技术,根据最新知识不断应用面板设计和分析流程可以确保为肺癌患者提供精准的医疗服务。对来自肺癌患者的样本进行的测试还确定了所有SNV,插入缺失和融合。结论基于当前的最新技术,根据最新知识不断应用面板设计和分析流程可确保为肺癌患者提供精准的医疗服务。对来自肺癌患者的样本进行的测试还确定了所有SNV,插入缺失和融合。结论基于当前的最新技术,根据最新知识不断应用面板设计和分析流程可以确保为肺癌患者提供精准的医疗服务。
更新日期:2020-05-24
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