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Performance validation of an amplicon-based targeted next-generation sequencing assay and mutation profiling of 648 Chinese colorectal cancer patients 期刊论文

编号：

c708df4d-4a08-47de-b087-5160b50aba26
作者：

Wang, Yajian^[1,2];Liu, Haijing^[3];Hou, Yingyong(侯英勇)^[4]Zhou, Xiaoyan(周晓燕)^[5]Liang, Li^[6];Zhang, Zhihong^[7];Shi, Huaiyin^[8,9];Xu, Sanpeng^[10];Hu, Peizhen^[11];Zheng, Zuyu^[12];Liu, Rui^[12];Tang, Tingdong^[12];Ye, Feng^[2,13];Liang, Zhiyong^[14,15];Bu, Hong^[1,2,13];
语种：

English
期刊：

VIRCHOWS ARCHIV ISSN：0945-6317 2018 年 472 卷 6 期 (959 - 968) ; JUN
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关键词：

Next-generation sequencing (NGS) Molecular test validation Colorectal cancer (CRC) Actionable variants
摘要：

Next-generation sequencing (NGS) has become a promising approach for tumor somatic mutation detection. However, stringent validation is required for its application on clinical specimens, especially for low-quality formalin-fixed paraffin-embedded (FFPE) tissues. Here, we validated the performance of an amplicon-based targeted NGS assay, OncoAim (TM) DNA panel, on both commercial reference FFPE samples and clinical FFPE samples of Chinese colorectal cancer (CRC) patients. Then we profiled the mutation spectrum of 648 Chinese CRC patients in a multicenter study to explore its clinical utility. This NGS assay achieved 100% test specificity and 95-100% test sensitivity for variants with mutant allele frequency (MAF) ae 5% when median read depth ae 500x. The orthogonal methods including amplification refractory mutation system (ARMS)-PCR and Sanger sequencing validated that NGS generated three false negatives (FNs) but no false positives (FPs) among 516 clinical samples for KRAS aberration detection. Genomic profiling of Chinese CRC patients with this assay revealed that 63.3% of the tumors harbored clinically actionable alterations. Besides the commonly mutated genes including TP53 (52.82%), KRAS (46.68%), APC (24.09%), PIK3CA (18.94%), SMAD4 (9.47%), BRAF (6.15%), FBXW7 (5.32%), and NRAS (4.15%), other less frequently mutated genes were also identified. Statistically significant association of specific mutated genes with certain clinicopathological features was detected, e.g., both BRAF and PIK3CA were more prevalent in right-side CRC (p < 0.001 and p = 0.002, respectively). We concluded this targeted NGS assay is qualified for clinical practice, and our findings could help the diagnosis and prognosis of Chinese CRC patients.
推荐引用方式
GB/T 7714：

Wang Yajian,Liu Haijing,Hou Yingyong, et al. Performance validation of an amplicon-based targeted next-generation sequencing assay and mutation profiling of 648 Chinese colorectal cancer patients [J].VIRCHOWS ARCHIV,2018,472(6):959-968.
APA：

Wang Yajian,Liu Haijing,Hou Yingyong,Zhou Xiaoyan,&Bu Hong.(2018).Performance validation of an amplicon-based targeted next-generation sequencing assay and mutation profiling of 648 Chinese colorectal cancer patients .VIRCHOWS ARCHIV,472(6):959-968.
MLA：

Wang Yajian, et al. "Performance validation of an amplicon-based targeted next-generation sequencing assay and mutation profiling of 648 Chinese colorectal cancer patients" .VIRCHOWS ARCHIV 472,6(2018):959-968.

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