机构：[1]Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China四川大学华西医院[2]Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China四川大学华西医院[3]Department of Pathology, Peking University Third Hospital, Beijing 100000, China[4]Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, China[5]Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China[6]Huayin Laboratory, Southern Medical University, Guangzhou 510515, China[7]Department of Pathology, First Affiliated Hospital, Nanjing Medical University, Nanjing 210000, China江苏省人民医院[8]Department of Pathology, Chinese PLA General Hospital and Chinese PLA Medical School, Beijing 100000, China[9]Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China华中科技大学同济医学院附属同济医院[10]Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China[11]Singlera Genomics Inc., Shanghai 201318, China[12]Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu 610041, China四川大学华西医院[13]Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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<yen> 5% when median read depth ae<yen> 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.
基金：
This work was supported by the funding from the National Key
Research and Development Plan of Precision Medical research in China
(2016YFC0906000), National Natural Science Foundation of China
(81401990), and Key Research and Development Project of
Department of Science and Technology in Sichuan Province
(2017SZ0005).
第一作者机构：[1]Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China[2]Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
通讯作者：
通讯机构：[2]Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China[12]Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu 610041, China
推荐引用方式(GB/T 7714)：
Yajian Wang,Haijing Liu,Yingyong Hou,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.doi:10.1007/s00428-018-2359-4.
APA：
Yajian Wang,Haijing Liu,Yingyong Hou,Xiaoyan Zhou,Li Liang...&Hong Bu.(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)
MLA：
Yajian Wang,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
