| Title | Performance validation of an amplicon-based targeted next-generation sequencing assay and mutation profiling of 648 Chinese colorectal cancer patients |
| Authors | Wang, Yajian Liu, Haijing Hou, Yingyong Zhou, Xiaoyan Liang, Li Zhang, Zhihong Shi, Huaiyin Xu, Sanpeng Hu, Peizhen Zheng, Zuyu Liu, Rui Tang, Tingdong Ye, Feng Liang, Zhiyong Bu, Hong |
| Affiliation | Sichuan Univ, West China Hosp, Dept Pathol, Chengdu 610041, Sichuan, Peoples R China. Sichuan Univ, West China Hosp, Pathol Lab, Chengdu 610041, Sichuan, Peoples R China. Peking Univ Third Hosp, Dept Pathol, Beijing 100000, Peoples R China. Fudan Univ, Zhongshan Hosp, Dept Pathol, Shanghai 200032, Peoples R China. Fudan Univ, Dept Pathol, Shanghai Canc Ctr, Shanghai 200032, Peoples R China. Southern Med Univ, Huayin Lab, Guangzhou 510515, Guangdong, Peoples R China. Nanjing Med Univ, Affiliated Hosp 1, Dept Pathol, Nanjing 210000, Jiangsu, Peoples R China. Chinese Peoples Liberat Army Gen Hosp, Dept Pathol, Beijing 100000, Peoples R China. Chinese PLA Med Sch, Beijing 100000, Peoples R China. Huazhong Univ Sci & Technol, Inst Pathol, Tongji Hosp, Tongji Med Coll, Wuhan 430030, Hubei, Peoples R China. Fourth Mil Med Univ, Xijing Hosp, Dept Pathol, Xian 710032, Shaanxi, Peoples R China. Singlera Genom Inc, Shanghai 201318, Peoples R China. Sichuan Univ, West China Hosp, Key Lab Transplant Engn & Immunol, Minist Hlth, Chengdu 610041, Sichuan, Peoples R China. Chinese Acad Med Sci, Dept Pathol, Peking Union Med Coll Hosp, Beijing 100730, Peoples R China. Peking Union Med Coll, Beijing 100730, Peoples R China. Sichuan Univ, West China Hosp, Pathol Lab, Chengdu 610041, Sichuan, Peoples R China. Ye, F (reprint author), Sichuan Univ, West China Hosp, Key Lab Transplant Engn & Immunol, Minist Hlth, Chengdu 610041, Sichuan, Peoples R China. |
| Keywords | Next-generation sequencing (NGS) Molecular test validation Colorectal cancer (CRC) Actionable variants GENE-MUTATIONS INTRATUMOR HETEROGENEITY MOLECULAR DIAGNOSTICS KRAS MUTATIONS BRAF DNA ADENOCARCINOMA ONCOLOGY SYSTEM NRAS |
| Issue Date | 2018 |
| Publisher | VIRCHOWS ARCHIV |
| Citation | VIRCHOWS ARCHIV. 2018, 472(6), 959-968. |
| Abstract | 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. |
| URI | http://hdl.handle.net/20.500.11897/513273 |
| ISSN | 0945-6317 |
| DOI | 10.1007/s00428-018-2359-4 |
| Indexed | SCI(E) PubMed |
| Appears in Collections: | 第三医院 |
