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

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™ 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) ≥ 5% when median read depth ≥ 500×. 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.

• Authors: Yajian Wang, Haijing Liu, Yingyong Hou, Xiaoyan Zhou, Li Liang, Zhihong Zhang, Huaiyin Shi, Sanpeng Xu, Peizhen Hu, Zuyu Zheng, Rui Liu, Tingdong Tang, Feng Ye, Zhiyong Liang, Hong Bu
• Journal: Virchows Archiv : an international journal of pathology (Virchows Arch) Vol. 472 Issue 6 Pg. 959-968 (Jun 2018) ISSN: 1432-2307 [Electronic] Germany
• PMID: 29705968 (Publication Type: Journal Article, Validation Study)

Chemical References

• ErbB Receptors

Topics

• Adult
• Aged
• Colonic Neoplasms (diagnosis, genetics)
• Colorectal Neoplasms (diagnosis, genetics)
• ErbB Receptors (genetics)
• Female
• High-Throughput Nucleotide Sequencing (methods)
• Humans
• Lung Neoplasms (genetics)
• Male
• Middle Aged
• Mutation (genetics)
• Young Adult