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28.04.2018 | Original Article | Ausgabe 6/2018

Virchows Archiv 6/2018

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

Zeitschrift:
Virchows Archiv > Ausgabe 6/2018
Autoren:
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
Wichtige Hinweise

Electronic supplementary material

The online version of this article (https://​doi.​org/​10.​1007/​s00428-018-2359-4) contains supplementary material, which is available to authorized users.

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.

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Zusatzmaterial
Fig. S1 (PDF 6 kb)
428_2018_2359_MOESM1_ESM.pdf
ESM 1 (PDF 970 kb)
428_2018_2359_MOESM2_ESM.pdf
ESM 2 (XLSX 386 kb)
428_2018_2359_MOESM3_ESM.xlsx
Literatur
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