Background Understanding the genetic basis of cancer risk is a major international endeavor. The emergence of next-generation sequencing (NGS) in late 2000’s has further accelerated the discovery of many cancer susceptibility genes. The use of targeted NGS-based multigene testing panels to provide comprehensive analysis of cancer susceptible genes has proven to be a viable option, with the accurate and robust detection of a wide range of clinically relevant variants in the targeted genes being crucial. Methods We have developed and validated a targeted NGS-based test for hereditary cancer risk assessment using Illumina’s NGS platform by analyzing the protein-coding regions of 35 hereditary cancer genes with a bioinformatics pipeline that utilizes standard practices in the field. This 35-gene hereditary cancer panel is designed to identify germline cancer-causing mutations for 8 different cancers: breast, ovarian, prostate, uterine, colorectal, pancreatic, stomach cancers and melanoma. The panel was validated using well-characterized DNA specimens [NIGMS Human Genetic Cell Repository], where DNA had been extracted using blood of individuals whose genetic variants had been previously characterized by the 1000 Genome Project and the Coriell Catalog. Results The 35-gene hereditary cancer panel shows high sensitivity (99.9%) and specificity (100%) across 4820 variants including single nucleotide variants (SNVs) and small insertions and deletions (indel; up to 25 bp). The reproducibility and repeatability are 99.8 and 100%, respectively. Conclusions The use of targeted NGS-based multigene testing panels to provide comprehensive analysis of cancer susceptible genes has been considered a viable option. In the present study, we developed and validated a 35-gene panel for testing 8 common cancers using next-generation sequencing (NGS). The performance of our hereditary cancer panel is assessed across a board range of variants in the 35 genes to support clinical use.

中文翻译：

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基于下一代测序的 35 基因遗传性癌症 panel 的开发和验证

背景 了解癌症风险的遗传基础是一项重大的国际努力。2000 年代后期新一代测序 (NGS) 的出现进一步加速了许多癌症易感基因的发现。使用基于 NGS 的靶向多基因检测组对癌症易感基因进行全面分析已被证明是一种可行的选择，准确和稳健地检测靶向基因中广泛的临床相关变异至关重要。方法 我们使用 Illumina 的 NGS 平台开发并验证了一种针对遗传性癌症风险评估的基于 NGS 的测试，方法是通过利用该领域标准实践的生物信息学管道分析 35 个遗传性癌症基因的蛋白质编码区域。这个 35 个基因的遗传性癌症小组旨在识别 8 种不同癌症的种系致癌突变：乳腺癌、卵巢癌、前列腺癌、子宫癌、结直肠癌、胰腺癌、胃癌和黑色素瘤。该小组使用充分表征的 DNA 样本 [NIGMS 人类遗传细胞库] 进行了验证，其中 DNA 是使用先前已通过 1000 基因组计划和科里尔目录表征的遗传变异的个体的血液提取的。结果 35 个基因的遗传性癌症 panel 在 4820 个变体中显示出高灵敏度 (99.9%) 和特异性 (100%)，包括单核苷酸变体 (SNV) 和小的插入和缺失（插入缺失；高达 25 bp）。再现性和重复性分别为 99.8% 和 100%。结论 使用基于 NGS 的靶向多基因检测组对癌症易感基因进行综合分析已被认为是一种可行的选择。在本研究中，我们开发并验证了一个包含 35 个基因的面板，用于使用下一代测序 (NGS) 测试 8 种常见癌症。我们的遗传性癌症小组的表现在 35 个基因的一系列变体中进行了评估，以支持临床使用。