The Validation and Clinical Implementation of BRCAplus: A Comprehensive High-Risk Breast Cancer Diagnostic Assay
The Validation and Clinical Implementation of BRCAplus: A Comprehensive High-Risk Breast Cancer Diagnostic Assay
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DOI：
10.1371/journal.pone.0097408
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发表时间：
2014-05-15
期刊：
影响因子：
3.7
通讯作者：
Elliott, Aaron M.
中科院分区：
文献类型：
--
作者：
Chong, Hansook Kim;Wang, Tao;Elliott, Aaron M.
乳腺癌是女性中最常见的癌症，10%的疾病归因于遗传因素。尽管BRCA1和BRCA2在遗传性病例中占很高的比例，但有超过25种易感基因对乳腺癌的风险有不同的影响。传统上，乳腺癌的种系检测是通过从BRCA1和BRCA2开始的Sanger双脱氧终止子测序以反射方式进行的。新一代测序（NGS）的引入使得能够同时检测与乳腺癌有关的所有基因，从而使诊断实验室提供大型、全面的基因面板。然而，一些医生倾向于只检测那些已建立监测和治疗方案的基因。基于NGS的BRCAplus检测利用基于定制平片PCR的靶富集设计和生物信息学管道，结合阵列比较基因组杂交（aCGH）来识别6个高危基因的突变：BRCA1、BRCA2、PTEN、TP53、CDH1和STK11。用250个先前表征的样品验证该方法，结果100%检测出3025个已知变异，分析特异性为99.99%。对前3000份用于检测的BRCAplus样本的临床表现分析显示，每个目标碱基对的平均覆盖率大于9000倍，从而具有出色的特异性和检测低水平嵌合和等位基因缺失的灵敏度。该检测的独特设计能够检测到以前检测所遗漏的致病性突变。随着大量NGS诊断测试的发布，临床医生了解不同测试设计的优点和局限性至关重要。
Breast cancer is the most commonly diagnosed cancer in women, with 10% of disease attributed to hereditary factors. Although BRCA1 and BRCA2 account for a high percentage of hereditary cases, there are more than 25 susceptibility genes that differentially impact the risk for breast cancer. Traditionally, germline testing for breast cancer was performed by Sanger dideoxy terminator sequencing in a reflexive manner, beginning with BRCA1 and BRCA2. The introduction of next-generation sequencing (NGS) has enabled the simultaneous testing of all genes implicated in breast cancer resulting in diagnostic labs offering large, comprehensive gene panels. However, some physicians prefer to only test for those genes in which established surveillance and treatment protocol exists. The NGS based BRCAplus test utilizes a custom tiled PCR based target enrichment design and bioinformatics pipeline coupled with array comparative genomic hybridization (aCGH) to identify mutations in the six high-risk genes: BRCA1, BRCA2, PTEN, TP53, CDH1, and STK11. Validation of the assay with 250 previously characterized samples resulted in 100% detection of 3,025 known variants and analytical specificity of 99.99%. Analysis of the clinical performance of the first 3,000 BRCAplus samples referred for testing revealed an average coverage greater than 9,000X per target base pair resulting in excellent specificity and the sensitivity to detect low level mosaicism and allele-drop out. The unique design of the assay enabled the detection of pathogenic mutations missed by previous testing. With the abundance of NGS diagnostic tests being released, it is essential that clinicians understand the advantages and limitations of different test designs.