The aim of this study was to assess the frequency of potentially actionable genomic alterations in breast cancer that could be targeted with approved agents or investigational drugs in clinical trials using a next-generation sequencing-based genomic profiling assay performed in a Clinical Laboratory Improvement Amendments-certified and College of American Pathologists-accredited commercial laboratory. Methods. Fifty-one breast cancers were analyzed, including primary tumor biopsies of 33 stage I-II and 18 stage IV cancers (13 soft tissue, 3 liver, and 2 bone metastases). We assessed 3,230 exons in 182 cancer-related genes and 37 introns in 14 genes often rearranged in cancer for base substitutions, indels, copy number alterations, and gene fusions. The average median sequencing depth was 1,154×. Results. We observed 158 genomic alterations in 55 genes in 48 of 51 (94%) tumors (mean 3.1, range 0-9). The average number of potentially therapeutically relevant alterations was similar in primary (1.6, range 0-4) and in heavily pretreated metastatic cancers (2.0, range 0-4) (p = .24). The most common actionable alterations were in PIK3CA (n = 9, phosphatidylinositol 3-kinase [PI3K]/mammalian target of rapamycin [mTOR] inhibitors), NF1 (n = 7, PI3K/mTOR/mitogen-activated protein kinase inhibitors), v-akt murine thymoma viral oncogene homolog 1-3 (n = 7, PI3K/mTOR/AKT inhibitors), BRCA1/2 (n = 6, poly[ADP-ribose] polymerase inhibitors), and CCND1,2 and CCNE (n = 8)/cycline dependent kinase (CDK)6 (n = 1) (CDK4/6 inhibitors), KIT (n = 1, imatinib/sunitinib), ALK (n = 1, crizotinib), FGFR1,2 (n = 5, fibroblast growth factor receptor inhibitors), and EGFR (n = 2, epidermal growth factor receptor inhibitors). Our sequencing assay also correctly identified all six cases with HER2 (ERBB2) amplification by fluorescence in situ hybridization when tumor content was adequate. In addition, two known activating HER2 mutations were identified, both in unamplified cases. Conclusion. Overall, 84% of cancers harbored at least one genomic alteration linked to potential treatment options. Systematic evaluation of the predictive value of these genomic alterations is critically important for further progress in this field.
摘要
背景 本研究的目的是，在获得临床实验室改进修正案认证及美国病理学家学会认可的商业实验室中，使用一种新一代测序型基因组分析技术对乳腺癌进行测序分析，以确定癌灶内那些可作为已批准药物或临床试验性药物治疗靶标的基因组突变的发生频率。
方法 我们共分析了 51 例癌灶，包括 33 例 I-II 期原发性肿瘤活检组织和 18 例 IV 期癌灶活检组织（13 例为软组织灶，3 例为肝脏病灶，2 例为骨转移灶）。我们对 182 个癌症相关基因的 3230 个外显子和 14 个在癌症中常发生重排之基因的 37 个内含子进行了测序，以查找其中的碱基替代、插入缺失、拷贝数突变和基因融合。平均中位测序深度为 1154×。
结果 我们在 51 个瘤灶的 48 个 (94%) 内的 55 个基因中发现了 158 个基因组突变（平均 3.1，范围为 0-9）。原发性癌灶和进行过多重预先治疗的转移癌灶中可作为潜在治疗靶标的平均突变数大体相似（前者为 1.6，范围为 0-4；后者为 2.0，范围为 0-4）(p = 0.24)。最常见的可靶定突变为 PIK3CA （n =9，磷脂酰肌醇 3-激酶 [PI3K]/雷帕霉素的哺乳类动物靶标 [mTOR] 抑制剂）、NF1 （n =7，PI3K/mTOR/丝裂原活化蛋白激酶抑制剂）、v-akt 鼠科胸腺瘤病毒致癌基因同源体 1-3（n =7，PI3K/mTOR/AKT 抑制剂）、 BRCA1/2 （n =6，聚[ADP-核糖]聚合酶抑制剂）、CCND 1,2 和 CCNE (n =8)/细胞周期素依赖性抑制剂 (CDK)6 (n = 1)（CDK4/6 抑制剂）、KIT （n =1，伊马替尼/舒尼替尼）、ALK （n =1，克唑替尼）、FGFR1,2 （n =5，成纤维细胞生长因子受体抑制剂）以及 EGFR （n =2，表皮生长因子受体抑制剂）。在肿瘤量充足的情况下，我们的测序分析还通过荧光原位杂交法，准确地鉴定出了所有六例 HER2 (ERBB2) 扩增突变。此外，我们还检测出了两例已知的活化 HER2 突变，均出现在非扩增病例中。
结论 总体而言，84% 的癌症存在至少一种可作为潜在治疗靶标的基因组突变。对这些基因组突变的预测价值进行系统性评估，对推动这一领域的进步具有重要意义。The Oncologist 2014;19:453–458
Keywords: Molecularly targeted therapy; Next-generation sequencing; Precision medicine; Predictive markers.