High-throughput oncogene mutation detection in human cancer

描述（由申请人提供）：“癌症代表一种基因组疾病；每个肿瘤都有一组不同的突变，这些突变激活致癌基因，使肿瘤抑制基因失活。在靶向治疗的时代，预计癌症的治疗决定将越来越多地基于肿瘤的基因组成，而不是起源组织。然而，大多数检测癌症基因突变的分子诊断都是昂贵的，仅针对单个基因位点提供信息，并且受到降解或间质混合基因组DNA的不利影响。因此，尽管体细胞癌遗传学前景光明，但目前仍无法大规模识别关键的致癌基因突变，并且无法以符合常规临床应用的方式进行识别。为了解决这些限制，本应用旨在采用高通量、基于质谱的基因分型技术来检测大量癌症基因中的体细胞突变。”在R21阶段，将开发一个基于SequenomTM iPLEX基因分型的平台，该平台将询问50个癌基因和选定肿瘤基因中的600多个点突变（或小插入/缺失）。该平台还将优化用于石蜡包埋肿瘤组织基因组DNA的癌症基因突变检测。在R33阶段，测试这种突变检测方法的可行性将在一个大而多样的肿瘤收集的研究中得到证明。在这里，高通量癌基因突变检测将在近2700个冷冻和石蜡包埋的肿瘤中进行，这些肿瘤跨越许多谱系，包括一些之前没有经历过基因组表征的肿瘤。在临床肿瘤样本中进行高通量突变检测的能力将使分子流行病学和转化肿瘤学的分子分析成为可能，包括靶向癌症治疗试验的患者分层。因此，这些研究提供了巨大的潜力，使研究人员和患者都能在合理的癌症治疗道路上受益。

DESCRIPTION (provided by applicant): ' Cancer represents a disease of the genome; each tumor harbors a distinct set of mutations that activate oncogenes and inactivate tumor suppressor genes. In the era of targeted therapeutics, it is expected that cancer treatment decisions will increasingly be made based on tumor genetic composition as opposed to tissue of origin. However, most molecular diagnostics that detect cancer gene mutations are expensive, informative for only a single genetic locus, and adversely affected by degraded or stromally admixed genomic DNA. Thus, despite the promise of somatic cancer genetics, at the present time it remains impractical to identify critical oncogene mutations on a large scale and in a manner compatible with routine clinical use. To address these limitations, this application aims to adapt a high-throughput, mass spectrometry- based genotyping technology to detect somatic mutations in a large panel of cancer genes.' In the R21 phase, a platform based on SequenomTM iPLEX genotyping will be developed that interrogates over 600 point mutations (or small insertions/deletions) across 50 oncogenes and selected tumor genes. This platform will also be optimized for cancer gene mutation detection in genomic DNA from paraffin-embedded tumor tissue. In the R33 phase, test the feasibility of this mutation detection approach will be demonstrated in a study of a large and diverse tumor collection. Here, high-throughput oncogene mutation detection will be performed on nearly 2,700 frozen and paraffin-embedded tumors spanning many lineages, including several that have not undergone prior genomic characterization. The ability to perform high-throughput mutation detection in clinical tumor samples will enable unprecedented molecular analyses applicable to molecular epidemiology and translational oncology, including patient stratification for targeted cancer therapeutic trials. These studies therefore offer immense potential to benefit investigators and patients alike on the path to rational cancer therapeutics.