Combined NGS tumor-based detection of germline Lynch syndrome mutations and prognostic classification of endometrial cancers

项目摘要 子宫内膜癌（EC）是美国最常见的妇科恶性肿瘤。大多数病例是散发的。 然而，4-5%患有EC的女性因为携带遗传性DNA错配修复而发病 (MMR)基因突变，因此，有林奇综合征（LS）。另外25%的EC已获得 缺陷DNA MMR，通常与MLH 1修复基因的表观遗传沉默相关。 在EC患者中识别LS为患者及其家人提供了预防癌症的机会 因此，建议在EC中进行基于肿瘤的LS筛查。认识 EC中的MMR缺陷和其他遗传异常在治疗计划中也很重要， 评估新疗法。 目前，LS筛查依赖于一系列的IHC和DNA测试，这些测试指导遗传咨询和检测， 生殖系突变然而，基于群体的生殖系突变测试是时间限制性的，因为 所有受试者都需要考前咨询，只有约1/20-1/25的受试者有LS， 其他癌症易感基因座的发现。我们建议发展稳健的、低成本的检测方法 使用可用于所有EC患者的肿瘤DNA来检测LS突变。我们的测试方法将确保 更多患有LS的EC患者及其患有LS突变的家庭成员可以从癌症加剧中受益 监视此外，所提出的肿瘤分析方法包括允许对肿瘤进行分类的测试。 分子EC亚型可以指导辅助治疗的选择。我们的实验设计是由 前所未有的生物标本资源与临床病理学数据相关联。我们的分析集中在使用 在CAP批准的实验室制备样本，为快速转化为临床检测铺平道路 发展 提出了三个具体的目标，使我们能够开发临床相关的肿瘤为基础的测试遗传 癌症易感性和分子分类分析，将为辅助治疗决策提供信息 进行进一步的翻译研究。 目的1：进一步开发基于肿瘤的生殖系LS突变、MSI和拷贝数检测的稳健方法。 号码变更 目的2：确定在所有新诊断的子宫内膜异位症患者中筛查Lynch综合征的有效性 癌症患者使用错配修复基因的前期下一代测序， 护理顺序测试。 目的3：确定临床适用的分子分类系统对预后的意义， 子宫内膜癌

PROJECT SUMMARY Endometrial cancer (EC) is the most common gynecologic malignancy in the US. Most cases are sporadic. However, 4-5% of women with EC develop their disease because they carry inherited DNA mismatch repair (MMR) gene mutations and, as such, have Lynch syndrome (LS). An additional 25% of ECs have acquired defective DNA MMR, typically associated with epigenetic silencing of the MLH1 repair gene. Identifying LS in EC patients provides opportunities for cancer prevention for the patient and her family members, and because of this, tumor-based screening for LS in EC has been recommended. Recognizing MMR deficiencies and other genetic abnormalities in ECs is also important in treatment planning and evaluation of new therapies. At present, LS screening relies on a series of IHC and DNA tests that guide genetic counseling and testing for germline mutations. Population-based germline mutation testing is, however, time-prohibitive because of the need for pre-test counseling for all subjects, with only ~1/20-1/25 having LS, and the potential for incidental findings for other cancer susceptibility loci. We propose development of robust, low-cost methods for detection of LS mutations using tumor DNAs that can be used for all EC patients. Our testing approach will ensure that more EC patients with LS, and their family members with LS mutations, can benefit from intensified cancer surveillance. Furthermore, the tumor analysis methods proposed include tests that allow for classification of molecular EC subtypes that can direct selection of adjuvant therapies. Our experimental design is powered by unprecedented biospecimen resources linked to clinicopathologic data. Our analyses are focused on use of specimens prepared in CAP-approved laboratories, paving the way for rapid translation to clinical test development. Three specific aims are proposed to allow us to develop clinically relevant tumor-based testing for inherited cancer susceptibility and profiling for molecular classifications that will inform adjuvant treatment decision making and further translational research. Aim 1: To further develop robust methods for tumor-based detection of germline LS mutations, MSI and copy number alterations. Aim 2: To determine the efficacy of screening for Lynch syndrome among all newly diagnosed endometrial cancer patients using upfront next-generation sequencing of mismatch repair genes as compared to standard of care sequential testing. Aim 3: To determine the prognostic significance of a clinically-applicable molecular classification system for endometrial cancers.