Validation of copy number changes by MLPA as predictors of relapse in Wilms tumor

验证 MLPA 的拷贝数变化作为肾母细胞瘤复发的预测因素

基本信息

批准号：
8028602
负责人：
Elizabeth J Perlman
金额：
$ 19.18万
依托单位：
LURIE CHILDREN'S HOSPITAL OF CHICAGO
依托单位国家：
美国
项目类别：
财政年份：
2011
资助国家：
美国
起止时间：
2011-09-09 至 2013-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8028602
关键词：
15q 16q 17p 22q Biological Assay Biological Markers Child Childhood Children&apos s Oncology Group Chromosomal translocation Chromosomes Chromosomes, Human, Pair 1 Clinical Constitutional Cytogenetic Analysis DNA Data Future Gene Expression Genes Goals Histology Isochromosomes Laboratories Ligation Loss of Heterozygosity Malignant neoplasm of kidney Measures Methylation Microsatellite Repeats Mutation National Wilms&apos Tumor Study Group Nephroblastoma Outcome Patients Prevalence Protocols documentation Reagent Recurrence Relapse Relative Risks Reporting Resources Risk Sampling Staging Technology Testing Tissues Toxic effect Unbalanced Translocation Uniparental Isodisomies Validation adverse outcome arm chemotherapy chromosome 1q gain cohort comparative genomic hybridization cost design flexibility follow-up high risk imprint improved reagent testing research clinical testing transcriptomics tumor

项目摘要

DESCRIPTION (provided by applicant): Favorable Histology Wilms Tumor (FHWT) is the most common malignant renal tumor of childhood. Approximately 15% of FHWT relapse, and of these only 50% survive. Currently, loss of heterozygosity (LOH) for chromosomes 1p and 16q have been demonstrated and validated to be associated with poor outcome for patients with FHWT. Children registered on the current Children's Oncology Group (COG) protocols are now stratified for therapy according to their 1p and 16q LOH status. However, both 1p and 16q LOH is present in only 5% of FHWT, and predicts only 9% of relapses. Additional markers for relapse are needed. Recently, multiple studies using multiple different technologies have independently concluded that 1q gain (identified in approximately 25% of FHWT) is a much stronger predictor of relapse in FHWT than LOH of either 1p or 16q. Furthermore, in some patients these markers are inter-related due to the presence of unbalanced chromosomal translocations. Alterations to several other loci have also been identified in FHWT due to their association with relapse or acquisition following relapse (15q gain, 17p loss, and 22q loss). These changes have not been tested and validated in prospectively identified patients. This study seeks to develop and validate an inexpensive, robust clinical assay that may be utilized to stratify patients in the next COG protocol. Multiplex Ligation-dependent Probe Amplification (MLPA), was chosen due its simplicity, flexibility, sensitivity, amenability to multiplexing, applicability to archival tissues, and availability within clinical laboratories. Aims 1-3: To analyze 250 FHWT registered on NWTS-4 for 1q, 1p, 16q, 15q, 17p, and 22 copy number using MLPA. Samples previously analyzed for 1p and 16q LOH will be studied using a commercially available MLPA test that detects copy number of subtelomeric loci on each chromosomal arm (46 total targets). Chromosomal regions significantly associated with survival will be identified, and multiple probes will be designed for each chromosomal region identified and these will be multiplexed into a single clinical test. Aim 4: To validate the targeted multiplex MLPA test developed in Aims 1-3 on an independent set of 600 FHWT registered on NWTS-5. A case-cohort of 600 patients enriched for relapse has been developed from NWTS-5. The association between copy number of each locus and survival will be determined. Relevance: This study will result in a robust clinical test that requires fewer resources and will result in more information than is currently available. The currently performed microsatellite analysis for 1p and 16q LOH costs ~$50/test for reagents alone and requires both constitutional and tumor DNA. A targeted MLPA test will cost only $5/test, and will require only tumor DNA. The final MLPA test will analyze a minimum of three loci with multiple targets per locus and will be capable of measuring 100 targets. With a conservative projected relative risk of 2.0 and a prevalence of 25%, a minimum of 40% of relapses will be predicted. If so validated, the MLPA assay will be used to stratify therapy in the COG protocol that is anticipated to open in 2013. PUBLIC HEALTH RELEVANCE: This study will design a robust, inexpensive clinical test that will predict the overall clinical outcome of patients with Wilms tumor. The immediate clinical impact of the analysis of 1q gain in Wilms tumor is the potential to improve the survival of approximately 30 children per year in the US alone. More significant is the potential long-term opportunity to decrease the therapy (and toxicity) of larger subsets of Wilms tumor that lack these markers of relapse.

描述（由申请人提供）：良好的组织学肾母细胞瘤（FHWT）是儿童最常见的恶性肾肿瘤。大约 15% 的 FHWT 会复发，其中只有 50% 能够存活。目前，1p 和 16q 染色体杂合性缺失 (LOH) 已被证明和验证与 FHWT 患者的不良预后相关。在当前儿童肿瘤学组 (COG) 方案中注册的儿童现在根据其 1p 和 16q LOH 状态进行分层治疗。然而，1p 和 16q LOH 仅出现在 5% 的 FHWT 中，并且预测仅 9% 的复发。需要额外的复发标记。最近，使用多种不同技术的多项研究独立得出结论，1q 增益（在大约 25% 的 FHWT 中发现）比 1p 或 16q 的 LOH 更能预测 FHWT 的复发。此外，在一些患者中，由于不平衡染色体易位的存在，这些标记物是相互关联的。 FHWT 中还发现了其他几个位点的改变，因为它们与复发或复发后的获得性相关（15q 增益、17p 丢失和 22q 丢失）。这些变化尚未在前瞻性确定的患者中进行测试和验证。本研究旨在开发和验证一种廉价、稳健的临床检测方法，可用于在下一个 COG 方案中对患者进行分层。选择多重连接依赖性探针扩增 (MLPA) 是因为其简单性、灵活性、敏感性、多重性的适应性、对档案组织的适用性以及在临床实验室中的可用性。目标 1-3：使用 MLPA 分析 NWTS-4 上注册的 250 个 FHWT 的 1q、1p、16q、15q、17p 和 22 拷贝数。先前分析的 1p 和 16q LOH 样本将使用市售的 MLPA 测试进行研究，该测试可检测每个染色体臂上亚端粒基因座的拷贝数（总共 46 个目标）。将鉴定与存活显着相关的染色体区域，并且将为鉴定的每个染色体区域设计多个探针，并将这些探针多重化到单个临床测试中。目标 4：在 NWTS-5 上注册的一组独立的 600 个 FHWT 上验证目标 1-3 中开发的目标多重 MLPA 测试。 NWTS-5 已开发出一个包含 600 名复发患者的病例队列。将确定每个基因座的拷贝数与存活之间的关联。相关性：这项研究将产生一个强大的临床测试，需要更少的资源，并将产生比目前可用的更多信息。目前针对 1p 和 16q LOH 进行的微卫星分析，仅试剂/测试的成本约为 50 美元，并且需要宪法 DNA 和肿瘤 DNA。靶向 MLPA 测试每次测试仅需 5 美元，并且仅需要肿瘤 DNA。最终的 MLPA 测试将分析至少三个基因座，每个基因座有多个目标，并且能够测量 100 个目标。保守预测相对风险为 2.0，患病率为 25%，预计复发率至少为 40%。如果得到验证，MLPA 检测将用于 COG 方案中的治疗分层，该方案预计于 2013 年开放。公共健康相关性：本研究将设计一种稳健、廉价的临床测试，以预测肾母细胞瘤患者的总体临床结果。对肾母细胞瘤 1q 增益进行分析的直接临床影响是，仅在美国每年就有可能提高约 30 名儿童的生存率。更重要的是，潜在的长期机会可以减少缺乏这些复发标志物的较大肾母细胞瘤亚型的治疗（和毒性）。