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

• 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
• 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' 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' 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

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（由申请方提供）：组织学良好的肾母细胞瘤（FHWT）是儿童期最常见的恶性肾肿瘤。大约15%的FHWT复发，其中只有50%存活。目前，染色体1 p和16 q的杂合性丢失（洛）已被证明和验证与FHWT患者的不良结局相关。根据1 p和16 q洛缺失状态，对目前儿童肿瘤组（COG）方案中登记的儿童进行治疗分层。然而，1 p和16 q洛仅在5%的FHWT中存在，并且仅预测9%的复发。需要额外的复发标志物。最近，使用多种不同技术的多项研究得出了独立的结论，即1 q增益（在约25%的FHWT中确定）是FHWT复发的更强预测因子，而不是1 p或16 q的洛。此外，在一些患者中，由于存在不平衡的染色体易位，这些标记物是相互关联的。在FHWT中也发现了几个其他基因座的改变，这是由于它们与复发或复发后的获得相关（15 q增加、17 p丢失和22 q丢失）。这些变化尚未在前瞻性识别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、灵敏度、对多重的适应性、对存档组织的适用性以及在临床实验室内的可用性。目的1-3：使用MLPA分析NWTS-4上登记的250例FHWT的1 q、1 p、16 q、15 q、17 p和22拷贝数。将使用市售MLPA试验研究先前分析的1 p和16 q洛样本，该试验检测每个染色体臂上亚端粒位点的拷贝数（共46个靶标）。将鉴定与存活率显著相关的染色体区域，并将为鉴定的每个染色体区域设计多个探针，这些探针将被多重纳入单一临床试验。目的4：在NWTS-5上注册的一组独立的600只FHWT上验证目的1-3中开发的靶向多重MLPA检测。从NWTS-5中开发了一个600例复发患者的病例队列。将确定每个基因座的拷贝数与存活率之间的关联。相关性：这项研究将产生一个强大的临床试验，需要更少的资源，并将产生比目前更多的信息。目前进行的1 p和16 q洛缺失的微卫星分析仅试剂成本约为50美元/次，并且需要体质和肿瘤DNA。一个有针对性的MLPA测试将只花费5美元/测试，将只需要肿瘤DNA。最终的MLPA测试将分析至少三个位点，每个位点有多个靶标，并且能够测量100个靶标。保守预测的相对危险度为2.0，患病率为25%，预测复发率至少为40%。如果经过验证，MLPA检测试剂盒将用于对COG方案中的治疗进行分层，该方案预计将于2013年开放。 公共卫生关系：这项研究将设计一个强大的，廉价的临床试验，将预测肾母细胞瘤患者的整体临床结果。在Wilms肿瘤中分析1 q增加的直接临床影响是仅在美国每年就有可能提高大约30名儿童的生存率。更重要的是，对于缺乏这些复发标志物的较大Wilms肿瘤子集，潜在的长期机会可以减少治疗（和毒性）。