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(申请人提供)：良性组织学肾母细胞瘤(FHWT)是儿童最常见的肾脏恶性肿瘤。大约15%的FHWT复发，其中只有50%存活。目前，染色体1p和16q的杂合性缺失(LOH)已被证实与FHWT患者的不良预后有关。在当前儿童肿瘤学小组(COG)方案中注册的儿童现在根据他们的1P和16Q杂合性缺失状态进行分层治疗。然而，1P和16Q杂合性缺失只存在于5%的FHWT中，并且只预测了9%的复发率。需要额外的复发标记物。最近，使用多种不同技术的多项研究独立地得出结论，1Q增加(在大约25%的FHWT中发现)是FHWT复发的更强的预测因子，而1P或16Q的LOH要强得多。此外，在一些患者中，由于存在不平衡的染色体易位，这些标记是相互关联的。在FHWT中也发现了其他几个基因座的改变，因为它们与复发或复发后的获得性相关(15q增加，17p丢失，22q丢失)。这些变化还没有在预期确定的患者中进行测试和验证。这项研究试图开发和验证一种廉价、可靠的临床检测方法，可用于在下一次COG方案中对患者进行分层。多重连接依赖的探针扩增(MLPA)，由于其简单、灵活、灵敏、对多重的适应性、对档案组织的适用性以及在临床实验室中的可用性而被选择。目标1-3：用MLPA分析NWTS-4上注册的250个FHWT的1q、1p、16q、15q、17p和22个拷贝数。之前分析的1P和16Q杂合性缺失的样本将使用商业上可用的MLPA测试进行研究，该测试检测每条染色体臂(总共46个靶点)上亚端粒基因座的拷贝数。将确定与生存显著相关的染色体区域，并将为每个已确定的染色体区域设计多个探针，这些探针将被多路传输到单个临床测试中。目的4：在NWTS-5注册的600个FHWT的独立集合上验证AIMS 1-3中开发的靶向多重MLPA测试。根据NWTS-5建立了一个由600名患者组成的病例队列，这些患者因复发而变得更加丰富。将确定每个基因座的拷贝数与存活率之间的关联。相关性：这项研究将导致一项强大的临床测试，它需要更少的资源，并将产生比目前可用的更多的信息。目前进行的1P和16Q杂合性缺失的微卫星分析仅试剂一项的成本约为50美元，并且需要组成DNA和肿瘤DNA。靶向MLPA测试每项测试只需5美元，而且只需要肿瘤DNA。最终的MLPA测试将分析至少三个轨迹，每个轨迹有多个目标，并将能够测量100个目标。保守预测的相对风险为2.0，流行率为25%，预计至少有40%的复发率。如果得到证实，MLPA检测将用于COG方案中的分层治疗，该方案预计将于2013年开始实施。 公共卫生相关性：这项研究将设计一种强大、廉价的临床测试，以预测肾母细胞瘤患者的总体临床结果。分析Wilms肿瘤的1Q增益的直接临床影响是，仅在美国就有可能提高每年约30名儿童的存活率。更重要的是，缺乏这些复发标志物的Wilms肿瘤较大亚群的潜在长期机会减少了治疗(和毒性)。