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（由申请人提供）：有利的组织学Wilms肿瘤（FHWT）是最常见的儿童恶性肾肿瘤。大约15％的FHWT复发，其中只有50％的生存。目前，已证明并验证了染色体1p和16Q的杂合性损失（LOH）与FHWT患者的预后不良有关。现在，根据当前儿童肿瘤学组（COG）方案注册的儿童现在根据其1P和16Q LOH身份进行治疗。但是，只有5％的FHWT中存在1P和16Q LOH，仅预测9％的复发。需要其他复发标记。最近，使用多种不同技术的多项研究已独立地得出结论，比1p或16q的LOH比LOH相比，FHWT中的1Q增益（在FHWT的大约25％中鉴定）是更强的预测指标。此外，在某些患者中，由于存在不平衡的染色体易位，这些标记相关。由于复发后的复发或获取（15Q增益，17p损失和22Q损失），FHWT中还发现了对其他几个基因座的改变。这些变化尚未在前瞻性鉴定的患者中进行测试和验证。这项研究旨在开发和验证一种廉价，可靠的临床测定法，该测定可能用于在下一个COG方案中对患者进行分层。选择多重结扎依赖性探针扩增（MLPA），由于其简单性，灵活性，灵敏度，对多重多重性，适用于档案组织的适用性以及临床实验室内的可用性。 AIMS 1-3：使用MLPA分析250 FHWT在NWTS-4上以1Q，1P，1P，16Q，16Q，15Q，17P和22拷贝数进行分析。先前分析了1P和16Q LOH的样本将使用市售的MLPA测试研究，该测试检测每个染色体臂上的亚端粒位点的拷贝数（46个总目标）。将确定与生存显着相关的染色体区域，并将为确定的每个染色体区域设计多个探针，并将这些探针多重复为单个临床测试。 AIM 4：验证在AIMS 1-3中开发的目标多重MLPA测试在NWTS-5上注册的600 FHWT集中开发的。 NWTS-5开发了一个富含复发的600例富含复发的患者的病例 - 霍特。将确定每个基因座和生存之间的拷贝数之间的关联。相关性：这项研究将导致一项强大的临床测试，该测试需要更少的资源，并且会产生比当前可用的更多信息。目前对1P和16Q LOH进行的微卫星分析的成本约为$ 50/仅用于试剂，并且需要宪法和肿瘤DNA。有针对性的MLPA测试的费用仅为5美元/测试，仅需要肿瘤DNA。最终的MLPA测试将至少分析每个基因座的三个基因座，并能够测量100个目标。保守的预计相对风险为2.0，患病率为25％，至少将预测40％的复发。如果经过验证，MLPA测定法将用于在预计将于2013年开放的COG方案中对治疗进行分层。 公共卫生相关性：这项研究将设计出健壮，廉价的临床测试，该测试将预测Wilms肿瘤患者的整体临床结果。 Wilms肿瘤中1Q增长分析的临床影响是仅在美国，每年约30名儿童的存活率。更重要的是潜在的长期机会减少缺乏这些复发标志的Wilms肿瘤的较大子集的治疗（和毒性）。