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

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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.