Detailed constitutional epigenetic and copy number analysis of the 11p15 growth regulatory region in Wilms tumour by MS-MLPA
Richard Scott, The Familial Wilms Tumour Collaboration, The Factors Associated with Childhood Tumours (FACT) Collaboration, Nazneen Rahman
Section of Cancer Genetics, Institute of Cancer Research, Sutton, UK
Background
Constitutional epigenetic and copy number defects at the imprinted 11p15 growth regulatory region have been reported in the overgrowth disorder Beckwith-Wiedemann syndrome and predispose to childhood cancer, particularly Wilms tumour. However, investigation of the region has been restricted by the complexity/technical difficulty of its comprehensive analysis.
Method
We customised and optimised a novel MS-MLPA assay capable of detecting the range of constitutional 11p15 defects described in individuals with overgrowth. We validated its use by blinded analysis of a ‘test set’ of 51 samples of known 11p15 status and 200 normal control samples. Genomic lymphocyte DNA from a series Wilms tumour cases was subsequently analysed with the assay. In samples with abnormalities, microsatellite analysis, bisulfite sequencing and/or direct sequencing was performed as appropriate.
Results
The customised assay correctly identified all samples in the blinded test and detected no abnormality in 200 normal control samples. A diverse range of 11p15 defects were identified in Wilms tumour cases including isolated H19 hypermethylation, uniparental disomy 11p15 and novel heritable copy number abnormalities. The phenotypes with which these defects presented varied from non-syndromic Wilms tumour to classic Beckwith-Wiedemann syndrome.
Conclusion
MS-MLPA is a robust and simple means of determining constitutional 11p15 status. The abnormalities detected Wilms tumour cases provide novel insights into pathogenic mechanisms and epigenotype-phenotype correlations at 11p15. Given the clinical implications for individuals harbouring these defects and the broad range of phenotypes with which they manifest, it is now realistic to consider constitutional 11p15 analysis in all individuals with Wilms tumour.
