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Series GSE95484 Query DataSets for GSE95484
Status Public on Mar 01, 2017
Title Wilms Tumor in Beckwith-Wiedemann Syndrome and Loss of Methylation at Imprinting Centre 2 [HumanOmni2.5M]
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Beckwith-Wiedemann syndrome (BWS) is an overgrowth syndrome caused by a variety of molecular changes on chromosome 11p15.5. Children with BWS have a significant risk of developing Wilms tumours with the degree of risk being dependent on the underlying molecular mechanism. In particular, only a relatively small number of children with loss of methylation at the centromeric imprinting centre (IC2) were reported to have developed Wilms tumour. Discontinuation of tumour surveillance for children with BWS and loss of methylation at IC2 has been proposed in several recent publications. We report here three children with BWS reported to have loss of methylation at IC2 on clinical testing who developed Wilms tumour or precursor lesions. Using multiple molecular approaches and multiple tissues, we reclassified one of these cases to paternal uniparental disomy for chromosome 11p15.5. These cases highlight the current challenges in definitively assigning tumour risk based on molecular classification in BWS. The confirmed cases of loss of methylation at IC2 also suggest that the risk of Wilms tumour in this population is not low as previously thought. Therefore, we recommend that for now, all children with a clinical diagnosis of BWS be screened for Wilms tumour by abdominal ultrasonography until the age of 8 regardless of the molecular classification.
 
Overall design 2 blood samples (Case 1 and Case 2) are genotyped on the Illumina HumanOmni2.5M SNP array (GPL20641). 3 blood samples (Case 1, Case 2, and Case 3) have methylation measured on the Illumina HumanMethylation450 Bead Chip array (GPL13534). 21 Control blood samples were analyzed on the HumanMethylation BeadChip Array, there were no controls used for the HumanOmni2.5M SNP array. Pyrosequencing and MS-MLPA in cases and controls were done as described in the associated publication. There are no replications in this submission.
 
Contributor(s) Jack B, Cheryl S, Sanaa C, Peter R, Dmitri S, Raveen B, Leslie S, Nicole P, Ronald G, Paul T, Armando L, Rosanna W
Citation(s) 28699632
Submission date Feb 28, 2017
Last update date May 02, 2018
Contact name Jack Brzezinski
E-mail(s) jack.brzezinski@mail.utoronto.ca
Organization name University of Toronto
Street address 555 University Avenue
City Toronto
State/province ON
ZIP/Postal code M5G1X8
Country Canada
 
Platforms (1)
GPL20641 Illumina HumanOmni2.5M-8v1-1_B [data table]
Samples (2)
GSM2515099 Blood Sample Case 1 [SNP]
GSM2515100 Blood Sample Case 2 [SNP]
This SubSeries is part of SuperSeries:
GSE95488 Wilms Tumor in Beckwith-Wiedemann Syndrome and Loss of Methylation at Imprinting Centre 2
Relations
BioProject PRJNA377267

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE95484_RAW.tar 405.9 Mb (http)(custom) TAR (of IDAT)
Processed data included within Sample table

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