Study

Comprehensive analysis of atypical teratoid rhabdoid tumour (ATRT) using genomic, epigenomic and transcriptomic techniques.

Study ID Alternative Stable ID Type
EGAS00001000506 Other

Study Description

ATRTs (Atypical teratoid rhabdoid tumours) represent one of the most aggressive pediatric brain cancers, but intriguingly exhibit few other recurrently mutated loci except for SMARCB1/hSNF5. We integrated whole genome (n=15), exome, copy number, gene expression and methylation analyses to comprehensively interrogate 64 ATRTs and observed that structural events were relatively frequent in the ATRT genome (~3 tumour). In addition to SMARCB1, which was targeted by structural events in a majority (49/64) of tumours, recurrent structural alterations targeting the LRP1B, CDH13, BCR and MKL1 loci were observed. We observed novel translocation events, including 2 targeting SMARCB1 which were detected only by NGS analyses. Significantly, integration of gene expression and methylation profiles with genomic analyses revealed ATRT comprise two sub-groups with distinct clinical and genetic features. Group 1 tumours were characterized by supra-tentorial brain location, focal intragenic alterations of SMARCB1 and a pro-neural gene expression signature with evidence of NOTCH pathway activation. ... (Show More)

Study Datasets 10 datasets.

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Dataset ID Description Technology Samples
EGAD00001004576
ATRT whole exome sequencing
Illumina HiSeq 2000,unspecified 32
EGAD00001004836
ATRT ChIPSeq H3K27ac
Illumina HiSeq 2500 3
EGAD00001004837
ATRT RNASeq
Illumina HiSeq 2500 4
EGAD00001004847
ATRT ATACSeq
Illumina HiSeq 2000 18
EGAD00010000710
ATRT genotyping blood
11
EGAD00010000712
ATRT genotyping
40
EGAD00010000789
ATRT expression
Illumina Human HT6-v3 Array,unknown 4
EGAD00010000790
ATRT expression
Illumina Human HT6-v3 Array,unknown 41
EGAD00010001433
ATRT methylation
Illumina HumanMethylation450 BeadChip 162
EGAD00010001546
ATRT expression
Illumina HumanHT-12 v4.0 Array 43

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