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Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways

Cancer Cell. Volume 29, Issue 3: p.394-406, 14 March 2016, 10.1016/j.ccell.2016.02.009

Malignant rhabdoid tumors (MRTs) are rare lethal tumors of childhood that most commonly occur in the kidney and brain. MRTs are driven by SMARCB1 loss, but the molecular consequences of SMARCB1 loss in extra-cranial tumors have not been comprehensively described and genomic resources for analyses of extra-cranial MRT are limited. To provide such data, we used whole-genome sequencing, whole-genome bisulfite sequencing, whole transcriptome (RNA-seq) and microRNA sequencing (miRNA-seq), and histone modification profiling to characterize extra-cranial MRTs. Our analyses revealed gene expression and methylation subgroups and focused on dysregulated pathways, including those involved in neural crest development.

This study characterized TARGET cases as described below:

40 Discovery Cases   29 Validation Cases
40 cases had mRNA-Seq   25 cases had mRNA-Seq
40 cases had miRNA-Seq   26 cases had miRNA-Seq
40 cases had WGBS   29 cases had WGBS
40 cases had methylation array   28 cases had methylation array
16 cases had ChIP-Seq   19 cases had ChIP-Seq
40 cases had WGS   29 cases had WGS


WGBS = Whole genome bisulfite sequencing, methylation array = Illumina’s Infinium MethylationEPIC (850K)

In order to access Controlled TARGET RT data using the links below, users must submit an application for Authorized Access via dbGaP as described on dbGaP’s TARGET Study Page. To begin the application process, please view the information and instructions provided on the dbGaP Authorized Access Login Page under “dbGaP Data Download”.

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