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”.

Supplemental Data Files

• Clinical
  • TARGET RT Clinical Data
  • TARGET RT Clinical Data (Controlled)
• mRNA-Seq
  • RT mRNA-Seq Level 3 Data
  • RT mRNA-Seq Level 3 Data (Controlled)
  • RT mRNA-Seq Metadata
• Bisulfite-Seq
  • TARGET RT Bisulfite-Seq Level 3 Data (Controlled)
  • TARGET RT Bisulfite-Seq Metadata
• ChIP-Seq
  • TARGET RT ChIP-Seq Level 3 Data (Controlled)
  • TARGET RT ChIP-Seq Metadata
• Methylation Array
  • RT Methylation Array Level 1 Data
  • RT Methylation Array Level 2 Data
  • RT Methylation Array Metadata
• WGS
  • RT WGS Level 3 Data (Controlled)
  • RT WGS Metadata

Additional Resources

• OCG TARGET Data Matrix (link is external) Office of Cancer Genomics
• SRA - SRP012000 (link is external) NCBI