A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor.

Nat Genet. Volume 49, Issue 10 p.1487-1494, 21 August 2017 10.1038/ng.3940

We performed genome-wide sequencing and analyzed mRNA and miRNA expression, DNA copy number, and DNA methylation in 117 Wilms tumors, followed by targeted sequencing of 651 Wilms tumors. In addition to genes previously implicated in Wilms tumors (WT1, CTNNB1, AMER1, DROSHA, DGCR8, XPO5, DICER1, SIX1, SIX2, MLLT1, MYCN, and TP53), we identified mutations in genes not previously recognized as recurrently involved in Wilms tumors, the most frequent being BCOR, BCORL1, NONO, MAX, COL6A3, ASXL1, MAP3K4, and ARID1A. DNA copy number changes resulted in recurrent 1q gain, MYCN amplification, LIN28B gain, and MIRLET7A loss. Unexpected germline variants involved PALB2 and CHEK2. Integrated analyses support two major classes of genetic changes that preserve the progenitor state and/or interrupt normal development.

This study characterized TARGET cases as described below:

GE=gene expression; CN=copy number, TCS=targeted capture sequencing

In order to access Controlled TARGET WT 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

• GDC Manifests
  • Controlled-Access Data Download Manifest (8 Files)
  • Open-Access Data Download Manifest (25 Files)
  • WGS CGI Files Download Manifest (82 Files)

• Copy Number Array
  • TARGET WT Copy number array Level 1 Data (Controlled)
  • TARGET WT Copy number array Level 2 Data (Controlled)
  • TARGET WT Copy number array Level 3 Data
  • TARGET WT Copy number array Metadata
• Gene Expression Array
  • TARGET WT Gene expression array Level 1 Data
  • TARGET WT Gene expression array Level 2 Data
  • TARGET WT Gene expression array Level 3 Data
  • TARGET WT Gene expression array Level 4 Data
  • TARGET WT Gene expression array Metadata
• mRNA-Seq
  • TARGET WT mRNA-Seq Level 3 data
  • TARGET WT mRNA-Seq Level 3 data (Controlled)
  • TARGET WT mRNA-Seq Metadata
• miRNA-Seq
  • TARGET WT miRNA-Seq Level 3 Data
  • TARGET WT miRNA-Seq Metadata
• Whole Exome Sequencing
  • TARGET WT WXS Level 3 Data
  • TARGET WT WXS Level 3 Data (Controlled)
  • TARGET WT WXS Design
  • TARGET WT WXS Metadata
• Methylation Array
  • TARGET WT Methylation array Level 1 Data (Controlled)
  • TARGET WT Methylation array Level 2 Data
  • TARGET WT Methylation array Level 3 Data
  • TARGET WT Methylation array Level 4 Data
  • TARGET WT Methylation array Metadata
• Whole Genome Sequencing
  • TARGET WT WGS Level 3 Data
  • TARGET WT WGS Level 3 Data (Controlled)
  • TARGET WT WGS Level 4 Data
  • TARGET WT WGS Metadata
• Targeted Capture Sequencing
  • TARGET WT Targeted Capture Sequencing Level 3 Data (Controlled)
  • TARGET WT Targeted Capture Sequencing Design
  • TARGET WT Targeted Capture Sequencing Metadata
• Miscellaneous Files
  • TARGET WT Sample Matrices
  • TARGET WT CGI Requested Reports (Controlled)

Additional Resources

• TARGET-WT at SRA (link is external) NCBI

Instructions for Data Download

Open Access Data

1. Download the appropriate manifest file from the publication page
2. Use the manifest file to download data using the GDC Data Transfer Tool (DTT) or the GDC API
   • GDC DTT ( Download, User's Guide)
   • GDC API ( User’s Guide)

Controlled Access Data

1. Download the appropriate manifest file from the publication page
2. Download a token from the GDC Data Portal
   • GDC Data Portal ( Launch, User’s Guide)
3. Use the manifest file and token to download data using the GDC DTT or the GDC API
   • GDC DTT ( Download, User’s Guide)
   • GDC API ( User’s Guide)

For assistance, please contact the GDC Help Desk: support@nci-gdc.datacommons.io.