Tyrosine kinome sequencing of pediatric acute lymphoblastic leukemia: a report from the Children's Oncology Group TARGET Project

Blood. Volume 121 Issue 3, p:485-488, 17 January 2013, 10.1182/blood-2012-04-422691

One recently identified subtype of pediatric B-precursor acute lymphoblastic leukemia (ALL) has been termed BCR-ABL1-like or Ph-like because of similarity of the gene expression profile to BCR-ABL1 positive ALL suggesting the presence of lesions activating tyrosine kinases, frequent alteration of IKZF1, and poor outcome. Prior studies demonstrated that approximately half of these patients had genomic lesions leading to CRLF2 overexpression, with half of such cases harboring somatic mutations in the Janus kinases JAK1 and JAK2. To determine whether mutations in other tyrosine kinases might also occur in ALL, we sequenced the tyrosine kinome and downstream signaling genes in 45 high-risk pediatric ALL cases with either a Ph-like gene expression profile or other alterations suggestive of activated kinase signaling. Aside from JAK mutations and 1 FLT3 mutation, no somatic mutations were found in any other tyrosine kinases, suggesting that alternative mechanisms are responsible for activated kinase signaling in high-risk ALL.

In order to access Controlled TARGET ALL 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

• GDC Manifests
  • Controlled-Access Data Download Manifest (6 Files)
  • Open-Access Data Download Manifest (22 Files)
  • WGS CGI Files Download Manifest (305 Files)

• Copy Number
  • TARGET ALL P2 Copy Number Array Level 1 Data (Controlled)
  • TARGET ALL P2 Copy Number Array Level 2 Data (Controlled)
  • TARGET ALL P2 Copy Number Array Level 3 Data
  • TARGET ALL P2 Copy Number Array Metadata
• Gene Expression Array
  • TARGET ALL P2 Gene Expression Array Level 1 Data
  • TARGET ALL P2 Gene Expression Array Level 2 Data
  • TARGET ALL P2 Gene Expression Array Level 3 Data
  • TARGET ALL P2 Gene Expression Array Metadata
• Methylation Array
  • TARGET ALL P2 Methylation Array Level 1 Data
  • TARGET ALL P2 Methylation Array Level 1 Data (Controlled)
  • TARGET ALL P2 Methylation Array Level 2 Data
  • TARGET ALL P2 Methylation Array Level 3 Data
  • TARGET ALL P2 Methylation Array Design Information
  • TARGET ALL P2 Methylation Array Metadata
• mRNA-Seq
  • TARGET ALL P2 mRNA-Seq Level 3 Data
  • TARGET ALL P2 mRNA-Seq Level 3 Data (Controlled)
  • TARGET ALL P2 mRNA-Seq Metadata
• miRNA-Seq
  • TARGET ALL P2 miRNA-Seq Level 3 Data
  • TARGET ALL P2 miRNA-Seq Metadata
• WGS
  • TARGET ALL P1 and P2 WGS L3 Data
  • TARGET ALL P1 and P2 WGS L3 Data (Controlled)
  • TARGET ALL P1 and P2 WGS L4 Data
  • TARGET ALL P2 and P2 WGS Metadata
• WXS
  • TARGET ALL P2 WXS Level 3 Data
  • TARGET ALL P2 WXS Level 3 Data (Controlled)
  • TARGET ALL P2 WXS Design Information
  • TARGET ALL P2 WXS Metadata
• Miscellaneous Files
  • TARGET ALL P2 Sample Matrix

Additional Resources

• TARGET-ALL-P2 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.