Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design

Cell Rep. Volume 29, Issue 6: p.:1675-1689, 5 November 2019, 10.1016/j.celrep.2019.09.071

Accelerating cures for children with cancer remains an immediate challenge as a result of extensive oncogenic heterogeneity between and within histologies, distinct molecular mechanisms evolving between diagnosis and relapsed disease, and limited therapeutic options. To systematically prioritize and rationally test novel agents in preclinical murine models, researchers within the Pediatric Preclinical Testing Consortium are continuously developing patient-derived xenografts (PDXs)-many of which are refractory to current standard-of-care treatments-from high-risk childhood cancers. Here, we genomically characterize 261 PDX models from 37 unique pediatric cancers; demonstrate faithful recapitulation of histologies and subtypes; and refine our understanding of relapsed disease. In addition, we use expression signatures to classify tumors for TP53 and NF1 pathway inactivation. We anticipate that these data will serve as a resource for pediatric oncology drug development and will guide rational clinical trial design for children with cancer.

Supplemental Data Files

• NBL
  • TARGET MDLS NBL Clinical Data
  • TARGET MDLS NBL WGS L3 Data
  • TARGET MDLS NBL WGS L3 Data (Controlled)
  • TARGET MDLS NBL WXS L3 Data (Controlled)
  • TARGET MDLS NBL WXS Design
  • TARGET MDLS NBL WXS Metadata
  • TARGET MDLS NBL Sample Matrix
• PPTP
  • TARGET MDLS PPTP Clinical Data
  • TARGET MDLS PPTP Copy Number Array L1 Data (Controlled)
  • TARGET MDLS PPTP Copy Number Array Metadata
  • TARGET MDLS PPTP Gene Expression Array L1 Data
  • TARGET MDLS PPTP Gene Expression Array L1 Metadata
  • TARGET MDLS PPTP WXS L3 Data
  • TARGET MDLS PPTP WXS Design Information
  • TARGET MDLS PPTP WXS Metadata
  • TARGET MDLS PPTP ID Mapping Information
  • TARGET MDLS PPTP Sample Matrix
• RT & ESC
  • TARGET MDLS RT and ESC Bisulfite-Seq Metadata
  • TARGET MDLS RT and ESC Bisulfite-Seq L3 Data (Controlled)
  • TARGET MDLS RT and ESC ChIP-Seq L3 Data (Controlled)
  • TARGET MDLS RT and ESC ChIP-Seq Metadata
  • TARGET MDLS RT and ESC mRNA-Seq L3 Data
  • TARGET MDLS RT and ESC mRNA-Seq L3 Data (Controlled)
  • TARGET MDLS RT and ESC mRNA-Seq Metadata
  • TARGET MDLS RT and ESC miRNA-Seq L3 Data
  • TARGET MDLS RT and ESC miRNA-Seq Metadata
  • TARGET MDLS RT and ESC WGS L3 Data (Controlled)
  • TARGET MDLS RT and ESC WGS Metadata

Additional Resources

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

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