TARGET’s Pan-Cancer Model Systems (MDLS)
Insufficient understanding of the biology of many childhood cancers limits the development of novel treatments for these young patients. Pan-cancer model systems, such as cell lines and xenografts, have been used in basic research to help expand the knowledge of cancer mechanisms and treatment response. Few model systems of pediatric cancers have been available to the research community. To address this need, Therapeutically Applicable Research to Generate Effective Treatments (TARGET) developed the Pan-Cancer Model Systems (MDLS) initiative to create models of high-risk or hard-to-treat childhood cancers.
Several of TARGET’s disease-specific projects were able to produce tumor cell lines or xenografts, with or without matched normal comparators, as well as some noncancerous tissues from the same organ. The TARGET MDLS initiative molecularly characterized these models by sequencing their DNA and/or RNA. These reagents are available for in vitro validation experiments, and their molecular characterization data is available through the Genomic Data Commons.
The cell lines and patient-derived xenograft models produced by MDLS includes:
- acute leukemia cell lines and xenografts with matched primary and/or relapsed tumor information
- neuroblastoma cell lines and xenografts with matched controls
- kidney tumor cell lines
- normal brain tissues
- embryonic stem cell lines (sequenced for some TARGET disease projects)
Additionally, TARGET has provided whole exome sequencing for 131 cell lines and xenografts from NCI’s Pediatric Preclinical Testing Program; many of these have associated expression and copy number data that will be made available through the Genomic Data Commons.
NCI’s Pediatric Preclinical Testing Program (PPTP)
The NCI-supported Pediatric Preclinical Testing Program was a comprehensive program to systematically evaluate new agents against molecularly characterized childhood solid tumor and leukemia models. The primary goal of the PPTP was to identify new agents that have the potential for significant activity when clinically evaluated against selected childhood cancers. The program was based on a substantial body of data showing that appropriate childhood cancer preclinical in vivo models could recapitulate the antitumor activity of known effective agents and prospectively identify novel agents subsequently shown to have clinical activity against specific cancers of children and adolescents.
The Pediatric Preclinical Testing Consortium (PPTC) is designed to produce reliable preclinical in vivo data using molecularly characterized patient-derived xenograft lines—data that may help clinical researchers prioritize which agents to pursue in pediatric clinical trials. PPTC, previously known as PPTP, has developed over 370 patient-derived xenograft models from high-risk childhood cancers. Effective prioritization of truly active agents for pediatric clinical testing is essential to future success in identifying more effective treatments for children with cancer.
PPTC RNA sequencing and whole exome sequencing data are available via the Sequence Read Archive Run Selector.
Nomenclature issue to note within the PPTC dataset: After release of the PPTC dataset, cases “TARGET-80-PPT045” and “TARGET-80-PPT046” were determined to be the same individual where all samples associated with the TARGET-80-PPT045 case barcode are diagnosis samples and those associated with the TARGET-80-PPT046 barcode are relapse samples. Since this determination was not made until after release, some sample barcodes do not accurately reflect the correct sample type codes for this case.
Specifically, both TARGET-80-PPT046-60A-99R and TARGET-80-PPT046-60A-01D are relapse xenograft samples, but they were originally assigned the “60” sample type code which is for primary xenograft samples. Therefore, the tissue codes for these two samples are incorrect.