Available Resources

Preclinical models of childhood solid tumors (GEMMs)

GEMM-derived tissue samples developed at St. Jude are available for a variety of pediatric solid tumors, including neuroblastoma, retinoblastoma and osteosarcoma. Available strains are detailed on the request form.

Protocols (ChIPSeq)

Protocols with various antibodies, targets and tissue types have been developed and validated at St. Jude and are available to be shared. Available ChIPSeq protocols are detailed on the request form under “Protocols & Reagents”.

Patient-derived orthotopic xenografts

Orthotopic patient derived xenografts (O-PDXs) have been created from a wide variety of pediatric solid tumors collected under the Molecular Analysis of Solid Tumors (MAST) protocol at St. Jude Children’s Research Hospital (ClinicalTrials.gov: NCT01050296). Most O-PDX models are available with a luciferase reporter gene integrated into the genome to enable monitoring of tumor engraftment and growth in vivo. Cryopreserved cells, fresh frozen tissue/cells, and formalin-fixed paraffin-embedded tissue blocks are available. See below for the full list of tumor types and samples. Extensive molecular and drug sensitivity data are available for the O-PDX models. For each of the O-PDX models, a characterization sheet will be provided when the samples are shipped (see example for SJNBL046_X or visual descriptions of the clonal evolution groups.) Characterization sheets can also be requested to help investigators select the appropriate O-PDX models for their studies. For the samples that have been added most recently, characterization is pending and the completed characterization sheets will be sent to requestors as soon as they are available.

The list of available tumors is updated every 6 months (January and July) after the samples have engrafted and sufficient vials have been cryopreserved for distribution.

Neuroblastoma samples

Symbols/Abbreviations: – = not available, mo = months, N = no, Tx = treatment, Y = yes, yr = years.
Pending = characterization is ongoing.

Osteosarcoma samples

Symbols/Abbreviations: F = female, M = male, Tx = treatment, yr = years.
Pending = characterization is ongoing.

Rhabdomyosarcoma samples

Symbols/Abbreviations: ARMS = alveolar rhabdomyosarcoma, ERMS = embryonal rhabdomyosarcoma, F = female, M = male, mo = months, Tx = treatment, yr = years.
Pending = characterization is ongoing.

Other samples

Symbols/Abbreviations: F = female, M = male, mo = months, Tx = treatment, yr = years.
Pending = characterization is ongoing.

Genomic, drug sensitivity and pharmacokinetic data

We offer data from molecular and drug sensitivity analyses of diverse pediatric solid tumors, patient-derived orthotopic xenografts and solid tumor cell lines. (Some cell lines are available; see the request form for details.)

While comprehensive raw datasets are not made available prior to publication, we are happy to accommodate many types of data requests to answer specific research questions.

Genomic sequencing and integrated epigenetic profiling have been performed on pediatric solid tumors and patient-derived orthotopic xenografts as part of the St. Jude-Washington University Pediatric Cancer Genome Project and is actively ongoing in St. Jude investigator-led labs. Available data may include:

• Whole genome sequencing (WGS)
• Whole exome sequencing (WES)
• RNA-seq
• Whole-genome bisulfite sequencing (WGBS)
• ChIP-seq

High-throughput drug screening (HTS) data are available for many pediatric solid tumor cell lines and orthotopic xenografts, including Ewing sarcoma, neuroblastoma, osteosarcoma, retinoblastoma and rhabdomyosarcoma. In addition, we offer preclinical pharmacokinetic data for a number of high-priority drugs that are being explored for activity against pediatric solid tumors. Current preclinical trial data is uploaded into OpenClinica for long-term data capture. Data from completed preclinical Phase I (tolerability), Phase II (small pilot efficacy study) and Phase III (randomized, placebo controlled) trials are available by request. For more details and descriptions of Phase I, II and III, please see Stewart et al, 2014 Cell Reports.

Integrated Rhabdomyosarcoma Database (iRDb)

We have collected and integrated genomic, epigenetic, proteomic and drug sensitivity data into a central database. The genomic data includes whole genome, exome and RNA-sequence as well as clonal analysis that allows us to reconstruct the clonal heterogeneity of the tumor and corresponding O-PDX. The epigenetic data includes whole genome bisulfite (WGBS) and ChIP-seq data for 8 histone marks and CTCF, Brd4 and RNA PolII for a total of over 750 ChIP-seq libraries. The data have been integrated to define chromatin states using chromatin Hidden Markov Modeling. Quantitative proteomic and phosphoproteomic data were obtained for RMS tumors using mass coded peptides derived from batches of 10 samples. Drug sensitivity data includes primary cultures of O-PDX tumors in high throughput drug screening of 168 oncology drugs in 10-point dose response in triplicate with biological replicates.