The Childhood Solid Tumor Network (CSTN) at St. Jude offers a comprehensive collection of scientific resources for academic researchers studying pediatric solid tumors and related biology. An overview of available samples and data is provided below; visit our request form for more detailed information. To receive updates on new resources emerging from the CSTN, subscribe to our e-newsletter.
Available resources include:
- NEW Patient-derived orthotopic xenografts (InteractiveData Portal)
- NEW Patient-derived iPSCs
- Orthotopic patient-derived xenografts
- Preclinical models of childhood solid tumors (GEMMs)
- Genomic, drug sensitivity and pharmacokinetic data
- Protocols (ChIPSeq, O-PDX propagation)
- Integrated Rhabdomyosarcoma Database (iRDb)
- Integrated Neuroblastoma Database (iNBDb)
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. Access resources.
Orthotopic patient-derived 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.
Access CSTN Data Portal 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 downloaded for each sample in the CSTN Data Portal 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 year after the new samples have engrafted and sufficient vials have been cryopreserved for distribution.

Induced pluripotent stem cells (iPSCs) have been created from 15 patients with retinoblastoma that have germline RB1 mutations collected under the RETCELL (A Study of Children with Heritable Retinoblastoma) protocol at St Jude Children’s Research Hospital (ClinicalTrials.gov NCT02193724). The clinical spectrum of disease varies from early diagnosis (Group A and/or B) to advanced bilateral disease (Group D and/or E). In addition, some participants were found to be unaffected or spontaneously regressed carriers of the heritable mutation or chromosomal abnormality. The RB1 mutations have been validated in each line and they have undergone complete characterization including trilineage differentiation, whole genome sequencing, karyotyping and 3D retinal organoid differentiation. Vials of cryopreserved cells are available upon request. Additional iPSC lines are being developed for other pediatric solid tumor types and the list of available lines will be updated every six months after they have been validated and characterized.
iPSC number | laterality (1) | sample | gene mutation; protein mutation |
---|---|---|---|
SJRB-iPSC-1 | OU | fibroblasts | nonsense |
SJRB-iPSC-2 | OU, asynchronous | fibroblasts | frameshift |
SJRB-iPSC-3 | OU | fibroblasts | nonsense |
SJRB-iPSC-4 | OU | blood | frameshift |
SJRB-iPSC-5 | OS | blood | deletion |
SJRB-iPSC-6 | OU | blood | frameshift |
SJRB-iPSC-7 | OU | blood | frameshift |
SJRB-iPSC-8 | trilateral | blood | nonsense |
SJRB-iPSC-9 | OU | blood | nonsense |
SJRB-iPSC-10 | N/A | blood | nonsense |
SJRB-iPSC-11 | OU | blood | splice |
SJRB-iPSC-12 | OD | blood | splice |
SJRB-iPSC-13 | OU | blood | large deletion |
SJRB-iPSC-14 | OU | blood | nonsense |
SJRB-iPSC-15 | OU | blood | nonsense |
1: OU, oculus uterque (both eyes); OS, oculus sinister (left eye); OD, oculus destrus (right eye), trilateral, OU disease with tumor in the pineal gland at diagnosis
2: Reese-Ellsworth staging (1-5) and International Classification of Intraocular Retinoblastoma (A-E)
We offer molecular and drug sensitivity data 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.) 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.
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.
Raw datasets are available through St. Jude Cloud, following an application and approval process for access.
Genomic sequencing and integrated epigenetic profiling have been performed on pediatric solid tumors and orthotopic patient-derived 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. Standard of Care regimens used in current preclinical trials are available in the appendix. 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.
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All PK reports can be found in the CSTN Data Portal.
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5-Fluorodeoxycytidine
5-Fluorouracil (5-FU)
6-Mercaptopurine
6-Thioguanine
7-Hydroxystaurosporine
Abiraterone Acetate
Actinomycin D
Afatinib
Alisertib
Arimidex
Arry-520
Artesunate
Aurorafin
Axinitib
Azacitidine
AZD-1775
AZD-4547
AZD-5363
AZD-7762
Binimetinib
Blenoxane
Bmn673 (Talazoparib)
Bms-777607
Bordoxolone
Bortezomib
Bosisunib
Brivudine
Buparlisib
Cabazitaxel
Cabozantinib
Carfilzomib
Ceritinib
Chlorambucil
Ciclopirox
Cladribine
Clofarabine
Cobimetinib
Crenolanib
Crizotinib
Cyclophosphamide
Cyt11387
Cytadren
Cytidine
Dabrafenib
Daclctisib
Dacogen
Daraprim
Dasatinib
Dexamthasone
Dfmo
Dihydroartemisinin (DHA)
Docetaxol
DoxorubicinENMD-981693
Enzalutamide
Erlotinib
Etoposide
Everolimus
Fedratinib
Floxuridine
Fludara
Fluphenazine HCL
Fluvastatin
Foretinib
Ganetespib
GDC-0068
GDC-0199
GDC-0994
Gedatolisib
Gefifinib
Gemcitabine
GMX-1778
Golotimod
Hydroxychloroquine
Idronoxil
Ifosfamide
Itraconazole
Ixabepilone
JQ1
Lapatinib
LEE011
Leflunomide
LGX-818
LY2157299
Masitinib
Mepacrine
Methotrexate
Midostaurin
Mithramycin
Mitomycin
Mitotane
Mitoxantrone
MK-2206
MK-8776
Motatenib Diphosphate
Mycophenolate Mofetil Hydrochloride
Namenda
Navitoclax
Neratinib
Niftfuimox
Nililonib
Nimtmuine
Noscapine
NSC-617593
NSC-714598 | NSC-286644Obatoclax
Olaparib
Omipalisib
Ouabain
Pacritnib
Palbociclib
Panobinostat
Pazopanib
PD 325901
Pemetrexed Disodium
Pentostatin
Pimasertib
Pioglitazone
Ponatinib
Rabusertib
Raltitrexed
Regorafenib
Retinoic Acid
RG7112
Romidepsin
Ruxolitinib
Selinexor
Selumetinib
Sirolimus
SN-38
Sorafenib
Streptozotocin
Sulindac
Sunitinib
Tamibarotene
Tamoxifen
Targretin Bexarotene
Taselisib
Tazarotene
Temozolomide
Temsirolimus
Tivantinib
Tivozanib
Topotecan
Trametinib
Trimetrexate
Trisenox
Vantndanib
VE821
Vemurafenib
Vinblastine
Vincristine
Vinorelbine
Vismodegib
Volelartib
Vorinostat
Vosaroxin -
Vincristine + Irinotecan (Low-dose protracted)
Vincristine + Irinotecan (High-dose 5 day dosing)
Vincristine + Irinotecan + Panobinostat
Vinorelbine + Cyclophosphamide
Panobinostat + Bortezomib
Vincristine + Dactinomycin + Cyclophosphamide
Cisplatin + Doxorubicin + Methotrexate + Ifosfamide + Etoposide (MAP/IE)
Gemcitabine + Docetaxel
Cyclophosphamide + Doxorubicin + Etoposide
Cisplatin + Etoposide
Irinotecan + Temozolomide
BMN-673 + Irinotecan + Temozolomide
Olaparib + Irinotecan + Temozolomide
Veliparib + Irinotecan + Temozolomide -
Rhabdomyosarcoma
SHRHB026_X1: Vincristine + Irinotecan
SHRHB026_X1: Panobinostat
SHRHB026_X1: Panobinostat + Bortezomib
SHRHB026_X1: Vincristine + Dactinomycin + CyclophosphamideSHRHB026_X2: Vincristine + Dactinomycin + Cyclophosphamide
SHRHB026_X2: Vinorelbine + CyclophosphamideSJRHB010927_X1: Vincristine + Dactinomycin + Cyclophosphamide
SJRHB012_Y: Vincristine + Irinotecan
SJRHB012_Y: Panobinostat + BortezomibSJRHB013759_X1: Vincristine + Irinotecan
SJRHB013759_X1: Panobinostat + BortezomibNeuroblastoma
SJNBL046_X: Cyclophosphamide + Doxorubicin + Etoposide / Cisplatin + Etoposide
SJNBL046_X: OSI-906 + BEZ-235
SJNBL046_X: OSI-906 + BKM-120NB5: Cyclophosphamide + Doxorubicin + Etoposide / Cisplatin + Etoposide
NB5: OSI-906 + BEZ-235
NB5: OSI-906 + BKM-120Ewing sarcoma
ES-8: Irinotecan + Temozolomide
ES-8: BMN-673 + Irinotecan + Temozolomide
ES-8: Olaparib + Irinotecan + Temozolomide
ES-8: Veliparib + Irinotecan + Temozolomide
EW-8: Irinotecan + Temozolomide
EW-8: BMN-673 + Irinotecan + Temozolomide
EW-8: Olaparib + Irinotecan + Temozolomide
EW-8: Veliparib + Irinotecan + Temozolomide
ES-6: Irinotecan + Temozolomide
ES-6: BMN-673 + Irinotecan + Temozolomide
ES-6: Olaparib + Irinotecan + Temozolomide
ES-2: Irinotecan + Temozolomide
ES-2: BMN-673 + Irinotecan + Temozolomide
ES-3: Irinotecan + Temozolomide
ES-3: BMN-673 + Irinotecan + Temozolomide -
Ewing sarcoma
ES-8: PARP inhibitor trial (BMN-673, Olaparib, Veliparib, Irinotecan, Temozolamide)

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 eight 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.
We have collected and integrated genomic, epigenetic, proteomic and drug-sensitivity data into a central database for neuroblastoma. We have focused on age at diagnosis because there is an inverse relationship between age at diagnosis and outcome. Moreover, ATRX mutations are significantly associated with older age at diagnosis so we have included several ATRX mutant NBs. The genomic data includes whole genome, exome and RNA-sequence (transcriptome) 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 eight histone marks and CTCF, Brd4 and RNA PolII for a total of over 350 ChIP-seq libraries. The data have been integrated to define chromatin states using chromatin Hidden Markov Modeling. 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.
About the Childhood Solid Tumor Network
Childhood solid tumors are often difficult to study and treat because they are rare and originate in the complex biological context of developing organs. CSTN was established to disseminate resources and data that have been developed at St. Jude Children’s Research Hospital, with the aim of stimulating basic research and speeding translation to the clinic.
The effort was launched in 2013 by Howard Hughes Medical Institute investigator Michael Dyer, PhD, of St. Jude Developmental Neurobiology, and Alberto Pappo, MD, of St. Jude Oncology.
For more information, contact us: CSTN@stjude.org