Disease Types

Our orthotopic patient-derived xenografts (O-PDXs) have been created from a 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). The CSTN data portal consists of data generated from these O-PDX. As of April 2020, there are over 20 diagnoses of pediatric solid tumors in the data portal with a variety of samples within different diagnoses.

Search O-PDX Samples

You can also search the large diversity of tumors found in the data portal, including:

Ewing Sarcoma

Ewing sarcoma is the second most common bone tumor in children and adolescents. Most Ewing sarcoma tumors have a translocation involving the EWS gene on chromosome 22 and the FLI1 gene on chromosome 11 (EWS-FLI1). Ewing sarcomas have stable genomes relative to those of osteosarcomas. In addition to mutations in TP53 (small subset of tumors), the only other significant recurrent mutations are in STAG2 and CDKN2A. Ewing sarcoma tumor cells have defects in DNA repair and are particularly sensitive to PARP inhibitors when combined with DNA-damaging agents.

Browse Ewing Sarcoma Samples | Browse Ewing Sarcoma Cohort Data

Neuroblastoma

Neuroblastoma is the most common extracranial solid tumor in children. Most patients with neuroblastoma are young (median age at diagnosis, 18 months) and approximately 40-50% have disseminated disease at first presentation. Amplification of the MYCN oncogene is one of the most frequent genetic lesions in neuroblastoma. Germline mutations in the transcription factor PHOX2B and in the ALK gene can predispose children to neuroblastoma. Recurrent somatic mutations in the ARID1A/1B genes and in the ATRX gene points to a role for epigenetics in neuroblastoma initiation and progression.

Browse Neuroblastoma Samples | Browse Neuroblastoma Cohort Data

Osteosarcoma

Osteosarcoma is the most common type of bone cancer in children and teens. Although most cases are sporadic, the risk of osteosarcoma is increased in individuals with various genetic diseases. Approximately 15-20% of patients have metastatic disease at the time of diagnosis, with lungs being the most common site. Children who have germline mutations in the RB1 gene and develop retinoblastoma as infants are predisposed to develop osteosarcoma in adolescence. Virtually all osteosarcomas have initiating mutations in the TP53 tumor suppressor gene. Many osteosarcoma tumors have translocations in the first intron of the gene that separate the promoter of the TP53 gene from the coding region, generating an inactive allele. Of all childhood cancers, osteosarcomas have the highest rate of chromosomal breaks leading to structural variations and copy number variations.

Browse Osteosarcoma Samples | Browse Osteosarcoma Cohort Data

Retinoblastoma

Retinoblastoma is a rare cancer of the developing retina that is usually diagnosed before three years of age. Retinoblastoma can be hereditary or sporadic, and approximately 40% of patients have a germline genetic defect in the retinoblastoma susceptibility gene, RB1. Retinoblastomas have relatively stable genomes and some tumors have only RB1 gene mutations. Overall, retinoblastomas are relatively homogenous tumors with features of retinal neurons and progenitor cells.

Browse Retinoblastoma Samples | Browse Retinoblastoma Cohort Data

Rhabdomyosarcoma

Rhabdomyosarcoma is the most common soft-tissue sarcoma of childhood and adolescence. Most rhabdomyosarcomas can be divided into two main subtypes based on presence or absence of a PAX-3-FOXO1 or PAX7-FOXO1 fusion: fusion positive (commonly referred to as alveolar rhabdomyosarcoma) or fusion negative (commonly referred to as embryonal rhabdomyosarcoma). Fusion-positive rhabdomyosarcoma tumors have stable genomes, similar to those of the Ewing’s sarcoma tumors, and lack high rates of recurrent mutations in known cancer or developmental pathways. These tumors can occur in all age groups and often affect the large muscles of the arms, legs, and trunk. Fusion-negative tumors have features of an unstable genome, with the most recurrently mutated pathway being the RAS signal transduction pathway. These tumors are seen most commonly in children under the age of 5 and often affect the head and neck, bladder, vagina, prostate, and testicles. Tumors formerly classified with alveolar histology that lacked the gene fusion have been found to clinically resemble fusion negative tumors, and recent efforts have been made to risk stratify patients based on fusion status.

Browse Rhabdomyosarcoma Samples | Browse Rhabdomyosarcoma Cohort Data

Additional Rare Tumors

CSTN has several rare pediatric tumors, including diverse sarcomas and blastomas. Examples of these diagnoses are Clear cell sarcoma, Desmoplastic small cell round tumor, Fibrosarcoma, Hepatoblastoma, High-grade sarcoma, Liposarcoma, Melanoma, Synovial sarcoma, Wilms tumor, Epithelioid sarcoma and Rhabdoid tumor.

Browse Samples for Additional Rare Tumors | Browse Cohort Data for Additional Rare Tumors

Methylation Classification

Single-cell/nucleus RNA-sequencing data set from patient tumors and associated O-PDX tumors. Samples are annotated based on histologic type, developmental state, and predicted cell cycle phase. Patient tumor datasets contain separate viewers for malignant nuclei (>111,000 nuclei) or non-malignant nuclei (>11,000 nuclei). O-PDX datasets contain a viewer for >100,000 cells

RMS