Genomes 4 Kids
St. Jude Cloud
Data Resource:  St. Jude Cloud
Point of Contact:  
Clay McLeod ; Jinghui Zhang,  
Project

About This Dataset
Eligible cancer patients treated at St. Jude Children's Research Hospital are offered three-platform next-generation sequencing testing. This testing generally includes whole-genome sequencing (WGS) and whole-exome sequencing (WES) of tumor and normal tissue, as well as RNA sequencing (RNA Sequencing) of their tumor. Many of those patients consent to research data sharing so that their information can be leveraged to find cures for future patients. The Clinical Genomics dataset is comprised of data from these samples and is broken down into three distinct project phases. The Clinical Pilot project was a retrospective study that evaluated the accuracy and demonstrated the feasibility of three-platform sequencing in a CAP/CLIA setting. The findings of this project were published in Nature Communications. The Genomes 4 Kids (G4K) followed the Clinical Pilot. The goal of this prospective study was to determine whether the three-platform sequencing protocol laid out in the Clinical Pilot project could generate results on a clinical timeline in practice and to evaluate the prevalence of actionable findings. The study concluded with just over 300 patients, and the publication is currently in review. After the completion of G4K, clinical genomics became a standard service. Real-time Clinical Genomics (RTCG) is a first of its kind initiative, whereby St. Jude began releasing data from the clinical NGS service consented for research use to St. Jude Cloud in monthly batches to give researchers access to valuable data as quickly as possible. Subsequent publications are expected in the future.
Core Data Elements
Number of Cases
307
Case Sex
Female (142); Male (165)
Case Age At Diagnosis
0 to 4 years (138); 5 to 9 years (75); 10 to 14 years (62); 15 to 19 years (29); 20 to 24 years (4)
Case Race
Asian (11); Black or African American (41); More Than One Race (19); Native Hawaiian or Other Pacific Islander (1); Other (1); White (234)
Case Ethnicity
Hispanic or Latino (49); Not Hispanic or Latino (258)
Case Disease Diagnosis
Acute Leukemias of Ambiguous Lineage (4); Acute Leukemias of Ambiguous Lineage; T-cell Acute Lymphoblastic Leukemia, NOS (1); Acute Megakaryoblastic Leukemia (5); Acute Megakaryoblastic Leukemia, KMT2A rearrangement (2); Acute Myeloid Leukemia (7); Acute Myeloid Leukemia, Core Binding Factor (6); Acute Myeloid Leukemia, KMT2A rearrangement (6); Acute Myeloid Leukemia, NPM1 alteration (1); Acute Promyelocytic Leukemia, PML-RARA (2); Alveolar Rhabdomyosarcoma (1); Alveolar Rhabdomyosarcoma; Spindle Cell Rhabdomyosarcoma (1); Atypical Teratoid/Rhabdoid Tumor (2); B-cell Acute Lymphoblastic Leukemia, BCR-ABL1 (2); B-cell Acute Lymphoblastic Leukemia, BCR-ABL1 like (7); B-cell Acute Lymphoblastic Leukemia, DUX4-IGH (4); B-cell Acute Lymphoblastic Leukemia, ETV6-RUNX1 (19); B-cell Acute Lymphoblastic Leukemia, ETV6-RUNX1 like (2); B-cell Acute Lymphoblastic Leukemia, Hyperdiploidy (22); B-cell Acute Lymphoblastic Leukemia, iAMP21 (4); B-cell Acute Lymphoblastic Leukemia, IGH-CEBPD (1); B-cell Acute Lymphoblastic Leukemia, KMT2A rearrangement (6); B-cell Acute Lymphoblastic Leukemia, MEF2D rearrangement (1); B-cell Acute Lymphoblastic Leukemia, NOS (2); B-cell Acute Lymphoblastic Leukemia, PAX5 alteration (6); Botryoid Type Embryonal Rhabdomyosarcoma (1); Carcinoma, NOS (1); Chondroblastic Osteosarcoma; Osteosarcoma (1); Chordoma (1); Clear Cell Sarcoma; Clear Cell Sarcoma of Kidney (1); Craniopharyngioma, Adamantinomatous Type (27); Desmoid/Aggressive Fibromatosis (2); Desmoplastic Small Round Cell Tumor (1); Dysgerminoma, Ovarian (1); Dysgerminoma, Pelvis (1); Embryonal Rhabdomyosarcoma (2); Embryonal Tumor with Multilayered Rosettes, Brain (1); Embryonal Tumor, Brain (1); Ependymomal Tumor (1); Ependymomal Tumor, Posterior Fossa (1); Ependymomal Tumor, Spinal Tumor; Myxopapillary Ependymoma, Posterior Fossa (1); Ependymomal Tumor, Supratentorial (3); Ependymomal Tumor; Ependymomal Tumor, Posterior Fossa (2); Ewing Sarcoma (4); Ewing Sarcoma; Papillary Thyroid Cancer (1); Fibromyxoid Sarcoma (1); Ganglioglioma (1); Germ Cell Tumor, Brain (1); Glioma, NOS (3); Hepatoblastoma (3); High-Grade Glioma, NOS (21); High-Grade Neuroepithelial Tumor (1); Hodgkin Lymphoma (1); Langerhans Cell Histiocytosis (1); Low-Grade Glioma, NOS (9); Medulloblastoma (11); Medulloblastoma, Group 3; Medulloblastoma (1); Medulloblastoma, SHH subtype (4); Melanoma (2); Meningioma (1); Miscellaneous Brain Tumor (1); Mixed Germ Cell Tumor, Testis (1); Mixed Myxopapillary Anaplastic Ependymoma, Spinal Tumor (1); Myelodysplastic Syndromes (1); Myxopapillary Ependymoma, Posterior Fossa (1); Neuroblastoma (13); Osteosarcoma (4); Papillary Renal Cell Carcinoma (1); Papillary Thyroid Cancer (2); Pineoblastoma (1); Retinoblastoma (28); Spindle Cell Sarcoma, NOS (1); Squamous Cell Carcinoma, NOS (1); T-cell Acute Lymphoblastic Leukemia, KMT2A rearrangement (2); T-cell Acute Lymphoblastic Leukemia, LMO2 rearrangement (2); T-cell Acute Lymphoblastic Leukemia, NOS (5); T-cell Acute Lymphoblastic Leukemia, TAL1 rearrangement (1); T-cell Acute Lymphoblastic Leukemia, TLX3 rearrangement (3); T-cell Lymphoblastic Lymphoma, NKX2 rearrangement (1); T-cell Lymphoblastic Lymphoma, NOS (1); Wilms (5); Wilms, Bilateral (2)
Case Tumor Site
Not Reported (307)
Number of Samples
567
Sample Assay Method
Multiple (524); RNA Sequencing (786); Whole Exome Sequencing (2,268); Whole Genome Sequencing (2,264)
Additional Data Elements
DATA REPOSITORY
Grant Information
P30CA021765
Cancer Center Support Grant
PROGRAM ID
PAR-17-095
Published In
https://doi.org/10.1158/2159-8290.CD-20-1631
SAMPLE TYPE
Diagnosis (258);  
Germline (304);  
Relapse (5);  
Charts
Male (165); Female (142)
165Male