Real-Time Clinical Genomics
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
2,633
Case Sex
Female (1,169); Male (1,369); Not Reported (95)
Case Age At Diagnosis
0 to 4 years (550); 5 to 9 years (312); 10 to 14 years (305); 15 to 19 years (250); 20 to 24 years (38); 35 to 39 years (1); Pediatric and Young Adult (<40 years) (1,177)
Case Race
American Indian or Alaska Native (13); Asian (62); Black or African American (346); More Than One Race (137); Other (31); White (1,881); Not Reported (161); Unknown (2)
Case Ethnicity
Hispanic or Latino (354); Not Hispanic or Latino (2,095); Not Reported (157); Unknown (27)
Case Disease Diagnosis
Acute Leukemia (2); Acute Lymphoblastic Leukemia (18); Acute Lymphocytic Leukemia (226); Acute Megakaryocytic Leukemia (6); Acute Monocytic Leukemia (10); Acute Myeloblastic Leukemia (4); Acute Myeloblastic Leukemia In Relapse (1); Acute Myelocytic Leukemia (77); Acute Myeloid Leukemia (7); Acute Myeloid Leukemia Associated With Down Syndrome (2); Acute Myelomonocytic Leukemia (8); Acute Promyelocytic Leukemia (3); Acute Unclassifiable Leukemia (1); Adenocarcinoma (2); Adenoma (1); Adrenal Cortical Carcinoma (2); Adrenocortical Carcinoma (4); Adrenocortical Tumor (1); Alveolar Rhabdomyosarcoma (1); Alveolar Soft Part Sarcoma (1); Anaplastic (8); Anaplastic Alk-Positive Large Cell of Lymphoma of Intrathoracic Lymph Node (1); Anaplastic Astrocytoma (1); Anaplastic Ependymoma (18); Anaplastic Gangioglioma (1); Anaplastic Ganglioglioma (2); Anaplastic Large Cell Lymphoma (1); Anaplastic Large Cell Medulloblastoma (1); Aneurysmal Bone Cyst (2); Aplastic Anemia (1); Astroblastoma (1); Astrocytoma (61); Astrocytoma Pilomyxoid (1); Atypical Choroid Plexus Papilloma (1); Atypical Melanocytic Neoplasm (2); Atypical Spitz Nevus (1); Atypical Spitz Tumor (2); Atypical Spitzoid Melanocytic Proliferation (2); Atypical Teratoid Rhabdoid Tumor (22); Atypical Teratoid Rhabdoid Tumor of Brain (1); B Cell Lymphoma W/ Features Intermediate Diffuse Large B Cell and Classical Hodgkin (1); B Lymphoblastic Leukemia (1); B-Cell Acute Lymphoblastic Leukemia (18); Bilateral Retinoblastoma (1); Blastoma Determined By Biopsy of Pituitary Gland (1); Burkitt Lymphoma (5); Cancer With Pulmonary Metastases (1); Carcinoma (6); Cellular Neurothekeoma (1); Childhood Intracranial Germinoma (1); Cholangiocarcinoma (1); Chondroblastoma (1); Chondroblastoma of Bone (1); Choroid Plexus Carcinoma (1); Choroid Plexus Papilloma Determined By Biopsy of Brain (1); Chronic Myelocytic Leukemia (2); Chronic Myelogenous Leukemia (2); Chronic Myeloid Leukemia (1); Clear Cell Sarcoma (1); CNS Embryonal Tumor (1); Colloid Cyst (1); Compound Spitz Melanocytic Neoplasm (1); Congenital Melanocytic Nevus (1); Craniopharyngioma (22); Craniopharyngioma In Pediatric Patient (1); Cyst (2); Cystic Nephroma (1); Dermatofibrosarcoma Protuberans (3); Desmoid Tumor (6); Desmoplastic Fibroma (1); Desmoplastic Small Round Cell Tumor (3); Diagnosis Pending (3); Diffuse Astrocytoma (1); Diffuse Glioma (1); Diffuse Glioneuronal Tumor (2); Diffuse Large B-Cell Lymphoma of Lymph Nodes of Multiple Regions (1); Diffuse Low Grade Glioma (1); Diffuse Midline Glioma (8); Dysembryoplastic Neuroepithelial Tumor (4); Dysembryoplastic Neuroepithelial Tumor of Brain (1); Dysgerminoma (2); Embryonal Neoplasm of Central Nervous System (1); Embryonal Rhabdomyosarcoma (4); Embryonal Sarcoma (1); Embryonal Tumor (1); Embryonal Tumor W/ Multilayered Rosettes (1); Ependymoma (25); Epithelioid Angiomyolipoma (1); Epithelioid Sarcoma (3); Ewing's Sarcoma (25); Fibrosarcoma (5); Fibrothecoma (1); Ganglioglioma (16); Ganglioneuroblastoma (2); Gastric Adenocarcinoma (1); Gastrointestinal Stromal Tumor (1); Germ Cell Tumor (2); Giant Cell Fibroblastoma (2); Giant Cell Tumor (1); Glioblastoma (19); Glioblastoma Multiforme (2); Glioma (25); Glioneuronal Tumor (2); Granulosa Cell Tumor (1); Group 4 Medulloblastoma (1); Hepatoblastoma (13); Hepatocellular Carcinoma (4); High Grade Glioma (5); High Grade Tumor (1); Histiocytoma (1); Hodgkin's Lymphoma (4); Infantile Fibrosarcoma (1); Inflammatory Myofibroblastic Tumor (2); Juvenile Granulosa Cell Tumor (2); Juvenile Myelomonocytic Leukemia (1); Juxtaglomerular Tumor (1); Langerhans Cell Histiocytosis (1); Leiomyoma (1); Leukemia (2); Lipoblastoma (3); Lipofibromatosis (1); Liver Cell Carcinoma (1); Low Grade Glioma of Brain (6); Lymphoma (21); Malignant Melanoma (8); Malignant Neoplasm (21); Malignant Peripheral Nerve Sheath Tumor (1); Malignant Rhabdoid Tumor (1); Malignant Tumor (2); Mature B-Cell Leukemia Burkitt-Type (2); Medullary Carcinoma (1); Medulloblastoma (119); Melanoma (19); Meningioma (2); Mesenchymal Tumor (1); Mesenchymal Tumor With Ewsr1-Atf1 Fusion (1); Mixed Germ Cell Tumor (4); Mixed Phenotype Acute Leukemia (2); Mucoepidermoid Carcinoma (2); Myelodysplastic Syndromes (1); Myeloid Sarcoma (1); Myoepithelial Carcinoma (1); Myofibroma (1); Myositis Ossificans (1); Nephroblastoma (2); Nephroblastomatosis (1); Nephroma (1); Neuroblastoma (55); Neurocytoma (1); Neuroendocrine Carcinoma (1); Neuroepithelial Tumor (14); Neuroma (1); Neuromuscular Choristoma (1); Nodule (1); Optic Pathway-Hypothalamic Glioma In Child (1); Osteosarcoma (42); Papillary Carcinoma (18); Papillary Thyroid Carcinoma (3); Papilloma (4); Paraganglioma (1); Pheochromocytoma (2); Pilocytic Astrocytoma (13); Pineal Parenchymal Tumor (1); Pineoblastoma (7); Plexiform Neurofibroma (1); Polymorphous Low Grade Neuroepithelial Tumor (1); Post-transplant Lymphoproliferative Disorder (1); Pre B-Cell Acute Lymphoblastic Leukemia (2); Pre B-Cell Acute Lymphoblastic Leukemia In Remission (3); Primary Germinoma of Pineal Gland (1); Primary Malignant Atypical Teratoid-Rhabdoid Tumor of Brain (1); Pseudoprogression of Neoplasm (1); RAF1 Fusion Positive Spindle Cell Neoplasm (1); Relapse AML (1); Renal Cell Carcinoma (8); Retinoblastoma (20); Rhabdoid Tumor (6); Rhabdomyosarcoma (49); Rosai-Dorfman Syndrome (1); Rosette-Forming Glioneuronal Tumor (1); Salivary Gland Anlage Tumor (1); Sarcoma (14); Schwannoma of Spinal Cord (1); Sebaceous Cell Carcinoma (1); Secondary Malignant Neoplasm Lymph Nodes of Head (1); Secondary Malignant Neoplasm of Brain (1); Seminoma (1); Sertoli-Leydig Cell Tumor (1); Sialoblastoma (1); Sickle Cell Disease (2); Soft Tissue Tumor (1); Solid Pseudopapillary Tumor (1); Spindle Cell Neoplasm With Plekhh2-Alk Fusion (1); Spindle Cell Rhabdomyosarcoma (1); Spindle Cell Sarcoma (2); Spindle Epithelial Tumor with Thymus-Like Differentiation (1); Spitzoid Neoplasm of Uncertain Malignant Potential (2); Squamous Cell Carcinoma (1); Supratentorial Ependymoma (1); Syndrome (3); Synovial Cell Sarcoma (1); Synovial Sarcoma (3); T Lymphoblastic Lymphoma (1); T-Cell Acute Lymphoblastic Leukemia (2); T-Cell Acute Lymphoblastic Leukemia In Remission (1); T-Cell Lymphoblastic Leukemia (1); T-Cell Lymphoma (2); Thymoma (1); Thyroid Carcinoma (1); Thyroid Papillary Carcinoma (1); TLL (1); Undifferentiated Round Cell Sarcoma (2); Unspecified B-Cell Lymphoma (1); Wilms' Tumor (62); Xanthoastrocytoma (1); Yolk Sac Tumor (5); Not Reported (1,215)
Case Tumor Site
Not Reported (2,633)
Number of Samples
5,196
Sample Assay Method
RNA Sequencing (683); Whole Exome Sequencing (4,134); Whole Genome Sequencing (379)
Additional Data Elements
DATA REPOSITORY
Grant Information
P30CA021765
Cancer Center Support Grant
SAMPLE TYPE
Diagnosis (2,800);  
Germline (2,335);  
Relapse (61);  
Charts
Male (1,369); Female (1,169); Not Reported (95)
1,369Male