Find research datasets worth reusing

openGEO-OpenDec 2020View details →

Epigenome analysis altered DNA methylation following chemotherapy in childhood cancer patients

GEO Series GSE162560. Homo sapiens. 96 samples. Type: Methylation profiling by array.

openGEO-OpenMar 2024View details →

Childhood cancer mutagenesis caused by a domesticated DNA transposase

GEO Series GSE249785. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.

openGEO-OpenDec 2020View details →

Epigenome analysis altered DNA methylation following chemotherapy in childhood cancer patients [undergoing and post therapy]

GEO Series GSE162554. Homo sapiens. 64 samples. Type: Methylation profiling by array.

openGEO-OpenDec 2020View details →

Epigenome analysis altered DNA methylation in survivors of childhood and young adult cancer [adult]

GEO Series GSE162559. Homo sapiens. 32 samples. Type: Methylation profiling by array.

openGEO-OpenMar 2022View details →

Genome-wide association studies identify novel genetic loci for epigenetic age acceleration among survivors of childhood cancer

GEO Series GSE197678. Homo sapiens. 2922 samples. Type: Methylation profiling by genome tiling array.

Childhood Cancer Data Initiative (CCDI): Genomic Analysis in Pediatric Malignancies

Pediatric solid tumors are highly heterogeneous, encompassing a large number of histotypes. The genomic landscape of these diseases is characterized by few single-nucleotide variants (SNVs) compared to adult cancers. In contrast, many exhibit a high prevalence of structural or epigenetic changes that alter gene expression, underlining the need for comprehensive genomic approaches such as whole-genome sequencing (WGS). Several studies have specifically addressed the clinical utility of genomic analysis in the pediatric and AYA cancer setting. Review of these studies point to key challenges that must be addressed in order to advance the routine use of genomics in this population.

Childhood Cancer Data Initiative (CCDI): Clonal Evolution During Metastatic Spread in High-Risk Neuroblastoma

The goal of this study is to deliver a detailed characterization of the patterns of disease dissemination at diagnosis, during progression and in response to therapy in high-risk neuroblastoma. Longitudinal and spatially distinct tumors were collected from patients. Clinical data includes diagnosis and treatment information. Biospecimen data includes whole genome sequencing (WGS) and whole transcriptome sequencing (WTS).

Childhood Cancer Data Initiative (CCDI): Pediatric In Vivo Testing Program -Sarcoma, Kidney, and Liver Cancers

The goal was to complete whole exome sequencing (WES) and RNA sequencing (RNA-Seq) on patient derived xenograft samples. Cancer in children is rare with approximately 15,700 new cases diagnosed annually in children 21 years or younger in the U.S. Through use of multimodality therapy (surgery, radiation therapy, and aggressive chemotherapy), 70% of patients will be 'cured' of their disease, and 5-year Event-Free Survival (EFS) exceeds 80%. Consequently, the number of patients that can be enrolled in phase I/II clinical trials is small, and most patients will have been extensively treated, hence drug/radiation resistant. Thus, preclinical studies that accurately translate into effective clinical therapy are an essential component of pediatric drug development. Our group has contributed to studies in the Pediatric Preclinical Testing Program (PPTP) and Pediatric Preclinical Testing Consortium (PPTC) that have led to clinical studies through Children's Oncology Group (COG). Of importance, we have developed and characterized over 330 Patient Derived Xenografts (PDX), developed from tumors both at diagnosis and relapse, that can be used to facilitate pediatric drug development as directed by FDA under the Research to Accelerate Cures and Equity for Children Act (RACE for Children Act).

Childhood Cancer Data Initiative (CCDI): Pediatric In Vivo Testing Program - Neuroblastoma

The goal of NCI's Pediatric In Vivo Testing Consortium (PIVOT) is to advance the development of effective treatments for pediatric cancers through preclinical in vivo testing of novel therapeutic agents. To design impactful experiments that can be rapidly translated to the clinic, PIVOT investigators require comprehensive genomic characterization of the patient-derived xenograft (PDX) models used across the consortium. This robust experimental design enhances collaboration with industry partners by providing proof-of-concept data for drugs in development. As part of this effort, neuroblastoma PDX models are being molecularly characterized to identify promising therapeutic candidates. The molecular profiling includes whole exome sequencing (WES), RNA-seq, MethylEPIC array, CytoSNP array, and DNA fingerprinting for quality control. Additionally, demographic and clinical data (e.g., diagnosis, disease site, disease status) are shared. These characterized PDX models, matched with patient tumors, guide model selection for preclinical drug testing.

Childhood Cancer Data Initiative (CCDI): Texas Pediatric Patient Derived Xenograft

The DNA/RNA samples of patients for which PDX models were developed were from a population of children, adolescents, and young adults from South Texas. Consent was obtained for collection of malignant and non-malignant tissue samples for genetic analysis and for the development of models to study new ways to treat cancer.

Childhood Cancer Data Initiative (CCDI): Single-Cell Atlas of NF1 Nerve Sheath Tumors

The worst outcome of NF1 is the development of the aggressive and highly metastatic malignant peripheral nerve sheath tumors (MPNST), which transform from benign plexiform neurofibroma (PN) and lack effective treatment. In this study, we performed single-cell RNA sequencing of 63 clinically annotated NF1-associated peripheral nerve sheath tumors, including 24 PN, 34 premalignant atypical neurofibromas, and 5 MPNSTs. These results improve the ability of identifying high-risk neurofibromas and provide a unique opportunity for early detection of MPNST.

Childhood Cancer Data Initiative (CCDI): Whole Genome Landscapes of Patient Derived Osteosarcoma Xenograft Models

Osteosarcoma is the most common primary bone malignancy in children and young adults and has few treatment options. As a result, there has been little improvement in survival outcomes over the past few decades. The need for models to test novel therapies is especially great for this disease because it is both rare and unresponsive to most therapies. To address this need, an NCI-funded consortium has characterized and utilized a panel of patient-derived xenograft models of osteosarcoma for drug testing. The exomes, transcriptomes, and copy number landscapes of these models have been described previously. This study adds whole-genome sequencing (WGS) and reverse-phase protein array profiling data, which can be correlated with drug testing results. In addition, four new osteosarcoma models are described for use by the research community.

PDX for Childhood Cancer Therapeutics

PCAT stores information of 324 PDX models spanning all major cancer types seen in children, including some very rare subtypes.

Childhood Cancer Survivor Study

The Childhood Cancer Survivor Study (CCSS), a component of the Long-Term Follow Up Study that began in 1994 and was funded by a grant from the National Cancer Institute, includes all participants with a confirmed diagnosis of cancer and 5 year survival, a cohort of 35,923 childhood cancer survivors diagnosed between 1970 and 1999. It also includes over 5,000 siblings of survivors who serve as the comparison group for the study. The CCSS cohort has been assembled through the efforts of 31 participating centers in the United States and Canada. CCSS is a resource in which to investigate current and future questions regarding consequences of therapy, genetic associations, disease processes and causation, interventions, and quality of life among childhood cancer survivors. The Childhood Cancer Survivor Study (CCSS) includes all participants with a confirmed diagnosis of cancer and 5 year survival, a cohort of 35,923 childhood cancer survivors diagnosed between 1970 and 1999. The CCSS cohort has been assembled through the efforts of 31 participating centers in the United States and Canada. CCSS is a resource in which to investigate current and future questions regarding consequences of therapy, genetic associations, disease processes and causation, interventions, and quality of life among childhood cancer survivors. This dataset outlines the demographic, primary cancer and treatment characteristics of the Overall CCSS Cohort (the Expansion Cohort as of January 2021 plus the Original Cohort).