CSER: Incorporation of Genomic Sequencing into Pediatric Cancer Care
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PROVIDER: PRJNA489747 | ENA |
REPOSITORIES: ENA
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Project description:CSER: Incorporation of Genomic Sequencing into Pediatric Cancer Care
| PRJNA489749 | ENA
Project description:<p>This project includes data derived from subjects enrolled in the BASIC3 (Baylor College of Medicine Advancing Sequencing in Childhood Cancer Care) study. BASIC3 is a National Genome Human Research Institute (NHGRI) and National Cancer Institute-funded Clinical Sequencing Exploratory Research (CSER) consortium project that focused on prospective implementation of clinical whole exome sequencing in the pediatric oncology clinic. The primary study objective were to integrate information from CLIA-certified germline and tumor exome sequencing into the care of newly diagnosed solid tumor patients at Texas Children's Cancer Center, and to perform parallel evaluation of the impact of tumor and germline exomes on families and physicians. </p> <p>Blood and frozen tumor (if available) samples were collected from children undergoing surgery or biopsy of newly diagnosed solid tumors and subjected to exome sequencing in a CLIA-certified laboratory. Germline and tumor (if applicable) exome sequencing reports were generated and submitted into the electronic health record and returned to each patient/family by their primary oncologist.</p> <p>In addition to the clinical exome sequencing, specific (optional) consent was requested for research sequencing studies. If this consent was obtained then research studies of some of the children and parents participating in the BASIC3 study (including tumor transcriptome and whole genome sequencing of blood and/or tumor) are performed.</p> <p><b>The Clinical Sequencing Exploratory Research Consortium Cohort is utilized in the following dbGaP sub-study.</b> To view molecular data, and derived variables collected in this sub-study, please click on the following sub-studies below or in the "Sub-study" box located on the right hand side of this top-level study page <a href="study.cgi?study_id=phs001683">phs001383</a> Clinical Sequencing Exploratory Research Consortium Cohort. <ul> <li><a href="study.cgi?study_id=phs001026">phs001026</a> BASIC3</li> <li><a href="study.cgi?study_id=phs001878">phs001878</a> GMKF BASIC3</li> </ul> </p>
| phs001683 | dbGaP
Project description:The Investigators will conduct a longitudinal, mixed-methods cohort study to assess primary and secondary psychosocial outcomes among 705 MyCode pediatric participants and their parents, and health behaviors of parents whose children receive an adult- or pediatric-onset genomic result. Data will be gathered via quantitative surveys using validated measures of distress, family functioning, quality of life, body image, perceived cancer/heart disease risk, genetic counseling satisfaction, genomics knowledge, and adjustment to genetic information; qualitative interviews with adolescents and parents; and electronic health records review of parents’ cascade testing uptake and initiation of risk reduction behaviors. The investigators will also conduct empirical and theoretical legal research to examine the loss of chance doctrine and its applicability to genomic research.
| 2296574 | ecrin-mdr-crc
Project description:CSER: Genomic Diagnosis in Children with Developmental Delay
| PRJNA315714 | ENA
Project description:CSER: The Use of Sequencing to Guide the Care of Cancer Patients
| PRJNA312991 | ENA
Project description:Genomic sequencing of Pediatric Rhabdomyosarcoma
| PRJNA238611 | ENA
Project description:Pediatric AML is an aggressive hematological malignancy associated with distinctive genomic features. We employed RNA-seq to study fusion genes and clinically relevant gene expression patterns in pediatric AML patients.
2023-05-02 | GSE222814 | GEO
Project description:Genomic Sequencing of Pediatric Rhabdoid Cancers
| PRJNA169040 | ENA
Project description:We determined whether we could identify clusters of children with critical asthma by plasma cytokine concentration. Differences in gene expression between the two clusters were analyzed using a targeted Nanostring immunology array. We performed a single-center, prospective, observational cohort study of 64 children ages 6 – 17 years admitted to a pediatric intensive care unit for an asthma attack between July 2019 to February 2021.
2022-07-15 | GSE208220 | GEO
Project description:Lymphoblastic lymphoma (LBL) is one of the most frequent occurring pediatric non-Hodgkin lymphomas. In the WHO classification scheme pediatric LBL is considered to be the same disease entity as pediatric acute lymphoblastic leukemia (ALL). However, it is unclear whether the genetic basis of pediatric LBL development is similar to that of pediatric ALL. We performed genome-wide analyses of copy number aberrations in 12 T-LBL and 7 precursor B-cell LBL pediatric cases using high-resolution SNP-based array CGH. Similar to what previously has been found in T-ALLs, T-LBLs exhibited recurrent deletions of the CDKN2A locus, occurring in 92% of the cases. Additionally, we detected deletions of RB1 (16%), duplications of MYB (16%) and an amplification of ABL1 in one case. These results show that, similar to T-ALL, the genomic alterations in T-LBL predominantly target genes involved in cell cycle progression. The majority of precursor B-cell LBLs was characterized by high-hyperdiploidy (71%), and showed high resemblance with high-hyperdiploid precursor B-cell ALLs. These results show that, similar to T-ALL, the genomic alterations in T-LBL predominantly target genes involved in cell cycle progression and that high-hyperdiploidy is a commen event in B-LBL. Taken together, our data suggest that pediatric LBLs and ALLs exhibit similar genomic abnormalities within confined immunophenotypic and cytogenetic subgroups, but that the representations of these subgroups differs between the two entities. Copy number detection was performed using CNAG2.0 software, Reference genomes are included in this data set Keywords: comparative genome hybridization
2009-02-01 | GSE12660 | GEO