scholarly journals Clinical targeted exome-based sequencing in combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors

2017 ◽  
pp. now294 ◽  
Author(s):  
Shakti H. Ramkissoon ◽  
Pratiti Bandopadhayay ◽  
Jaeho Hwang ◽  
Lori A. Ramkissoon ◽  
Noah F. Greenwald ◽  
...  
Keyword(s):  
Brain Tumors ◽  
Precision Medicine ◽  
Copy Number ◽  
Pediatric Brain Tumors ◽  
Genome Wide ◽  
Medicine Analysis ◽  
Pediatric Brain

scholarly journals GENE-09. PRECISION MEDICINE ANALYSIS OF 203 PEDIATRIC BRAIN TUMORS REVEALS CLINICALLY RELEVANT GENOMIC ALTERATIONS

2017 ◽  
Vol 19 (suppl_4) ◽  
pp. iv20-iv20 ◽  
Author(s):  
Pratiti Bandopadhayay ◽  
Shakti Ramkissoon ◽  
Jaeho Hwang ◽  
Lori Ramkissoon ◽  
Noah Greenwald ◽  
...  
Keyword(s):  
Brain Tumors ◽  
Precision Medicine ◽  
Pediatric Brain Tumors ◽  
Genomic Alterations ◽  
Medicine Analysis ◽  
Pediatric Brain

scholarly journals EPT-20CLINICAL TARGETED EXOME-BASED SEQUENCING IN COMBINATION WITH GENOME WIDE COPY NUMBER PROFILING: A CLIA CERTIFIED APPROACH FOR PRECISION MEDICINE IN 203 PEDIATRIC BRAIN TUMOR PATIENTS

2016 ◽  
Vol 18 (suppl 3) ◽  
pp. iii28.2-iii28 ◽  
Author(s):  
Pratiti Bandopadhayay ◽  
Shakti Ramkissoon ◽  
Jaeho Hwang ◽  
Lori Ramkissoon ◽  
Adrian Dubuc ◽  
...  
Keyword(s):  
Brain Tumor ◽  
Precision Medicine ◽  
Copy Number ◽  
Pediatric Brain Tumor ◽  
Tumor Patients ◽  
Genome Wide ◽  
Pediatric Brain

Clinical Application of Whole Genome Array Improves the Diagnosis of Pediatric Brain Tumors

2017 ◽  
Vol 25 (8) ◽  
pp. 688-695 ◽  
Author(s):  
Lina Shao ◽  
Sue Miller ◽  
Carl Koschmann ◽  
Sandra Camelo-Piragua
Keyword(s):  
High Resolution ◽  
Brain Tumors ◽  
Copy Number ◽  
Essential Role ◽  
Pediatric Brain Tumors ◽  
Whole Genome ◽  
Diagnosis And Prognosis ◽  
Genetic Abnormalities ◽  
Genome Array ◽  
Pediatric Brain

Pediatric brain tumors are the leading cause of childhood cancer mortality. Recurring genetic abnormalities play an essential role in the diagnosis and prognosis of pediatric brain tumors. However, clinical workup has not routinely included whole genome assessment. Here, we present high resolution whole genome array results in 11 pediatric brain tumors. Array identified clinically relevant abnormalities in all samples. Copy number aberrations with targeted therapy implication, GOPC-ROS1 fusion, CDK4 amplification, and NF1 deletion, were detected in 3 cases. In addition, array detected recurring genetic abnormalities, including KIAA1549-BRAF fusion, 19q13.42 amplification, i(17q), and monosomy 6, which assisted accurate histological diagnosis in pediatric brain tumors. In conclusion, our results show that whole genome high-resolution array detects diagnostic and treatment-relevant copy number abnormalities in pediatric brain tumors.

scholarly journals Blood-brain barrier–adapted precision medicine therapy for pediatric brain tumors

2017 ◽  
Vol 188 ◽  
pp. 27.e1-27.e14 ◽  
Author(s):  
Bernard L. Marini ◽  
Lydia L. Benitez ◽  
Andrew H. Zureick ◽  
Ralph Salloum ◽  
Angela C. Gauthier ◽  
...  
Keyword(s):  
Brain Tumors ◽  
Precision Medicine ◽  
Blood Brain Barrier ◽  
Pediatric Brain Tumors ◽  
Brain Barrier ◽  
Blood Brain ◽  
Pediatric Brain

scholarly journals A pediatric brain tumor atlas of genes deregulated by somatic genomic rearrangement

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yiqun Zhang ◽  
Fengju Chen ◽  
Lawrence A. Donehower ◽  
Michael E. Scheurer ◽  
Chad J. Creighton
Keyword(s):  
Brain Tumor ◽  
Brain Tumors ◽  
Tyrosine Kinases ◽  
Pediatric Brain Tumor ◽  
Pediatric Brain Tumors ◽  
Altered Expression ◽  
Critical Pathways ◽  
Cis Regulation ◽  
Or Gene ◽  
Pediatric Brain

AbstractThe global impact of somatic structural variants (SSVs) on gene expression in pediatric brain tumors has not been thoroughly characterised. Here, using whole-genome and RNA sequencing from 854 tumors of more than 30 different types from the Children’s Brain Tumor Tissue Consortium, we report the altered expression of hundreds of genes in association with the presence of nearby SSV breakpoints. SSV-mediated expression changes involve gene fusions, altered cis-regulation, or gene disruption. SSVs considerably extend the numbers of patients with tumors somatically altered for critical pathways, including receptor tyrosine kinases (KRAS, MET, EGFR, NF1), Rb pathway (CDK4), TERT, MYC family (MYC, MYCN, MYB), and HIPPO (NF2). Compared to initial tumors, progressive or recurrent tumors involve a distinct set of SSV-gene associations. High overall SSV burden associates with TP53 mutations, histone H3.3 gene H3F3C mutations, and the transcription of DNA damage response genes. Compared to adult cancers, pediatric brain tumors would involve a different set of genes with SSV-altered cis-regulation. Our comprehensive and pan-histology genomic analyses reveal SSVs to play a major role in shaping the transcriptome of pediatric brain tumors.

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