NDLI: ASSESSING THE UTILITY OF CLINICAL TUMOR SEQUENCING IN THE PEDIATRIC NEURO-ONCOLOGY CLINIC

Content Provider	PubMed Central
Author	Parsons, D. Williams Roy, Angshumoy Monzon, Federico A. López-terrada, Dolores H. Chintagumpala, Murali M. Berg, Stacey L. Hilsenbeck, Susan G. Wang, Tao Adesina, Adekunle M. Li, Xiao-nan Kerstein, Robin A. Scollon, Sarah Bergstrom, Katie Street, Richard L. Mccullough, Laurence B. Mcguire, Amy L. Ramamurthy, Uma Wheeler, David A. Eng, Christine M. Yang, Yaping Reid, Jeff G. Muzny, Donna M. Gibbs, Richard A. Plon, Sharon E.
Copyright Year	2014
Abstract	BACKGROUND: Additional insight into the molecular alterations driving pediatric central nervous system (CNS) tumors is urgently needed, given the significant morbidity and mortality associated with these cancers and the relative paucity of effective chemotherapeutic options. Advances in sequencing technologies now allow for provision of genome-scale data to oncologists caring for pediatric cancer patients but current experience with the clinical application of genomic sequencing is limited. The goal of the BASIC3 (Baylor Advancing Sequencing into Childhood Cancer Care) study is to determine the clinical impact of incorporating CLIA-certified tumor and constitutional whole exome sequencing (WES) into the care of children with newly diagnosed solid tumors. METHODS: The study follows pediatric patients with newly diagnosed CNS and non-CNS solid tumors (target enrollment n = 280) at Texas Children's Cancer Center for two years after performing CLIA-certified whole exome sequencing (WES) of blood and frozen tumor samples. Results are deposited into the electronic medical record and disclosed to families by their oncologist and a genetic counselor. The potential impact of tumor exome findings on clinical decision-making is assessed through review of the medical record and through surveys of the oncologists regarding prioritization of treatment options in the hypothetical event of tumor recurrence. RESULTS: To date, 133 subjects have been enrolled, including 47 patients with CNS tumors (35%) comprising a diverse representation of diagnoses. Despite limited diagnostic biopsies in many patients, tumor samples adequate for WES were obtained from 33/47 (70%) patients. Tumor WES results have been reported for the first 22 CNS tumors, revealing a median of 7 (range of 0 to 25) protein-altering mutations per tumor, including alterations of known cancer genes such as ARID1A, SMARCA4, BRAF, CTNNB1, DDX3X, NF2, FANCA, and NOTCH3. Notably, 12/22 (55%) tumors were found to harbour mutations only in genes not known to be recurrently altered in human cancers. CONCLUSIONS: These results demonstrate the feasibility of routine tumor WES in the pediatric neuro- oncology clinic. Potentially clinically-relevant mutations can be identified in a substantial proportion of patients but early results suggest that integration of parallel genomic technologies (e.g. RNAseq) to identify genetic alterations not detectable by WES will be necessary; such studies are ongoing. Orthotopic xenograft models and cell lines are being established to allow in vitro and in vivo analysis of tumors containing alterations of interest. Data further assessing the clinical utility of the tumor exomes are under study. Supported by NHGRI/NCI 1U01HG006485. SECONDARY CATEGORY: Neuropathology & Tumor Biomarkers.
Related Links	http://dx.doi.org/10.1093/neuonc/nou208.5
Starting Page	24
File Format	PDF
ISSN	15235866
e-ISSN	15235866
Journal	Neuro-Oncology
Issue Number	Suppl 3
Volume Number	16
Language	English
Publisher	Oxford University Press
Publisher Date	2014-07-01
Access Restriction	Open
Rights Holder	Oxford University Press
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Cancer Research Neurology (clinical) Oncology

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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