Title |
Clinical targeted exome-based sequencing in combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors
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Published in |
Neuro-Oncology, January 2017
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DOI | 10.1093/neuonc/now294 |
Pubmed ID | |
Authors |
Shakti H Ramkissoon, Pratiti Bandopadhayay, Jaeho Hwang, Lori A Ramkissoon, Noah F Greenwald, Steven E Schumacher, Ryan O'Rourke, Nathan Pinches, Patricia Ho, Hayley Malkin, Claire Sinai, Mariella Filbin, Ashley Plant, Wenya Linda Bi, Michael S Chang, Edward Yang, Karen D Wright, Peter E Manley, Matthew Ducar, Sanda Alexandrescu, Hart Lidov, Ivana Delalle, Liliana C Goumnerova, Alanna J Church, Katherine A Janeway, Marian H Harris, Laura E MacConaill, Rebecca D Folkerth, Neal I Lindeman, Charles D Stiles, Mark W Kieran, Azra H Ligon, Sandro Santagata, Adrian M Dubuc, Susan N Chi, Rameen Beroukhim, Keith L Ligon |
Abstract |
Clinical genomics platforms are needed to identify targetable alterations, but implementation of these technologies and best practices in routine clinical pediatric oncology practice are not yet well established. Profile is an institution-wide prospective clinical research initiative that uses targeted sequencing to identify targetable alterations in tumors. OncoPanel, a multiplexed targeted exome-sequencing platform that includes 300 cancer-causing genes, was used to assess single nucleotide variants and rearrangements/indels. Alterations were annotated (Tiers 1-4) based on clinical significance, with Tier 1 alterations having well-established clinical utility. OncoCopy, a clinical genome-wide array comparative genomic hybridization (aCGH) assay, was also performed to evaluate copy number alterations and better define rearrangement breakpoints. Cancer genomes of 203 pediatric brain tumors were profiled across histological subtypes, including 117 samples analyzed by OncoPanel, 146 by OncoCopy, and 60 tumors subjected to both methodologies. OncoPanel revealed clinically relevant alterations in 56% of patients (44 cancer mutations and 20 rearrangements), including BRAF alterations that directed the use of targeted inhibitors. Rearrangements in MYB-QKI, MYBL1, BRAF, and FGFR1 were also detected. Furthermore, while copy number profiles differed across histologies, the combined use of OncoPanel and OncoCopy identified subgroup-specific alterations in 89% (17/19) of medulloblastomas. The combination of OncoPanel and OncoCopy multiplex genomic assays can identify critical diagnostic, prognostic, and treatment-relevant alterations and represents an effective precision medicine approach for clinical evaluation of pediatric brain tumors. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 6 | 43% |
Kuwait | 1 | 7% |
Montenegro | 1 | 7% |
Ireland | 1 | 7% |
United Kingdom | 1 | 7% |
Unknown | 4 | 29% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 6 | 43% |
Members of the public | 4 | 29% |
Practitioners (doctors, other healthcare professionals) | 3 | 21% |
Science communicators (journalists, bloggers, editors) | 1 | 7% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United Kingdom | 1 | 1% |
Unknown | 75 | 99% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 12 | 16% |
Other | 10 | 13% |
Student > Ph. D. Student | 9 | 12% |
Student > Master | 9 | 12% |
Student > Bachelor | 5 | 7% |
Other | 15 | 20% |
Unknown | 16 | 21% |
Readers by discipline | Count | As % |
---|---|---|
Medicine and Dentistry | 24 | 32% |
Biochemistry, Genetics and Molecular Biology | 14 | 18% |
Agricultural and Biological Sciences | 10 | 13% |
Computer Science | 3 | 4% |
Neuroscience | 3 | 4% |
Other | 7 | 9% |
Unknown | 15 | 20% |