Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma Journal Article


Authors: Wrzeszczynski, K. O.; Frank, M. O.; Koyama, T.; Rhrissorrakrai, K.; Robine, N.; Utro, F.; Emde, A. K.; Chen, B. J.; Arora, K.; Shah, M.; Vacic, V.; Norel, R.; Bilal, E.; Bergmann, E. A.; Vogel, J. L. M.; Bruce, J. N.; Lassman, A. B.; Canoll, P.; Grommes, C.; Harvey, S.; Parida, L.; Michelini, V. V.; Zody, M. C.; Jobanputra, V.; Royyuru, A. K.; Darnell, R. B.
Article Title: Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma
Abstract: Objective: To analyze a glioblastoma tumor specimen with 3 different platforms and compare potentially actionable calls from each. Methods: Tumor DNA was analyzed by a commercial targeted panel. In addition, tumor-normal DNA was analyzed by whole-genome sequencing (WGS) and tumor RNA was analyzed by RNA sequencing (RNA-seq). The WGS and RNA-seq data were analyzed by a team of bioinformaticians and cancer oncologists, and separately by IBM Watson Genomic Analytics (WGA), an automated system for prioritizing somatic variants and identifying drugs. Results: More variants were identified by WGS/RNA analysis than by targeted panels. WGA completed a comparable analysis in a fraction of the time required by the human analysts. Conclusions: The development of an effective human-machine interface in the analysis of deep cancer genomic datasets may provide potentially clinically actionable calls for individual patients in a more timely and efficient manner than currently possible. ClinicalTrials.gov identifier: NCT02725684. Copyright © 2017 The Author(s).
Keywords: clinical article; controlled study; human tissue; aged; sequence analysis; single nucleotide polymorphism; case report; bevacizumab; cancer growth; treatment duration; cancer radiotherapy; temozolomide; nuclear magnetic resonance imaging; brain tumor; cancer diagnosis; gene targeting; computer assisted tomography; multiple cycle treatment; tumor volume; lomustine; rna; genome analysis; confusion; death; dna; glioblastoma; genomics; headache; tumor growth; tumor gene; dna determination; brain surgery; brain ventricle peritoneum shunt; rna sequence; parietal lobe; deterioration; drug identification; walking difficulty; oncologist; indel mutation; human; male; priority journal; article; whole genome sequencing; agnosia; watson genomic analytics
Journal Title: Neurology-Genetics
Volume: 3
Issue: 4
ISSN: 2376-7839
Publisher: Lippincott Williams & Wilkins  
Date Published: 2017-08-01
Start Page: e164
Language: English
DOI: 10.1212/nxg.0000000000000164
PROVIDER: scopus
PMCID: PMC5506390
PUBMED: 28740869
DOI/URL:
Notes: Article -- Export Date: 1 October 2018 -- Source: Scopus
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  1. Christian Grommes
    126 Grommes