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August 2017; 3 (4) ArticleOpen Access

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

Kazimierz O. Wrzeszczynski, Mayu O. Frank, Takahiko Koyama, Kahn Rhrissorrakrai, Nicolas Robine, Filippo Utro, Anne-Katrin Emde, Bo-Juen Chen, Kanika Arora, Minita Shah, Vladimir Vacic, Raquel Norel, Erhan Bilal, Ewa A. Bergmann, Julia L. Moore Vogel, Jeffrey N. Bruce, Andrew B. Lassman, Peter Canoll, Christian Grommes, Steve Harvey, Laxmi Parida, Vanessa V. Michelini, Michael C. Zody, Vaidehi Jobanputra, Ajay K. Royyuru, Robert B. Darnell
First published July 11, 2017, DOI: https://doi.org/10.1212/NXG.0000000000000164
Kazimierz O. Wrzeszczynski
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Mayu O. Frank
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
NP, MS
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Takahiko Koyama
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Kahn Rhrissorrakrai
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Nicolas Robine
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Filippo Utro
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Anne-Katrin Emde
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Bo-Juen Chen
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Kanika Arora
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Minita Shah
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Vladimir Vacic
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Raquel Norel
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Erhan Bilal
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Ewa A. Bergmann
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Julia L. Moore Vogel
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Jeffrey N. Bruce
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Andrew B. Lassman
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Peter Canoll
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Christian Grommes
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Steve Harvey
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Laxmi Parida
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Vanessa V. Michelini
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
BS
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Michael C. Zody
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Vaidehi Jobanputra
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Ajay K. Royyuru
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Robert B. Darnell
From the New York Genome Center (K.O.W., M.O.F., N.R., A.-K.E., B.-J.C., K.A., M.S., V.V., E.A.B., J.L.M.V., M.C.Z., V.J., R.B.D.); IBM Thomas J. Watson Research Center (T.K., K.R., F.U., R.N., E.B., L.P., A.K.R.); Columbia University Medical Center (J.N.B., A.B.L., P.C., V.J.); Memorial Sloan-Kettering Cancer Center (C.G.), New York, NY; IBM Watson Health (S.H., V.V.M.), Boca Raton, FL; Laboratory of Molecular Neuro-Oncology (M.O.F., R.B.D.), and Howard Hughes Medical Institute (R.B.D.), The Rockefeller University, New York, NY. B.-J.C. is currently affiliated with Google, New York, NY. V.V. is currently affiliated with 23andMe, Inc., Mountain View, CA. E.A.B. is currently affiliated with Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Full PDF
Citation
Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma
Kazimierz O. Wrzeszczynski, Mayu O. Frank, Takahiko Koyama, Kahn Rhrissorrakrai, Nicolas Robine, Filippo Utro, Anne-Katrin Emde, Bo-Juen Chen, Kanika Arora, Minita Shah, Vladimir Vacic, Raquel Norel, Erhan Bilal, Ewa A. Bergmann, Julia L. Moore Vogel, Jeffrey N. Bruce, Andrew B. Lassman, Peter Canoll, Christian Grommes, Steve Harvey, Laxmi Parida, Vanessa V. Michelini, Michael C. Zody, Vaidehi Jobanputra, Ajay K. Royyuru, Robert B. Darnell
Neurol Genet Aug 2017, 3 (4) e164; DOI: 10.1212/NXG.0000000000000164

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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.

GLOSSARY

CNV=
copy number variant;
EGFR=
epidermal growth factor receptor;
GATK=
Genome Analysis Toolkit;
GBM=
glioblastoma;
IRB=
institutional review board;
NLP=
Natural Language Processing;
NYGC=
New York Genome Center;
RNA-seq=
RNA sequencing;
SNV=
single nucleotide variant;
SV=
structural variant;
TCGA=
The Cancer Genome Atlas;
TPM=
transcripts per million;
VCF=
variant call file;
VUS=
variants of uncertain significance;
WGA=
Watson Genomic Analytics;
WGS=
whole-genome sequencing

Footnotes

  • ↵* These authors contributed equally to the manuscript.

  • Funding information and disclosures are provided at the end of the article. Go to Neurology.org/ng for full disclosure forms. The Article Processing Charge was funded by the authors.

  • Supplemental data at Neurology.org/ng

  • Received December 12, 2016.
  • Accepted in final form April 19, 2017.
  • Copyright © 2017 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.

This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND), which permits downloading and sharing the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal.

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