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Research Article

Convergence of Mutation and Epigenetic Alterations Identifies Common Genes in Cancer That Predict for Poor Prognosis

  • Timothy A Chan,

    Affiliations: Cancer Biology Program, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America, Department of Radiation Oncology and Molecular Radiation Sciences, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America

    ¤ Current address: Human Oncology and Pathogenesis Program and Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America

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  • Sabine Glockner,

    Affiliations: Cancer Biology Program, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America, Department of Surgery, Johns Hopkins Hospital, Baltimore, Maryland, United States of America

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  • Joo Mi Yi,

    Affiliation: Cancer Biology Program, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America

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  • Wei Chen,

    Affiliations: Cancer Biology Program, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America, Predoctoral Training Program in Human Genetics, The Johns Hopkins University, Baltimore, Maryland, United States of America

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  • Leander Van Neste,

    Affiliation: Department of Molecular Biotechnology, Ghent University, Ghent, Belgium

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  • Leslie Cope,

    Affiliation: Biometry and Clinical Trials Division, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America

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  • James G Herman,

    Affiliation: Cancer Biology Program, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America

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  • Victor Velculescu,

    Affiliations: Ludwig Center for Cancer Genetics and Therapeutics, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America, Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America

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  • Kornel E Schuebel mail,

    To whom correspondence should be addressed. E-mail: sbaylin@jhmi.edu (SBB); kornels@jhmi.edu (KES); nahuja@jhmi.ed (NA)

    Affiliation: Cancer Biology Program, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America

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  • Nita Ahuja mail,

    To whom correspondence should be addressed. E-mail: sbaylin@jhmi.edu (SBB); kornels@jhmi.edu (KES); nahuja@jhmi.ed (NA)

    Affiliations: Cancer Biology Program, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America, Department of Surgery, Johns Hopkins Hospital, Baltimore, Maryland, United States of America

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  • Stephen B Baylin mail

    To whom correspondence should be addressed. E-mail: sbaylin@jhmi.edu (SBB); kornels@jhmi.edu (KES); nahuja@jhmi.ed (NA)

    Affiliations: Cancer Biology Program, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America, Predoctoral Training Program in Human Genetics, The Johns Hopkins University, Baltimore, Maryland, United States of America

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  • Published: May 27, 2008
  • DOI: 10.1371/journal.pmed.0050114

About the Authors

Timothy A Chan, Sabine Glockner, Joo Mi Yi, Wei Chen, James G Herman, Kornel E Schuebel, Nita Ahuja, Stephen B Baylin
Cancer Biology Program, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America
Timothy A Chan
Department of Radiation Oncology and Molecular Radiation Sciences, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America
Sabine Glockner, Nita Ahuja
Department of Surgery, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
Wei Chen, Stephen B Baylin
Predoctoral Training Program in Human Genetics, The Johns Hopkins University, Baltimore, Maryland, United States of America
Leander Van Neste
Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
Leslie Cope
Biometry and Clinical Trials Division, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America
Victor Velculescu
Ludwig Center for Cancer Genetics and Therapeutics, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America
Victor Velculescu
Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, United States of America

Corresponding Authors

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

TAC and SBB designed the study. TAC and SG performed the experiments for the study. TAC, VV, KES, and SBB analyzed the data and interpreted the results. TAC, WC, LVN, LC, and JGH contributed bioinformatics and statistical analysis to the research effort. TAC and SBB wrote the manuscript. NA enrolled patients and helped analyze the clinical outcomes data. JMY performed a portion of the bisulfite sequencing analysis of the common target.