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Research Article

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data

  • Alexander R. Macalalad,

    Affiliations: Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America, Department of Biostatistics, Harvard University, Boston, Massachusetts, United States of America

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  • Michael C. Zody,

    Affiliation: Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America

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  • Patrick Charlebois,

    Affiliation: Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America

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  • Niall J. Lennon,

    Affiliation: Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America

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  • Ruchi M. Newman,

    Affiliation: Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America

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  • Christine M. Malboeuf,

    Affiliation: Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America

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  • Elizabeth M. Ryan,

    Affiliation: Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America

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  • Christian L. Boutwell,

    Affiliation: Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

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  • Karen A. Power,

    Affiliation: Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

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  • Doug E. Brackney,

    Affiliation: Department of Pathology, University of New Mexico School of Medicine, Albuquerque, New Mexico, United States of America

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  • Kendra N. Pesko,

    Affiliation: Department of Pathology, University of New Mexico School of Medicine, Albuquerque, New Mexico, United States of America

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  • Joshua Z. Levin,

    Affiliation: Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America

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  • Gregory D. Ebel,

    Affiliation: Department of Pathology, University of New Mexico School of Medicine, Albuquerque, New Mexico, United States of America

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  • Todd M. Allen,

    Affiliation: Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America

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  • Bruce W. Birren,

    Affiliation: Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America

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  • Matthew R. Henn mail

    mhenn@broadinstitute.org

    Affiliation: Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America

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  • Published: March 15, 2012
  • DOI: 10.1371/journal.pcbi.1002417

About the Authors

Alexander R. Macalalad, Michael C. Zody, Patrick Charlebois, Niall J. Lennon, Ruchi M. Newman, Christine M. Malboeuf, Elizabeth M. Ryan, Joshua Z. Levin, Bruce W. Birren, Matthew R. Henn
Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
Alexander R. Macalalad
Department of Biostatistics, Harvard University, Boston, Massachusetts, United States of America
Christian L. Boutwell, Karen A. Power, Todd M. Allen
Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
Doug E. Brackney, Kendra N. Pesko, Gregory D. Ebel
Department of Pathology, University of New Mexico School of Medicine, Albuquerque, New Mexico, United States of America

Corresponding Author

Email: mhenn@broadinstitute.org

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: ARM MRH. Performed the experiments: ARM MCZ PC MRH. Analyzed the data: ARM MCZ PC TMA MRH. Contributed reagents/materials/analysis tools: ARM MCZ PC NJL RMN CMM EMR CLB KAP DEB KNP JZL GDE TMA BWB MRH. Wrote the paper: ARM MCZ MRH.