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Research Article

Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions

  • Soumya Raychaudhuri mail,

    soumya@broad.mit.edu (SR); mjdaly@broad.mit.edu (MJD)

    Affiliations: Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America

    X
  • Robert M. Plenge,

    Affiliations: Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America, Harvard Medical School – Partners HealthCare Center for Genetics and Genomics, Boston, Massachusetts, United States of America

    X
  • Elizabeth J. Rossin,

    Affiliations: Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America, Harvard-MIT Health Sciences and Technology, Cambridge, Massachusetts, United States of America

    X
  • Aylwin C. Y. Ng,

    Affiliations: Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America, Gastroenterology Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America

    X
  • International Schizophrenia Consortium,
  • Shaun M. Purcell,

    Affiliations: Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America

    X
  • Pamela Sklar,

    Affiliations: Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America

    X
  • Edward M. Scolnick,

    Affiliations: Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America

    X
  • Ramnik J. Xavier,

    Affiliations: Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America, Gastroenterology Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America

    X
  • David Altshuler,

    Affiliations: Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America, Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America, Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America

    X
  • Mark J. Daly mail

    soumya@broad.mit.edu (SR); mjdaly@broad.mit.edu (MJD)

    Affiliations: Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America

    X
  • Published: June 26, 2009
  • DOI: 10.1371/journal.pgen.1000534

About the Authors

Soumya Raychaudhuri, Robert M. Plenge, Elizabeth J. Rossin, David Altshuler, Mark J. Daly
Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
Soumya Raychaudhuri, Elizabeth J. Rossin, Shaun M. Purcell, Pamela Sklar, Edward M. Scolnick, David Altshuler, Mark J. Daly
Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
Soumya Raychaudhuri, Robert M. Plenge
Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
Robert M. Plenge
Harvard Medical School – Partners HealthCare Center for Genetics and Genomics, Boston, Massachusetts, United States of America
Elizabeth J. Rossin
Harvard-MIT Health Sciences and Technology, Cambridge, Massachusetts, United States of America
Aylwin C. Y. Ng, Ramnik J. Xavier
Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
Aylwin C. Y. Ng, Ramnik J. Xavier
Gastroenterology Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
Shaun M. Purcell, Pamela Sklar, Edward M. Scolnick
Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
Shaun M. Purcell, Pamela Sklar
Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
Pamela Sklar, Edward M. Scolnick
Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America
David Altshuler
Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
David Altshuler
Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
David Altshuler
Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America

Corresponding Authors

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: SR RMP EJR SMP PS DA MJD. Performed the experiments: SR EJR ACYN International Schizophrenia Consortium. Analyzed the data: SR ACYN EMS RJX MJD. Contributed reagents/materials/analysis tools: SR International Schizophrenia Consortium EMS DA MJD. Wrote the paper: SR RMP EJR ACYN SMP PS EMS RJX DA MJD. Critically read and contributed to the final manuscript: SR RMP SJR ACYN SMP PS EMS RJX DA MJD.