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Metagenomic biomarker discovery and explanation

Nicola Segata1, Jacques Izard23, Levi Waldron1, Dirk Gevers4, Larisa Miropolsky1, Wendy S Garrett567 and Curtis Huttenhower1*

Author Affiliations

1 Department of Biostatistics, 677 Huntington Avenue, Harvard School of Public Health, Boston, MA 02115, USA

2 Department of Molecular Genetics, 245 First Street, The Forsyth Institute, Cambridge, MA 02142, USA

3 Department of Oral Medicine, Infection and Immunity, 188 Longwood Ave, Harvard School of Dental Medicine, Boston, MA 02115, USA

4 Microbial Sequencing Center, 7 Cambridge Center, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

5 Department of Immunology and Infectious Diseases, 665 Huntington Avenue, Harvard School of Public Health, Boston, MA 02115, USA

6 Department of Medicine, 75 Francis Street, Harvard Medical School, Boston, MA 02115, USA

7 Department of Medical Oncology, 44 Binney Street, Dana-Farber Cancer Institute, MA 02215, USA

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Genome Biology 2011, 12:R60  doi:10.1186/gb-2011-12-6-r60

Published: 24 June 2011

Abstract

This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/ webcite.