Metagenomic biomarker discovery and explanation |
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| Authors: | Nicola Segata Jacques Izard Levi Waldron Dirk Gevers Larisa Miropolsky Wendy S Garrett Curtis Huttenhower |
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| Institution: | (1) Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA;(2) Department of Molecular Genetics, The Forsyth Institute, 245 First Street, Cambridge, MA 02142, USA;(3) Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, 188 Longwood Ave, Boston, MA 02115, USA;(4) Microbial Sequencing Center, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA;(5) Department of Immunology and Infectious Diseases, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA;(6) Department of Medicine, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA;(7) Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Kragujevac, MA 02215, USA |
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| 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
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