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06 April 2023
Article (Scientific journals)
Results and Lessons Learned from the sbv IMPROVER Metagenomics Diagnostics for Inflammatory Bowel Disease Challenge
Khachatryan, Lusine; Xiang, Yang; Ivanov, Artem et al.
2023In Scientific Reports, in press
Peer reviewed


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The original publication is available at: https://doi.org/10.1038/s41598-023-33050-0

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Keywords :
Gut microbiota; Inflammatory bowel disease; Metagenomics; Non-invasive diagnostics; Diagnosis; Crohn's Disease; Ulcerative Colitis; classification; supervised; machine learning
Abstract :
[en] A growing body of evidence links gut microbiota changes with inflammatory bowel disease (IBD), raising the potential benefit of exploiting metagenomics data for non-invasive IBD diagnostics. The sbv IMPROVER Metagenomics Diagnosis for Inflammatory Bowel Disease Challenge (MEDIC) investigated computational metagenomics methods for discriminating IBD and nonIBD subjects. Participants in this challenge were given independent training and test metagenomics data from IBD and nonIBD subjects, which could be wither either raw read data (sub-challenge 1, SC1) or processed taxonomy- and function-based profiles (sub-challenge 2, SC2). A total of 81 anonymized submissions were received between September 2019 and March 2020. Most participants’ predictions performed better than random predictions in classifying IBD vs nonIBD, Ulcerative Colitis (UC) vs nonIBD, and Crohn’s Disease (CD) vs nonIBD. However, discrimination between UC and CD remains challenging, with the classification quality similar to the set of random predictions. We analyzed the class prediction accuracy, the metagenomics features by the teams, and computational methods used. These results will be openly shared with the scientific community to help advance IBD research and illustrate the application of a range of computational methodologies for effective metagenomic classification.
Research center :
- Luxembourg Centre for Systems Biomedicine (LCSB): Biomedical Data Science (Glaab Group)
Disciplines :
Life sciences: Multidisciplinary, general & others
Human health sciences: Multidisciplinary, general & others
Immunology & infectious disease
Author, co-author :
Khachatryan, Lusine
Xiang, Yang
Ivanov, Artem
Glaab, Enrico ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Biomedical Data Science
Graham, Garrett
Granata, Ilaria
Giordano, Maurizio
Maddalena, Lucia
Piccirillo, Marina
Manipur, Ichcha
Baruzzo, Giacomo
Cappellato, Marco
Avot, Batiste
Stan, Adrian
Battey, James
Lo Sasso, Giuseppe
Boue, Stephanie
Ivanov, Nikolai V.
Peitsch, Manuel C.
Hoeng, Julia
Falquet, Laurent
Di Camillo, Barbara
Guarracino, Mario
Ulyantsev, Vladimir
Sierro, Nicolas
Poussin, Carine
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External co-authors :
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Title :
Results and Lessons Learned from the sbv IMPROVER Metagenomics Diagnostics for Inflammatory Bowel Disease Challenge
Publication date :
Journal title :
Scientific Reports
Publisher :
Nature Publishing Group
Volume :
in press
Peer reviewed :
Peer reviewed
Focus Area :
Systems Biomedicine


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