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HOMINID: A framework for identifying associations between host genetic variation and microbiome composition

Joshua Lynch, Karen Tang, Sambhawa Priya, Joanna Sands, Margaret Sands, Evan Tang, Sayan Mukherjee, Dan Knights, Ran Blekhman
doi: https://doi.org/10.1101/081323
Joshua Lynch
1Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
2Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
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Karen Tang
1Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
2Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
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Sambhawa Priya
1Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
2Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
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Joanna Sands
1Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
2Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
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Margaret Sands
1Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
2Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
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Evan Tang
1Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
2Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
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Sayan Mukherjee
3Departments of Statistical Science, Mathematics, and Computer Science, Duke University, Durham, NC, USA
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Dan Knights
4Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
5Biotechnology Institute, University of Minnesota, Minneapolis, MN, USA
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  • For correspondence: blekhman@umn.edu dknights@umn.edu
Ran Blekhman
1Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
2Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
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  • For correspondence: blekhman@umn.edu dknights@umn.edu
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Abstract

Recent studies have uncovered a strong effect of host genetic variation on the composition of host-associated microbiota. Here, we present HOMINID, a computational approach based on Lasso linear regression, that given host genetic variation and microbiome composition data, identifies host SNPs that are correlated with microbial taxa abundances. Using simulated data we show that HOMINID has accuracy in identifying associated SNPs, and performs better compared to existing methods. We also show that HOMINID can accurately identify the microbial taxa that are correlated with associated SNPs. Lastly, by using HOMINID on real data of human genetic variation and microbiome composition, we identified 13 human SNPs in which genetic variation is correlated with microbiome taxonomic composition across body sites. In conclusion, HOMINID is a powerful method to detect host genetic variants linked to microbiome composition, and can facilitate discovery of mechanisms controlling host-microbiome interactions.

Availability and implementation Software, code, tutorial, installation and setup details, and synthetic data are available in the project homepage: https://github.com/blekhmanlab/hominid.

Real dataset used here is from Blekhman et al. (Blekhman et al. 2015); 16S rRNA gene sequence data and OTU tables are available on the HMP DACC website (www.hmpdacc.org), and host genetic data are deposited in dbGaP under project number phs000228.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 21, 2017.
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HOMINID: A framework for identifying associations between host genetic variation and microbiome composition
Joshua Lynch, Karen Tang, Sambhawa Priya, Joanna Sands, Margaret Sands, Evan Tang, Sayan Mukherjee, Dan Knights, Ran Blekhman
bioRxiv 081323; doi: https://doi.org/10.1101/081323
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HOMINID: A framework for identifying associations between host genetic variation and microbiome composition
Joshua Lynch, Karen Tang, Sambhawa Priya, Joanna Sands, Margaret Sands, Evan Tang, Sayan Mukherjee, Dan Knights, Ran Blekhman
bioRxiv 081323; doi: https://doi.org/10.1101/081323

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