GigaScience
GigaScience
5 years ago

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

Sayan Mukherjee, Margaret Sands, Evan Tang, Joanna Sands, Joshua Lynch, Ran Blekhman, Dan Knights, Karen Tang, Sambhawa Priya
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 taxonomic 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.

Publisher URL: http://doi.org/10.1093/gigascience/gix107

DOI: 10.1093/gigascience/gix107

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