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

Dataset type: Software, Genomic
Data released on November 01, 2017

Lynch J; Tang K; Priya S; Sands J; Sands M; Tang E; Mukherjee S; Knights D; Blekhman R (2017): Supporting data for "HOMINID: A framework for identifying associations between host genetic variation and microbiome composition" GigaScience Database. http://dx.doi.org/10.5524/100367

DOI10.5524/100367

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.

Additional details

Read the peer-reviewed publication(s):

Lynch, J., Tang, K., Priya, S., Sands, J., Sands, M., Tang, E., … Blekhman, R. (2017). HOMINID: a framework for identifying associations between host genetic variation and microbiome composition. GigaScience, 6(12), 1–7. doi:10.1093/gigascience/gix107

Additional information:

https://github.com/blekhmanlab/hominid

http://z.umn.edu/genemicrobe

Accessions (data not in GigaDB):

dbGAP: phs000228.v3.p1





File NameSample IDData TypeFile FormatSizeRelease Date 
Tabular dataTSV119.84 KB2017-10-27
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Tabular dataTSV119.13 KB2017-10-27
Tabular dataTSV119.13 KB2017-10-27
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Funding body Awardee Award ID Comments
American Cancer Society R Blekhman 124166-IRG-58-001-55-IRG53
Alfred P. Sloan Foundation R Blekhman
The Randy Shaver Cancer Research and Community Fund R Blekhman
Date Action
November 1, 2017 Dataset publish
January 9, 2018 Manuscript Link added : 10.1093/gigascience/gix107