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Data released on November 01, 2017

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

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 RIS BibTeX Text

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.

Contact Submitter

Additional information:

https://github.com/blekhmanlab/hominid

http://z.umn.edu/genemicrobe

Accessions (data not in GigaDB):

dbGAP: phs000228.v3.p1

Keywords:

microbiome host genetics association machine learning 

Software, Genomic

http://gigadb.org/images/data/cropped/100367.jpg

Funding:

  • Funding body - American Cancer Society
  • Award ID - 124166-IRG-58-001-55-IRG53
  • Awardee - R Blekhman
  • Funding body - Alfred P. Sloan Foundation
  • Awardee - R Blekhman
  • Funding body - The Randy Shaver Cancer Research and Community Fund
  • Awardee - R Blekhman

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File NameSample IDFile TypeFile FormatSizeRelease Date 
Tabular dataTSV122.64 KB2017-10-27
Tabular dataTSV75.5 KB2017-10-27
Tabular dataTSV107.56 KB2017-10-27
Tabular dataTSV127.77 KB2017-10-27
GitHub archivearchive25.61 MB2017-10-27
Tabular dataTSV187.9 KB2017-10-27
Tabular dataTSV114.18 KB2017-10-27
Tabular dataTSV116.18 KB2017-10-27
ReadmeTEXT2.46 KB2017-10-27
Tabular dataTSV167.63 KB2017-10-27
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