Fast and accurate exhaustive higher-order epistasis search with BitEpi.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
05 08 2021
05 08 2021
Historique:
received:
19
03
2021
accepted:
20
07
2021
entrez:
6
8
2021
pubmed:
7
8
2021
medline:
7
8
2021
Statut:
epublish
Résumé
Complex genetic diseases may be modulated by a large number of epistatic interactions affecting a polygenic phenotype. Identifying these interactions is difficult due to computational complexity, especially in the case of higher-order interactions where more than two genomic variants are involved. In this paper, we present BitEpi, a fast and accurate method to test all possible combinations of up to four bi-allelic variants (i.e. Single Nucleotide Variant or SNV for short). BitEpi introduces a novel bitwise algorithm that is 1.7 and 56 times faster for 3-SNV and 4-SNV search, than established software. The novel entropy statistic used in BitEpi is 44% more accurate to identify interactive SNVs, incorporating a p-value-based significance testing. We demonstrate BitEpi on real world data of 4900 samples and 87,000 SNPs. We also present EpiExplorer to visualize the potentially large number of individual and interacting SNVs in an interactive Cytoscape graph. EpiExplorer uses various visual elements to facilitate the discovery of true biological events in a complex polygenic environment.
Identifiants
pubmed: 34354094
doi: 10.1038/s41598-021-94959-y
pii: 10.1038/s41598-021-94959-y
pmc: PMC8342486
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
15923Informations de copyright
© 2021. The Author(s).
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