PT  - JOURNAL ARTICLE
AU  - Arash Bayat
AU  - Brendan Hosking
AU  - Yatish Jain
AU  - Cameron Hosking
AU  - Natalie Twine
AU  - Denis C. Bauer
TI  - BitEpi: A Fast and Accurate Exhaustive Higher-Order Epistasis Search
AID  - 10.1101/858282
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 858282
4099  - http://biorxiv.org/content/early/2019/12/01/858282.short
4100  - http://biorxiv.org/content/early/2019/12/01/858282.full
AB  - Motivation Higher-order epistatic interactions can be the driver for complex genetic diseases. An exhaustive search is the most accurate method for identifying interactive SNPs. While there is a fast bitwise algorithm for pairwise exhaustive searching (BOOST), higher-order exhaustive searching has yet to be efficiently optimized.Results In this paper, we introduce BitEpi, a program to detect and visualize higher-order epistatic interactions using an exhaustive search. BitEpi introduces a novel bitwise algorithm that can perform higher-order analysis more quickly and is the first bitwise algorithm to search for 4-SNP interactions. Furthermore, BitEpi increases detection accuracy by using a novel entropy-based power analysis. BitEpi visualizes significant interactions in a publication-ready interactive graph. BitEpi is 56 times faster than MDR for 4-SNP searching and is up to 1.33 and 2.09 times more accurate than BOOST and MPI3SNP respectively.Availability Codes and data are publicly available on GitHub https://github.com/aehrc/BitEpi. BitEpi is also available on CodeOcean https://doi.org/10.24433/CO.3671084.v1.Contact: Arash.Bayat{at}csiro.au - Denis.Bauer{at}csiro.auSupplementary information Supplementary data are available at bioRxiv online.