Epistasis detection software tools | Genome-wide association analysis

It is becoming clear that most human diseases have a complex etiology that cannot be explained by single nucleotide polymorphisms (SNPs) or simple additive combinations; the general consensus is that they are caused by combinations of multiple…

It is becoming clear that most human diseases have a complex etiology that cannot be explained by single nucleotide polymorphisms (SNPs) or simple additive combinations; the general consensus is that they are caused by combinations of multiple genetic variations. The limited success of some genome-wide association studies is partly a result of this focus on single genetic markers. A more promising approach is to take into account epistasis, by considering the association of multiple SNP interactions with disease. Source text: Upton et al., 2015.

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A method for genome-wide case-control studies. BEAM treats the…

A method for genome-wide case-control studies. BEAM treats the disease-associated markers and their interactions via a bayesian partitioning model and computes, via Markov chain Monte Carlo, the…

Discovers genome-phenome relationship using Bayesian Networks (BNs). MBS…

Discovers genome-phenome relationship using Bayesian Networks (BNs). MBS employs the extended greedy search and learn directed acyclic graph (DAG) models that contain two or more predictors in the…

Allows to make epistasis detection based on hierarchical representation of…

Allows to make epistasis detection based on hierarchical representation of linkage disequilibrium (LD). LinDen reduces the number of tests performed in epistasis detection. It uses correlations…

Provides a convenient single interface for accessing multiple publicly…

Provides a convenient single interface for accessing multiple publicly available human genetic data sources that have been compiled in the supporting database of the Library of Knowledge Integration…

Permits the study of single nucleotide polymorphism (SNP)–SNP interactions…

Permits the study of single nucleotide polymorphism (SNP)–SNP interactions with or without marginal effects. TS-GSIS provides valid variable selection for the analysis of quantitative and disease…

An efficient family-based gene-gene interaction test for trios (i.e., two…

An efficient family-based gene-gene interaction test for trios (i.e., two parents and one affected sib). The GCORE compares interlocus correlations at two SNPs between the transmitted and…

A tool for epistasis analysis based on functional regression model. The…

A tool for epistasis analysis based on functional regression model. The proposed method was applied to exome sequence data from the NHLBI's Exome Sequencing Project (ESP) and CHARGE-S study. We…

A general measure for epistasis testing. W-test is fast, model-free, and…

A general measure for epistasis testing. W-test is fast, model-free, and powerful. We have demonstrated that the W-test has robust power for linear and non-linear genetic models over a range of…

A Markov chain Monte Carlo-based method using genotype summary data to obtain…

A Markov chain Monte Carlo-based method using genotype summary data to obtain consistent estimates of epistasis effects in meta-analysis. We defined a series of conditions to generate simulation data…

Allows performing a complete search for significant single nucleotide…

Allows performing a complete search for significant single nucleotide polymorphism (SNP) main effects and SNP x SNP interactions. PSESM was implemented in order to give scan results rapidly despite…

Can take into account double knockouts and infer more complex network…

Can take into account double knockouts and infer more complex network signalling pathways. EpiNEM incorporates logical functions that describe interactions between regulators. The epiNEM method can…

Assesses pathogenicity of Mendelian germline sequence variants. ClinGen…

Assesses pathogenicity of Mendelian germline sequence variants. ClinGen Pathogenicity Calculator allows users to enter the applicable American College of Medical Genetics and Genomics /Association…

An efficient gene-gene interaction test for discordant sib pairs (DSPs), which…

An efficient gene-gene interaction test for discordant sib pairs (DSPs), which is suitable for genome-wide interaction analysis for single nucleotide polymorphisms (SNP) pairs in DSPs. We used…

Allows users to locate coherent sets of single-nucleotide polymorphisms…

Allows users to locate coherent sets of single-nucleotide polymorphisms (SNP)-SNP interactions included in Genome-wide association studies (GWAS) cohorts. BridGe focuses on two structures: “between…

Identifies interactive effects in high-dimensional datasets. MBS-IGain employs…

Identifies interactive effects in high-dimensional datasets. MBS-IGain employs information gain to determine whether to add a predictor on a given beam rather than using the score. It uses the score…

Obtains the significance of a multi-locus model, even a high-order model…

Obtains the significance of a multi-locus model, even a high-order model through a regression framework with a semi-parametric correction procedure for controlling Type I error rates. UM-MDR avoids…

Takes non-hierarchical models, inheritance modes and mode coding direction into…

Takes non-hierarchical models, inheritance modes and mode coding direction into consideration. SIPI can intensively and effectively search pairwise SNP–SNP interactions. It detects 45 interaction…

Employs a cutting-edge method to enumerate statistically significant SNP…

Employs a cutting-edge method to enumerate statistically significant SNP combinations from genome-wide case-control data. LAMPLINK is implemented as a set of additional functions to PLINK, and hence…

An integrative mixture model. JBASE explores two major reasons of missing…

An integrative mixture model. JBASE explores two major reasons of missing heritability: interactions between genetic variants, a phenomenon known as epistasis and phenotypic heterogeneity, addressed…

Allows to identify epistatic interactions, which is based on ant colony…

Allows to identify epistatic interactions, which is based on ant colony optimization (ACO) algorithm. Highlights of epiACO are the introduced fitness function Svalue, path selection strategies, and a…

Employs an opportunistic evolutionary strategy designed to maximally utilize an…

Employs an opportunistic evolutionary strategy designed to maximally utilize an arbitrary collection of distributed compute nodes. Crush-MDR is a multi-objective evolutionary search engine for…

A web server-based tool for analysing polygenic epistatic effects. PEPIS is…

A web server-based tool for analysing polygenic epistatic effects. PEPIS is based on a linear mixed model that has been used to predict the performance of hybrid rice. It includes two main…

A compressed sensing method that can reconstruct nonlinear genetic models…

A compressed sensing method that can reconstruct nonlinear genetic models (i.e., including epistasis, or gene-gene interactions) from phenotype-genotype (GWAS) data. Our method uses L1-penalized…

Handles multi-locus hypotheses by computing the posterior probability of a…

Handles multi-locus hypotheses by computing the posterior probability of a hypothesis. BNPP allows users to compute the posterior probability of multi-locus models. It represents models where a…

A software tool that is able to detect multiple sets of significant gene-gene…

A software tool that is able to detect multiple sets of significant gene-gene and/or gene-environment interactions in relation to a trait of interest, while efficiently controlling type I error…

A software tool for genome-wide interaction analysis (GWIA) of case-control SNP…

A software tool for genome-wide interaction analysis (GWIA) of case-control SNP data and quantitative traits. SNPs are selected for joint analysis using a priori information. Sources of information…

Performs inference simultaneously for all single nucleotide polymorphism (SNP)…

Performs inference simultaneously for all single nucleotide polymorphism (SNP) positions in a much higher dimension. SuperDCA is a method uses for Direct Coupling Analysis (DCA) of input genome…

Intends to decode three-way interactions from cancer expression data. xSyn was…

Intends to decode three-way interactions from cancer expression data. xSyn was developed by using Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and synergy. It can be used to explore…

Provides algorithms for training and evaluating several types of Boltzmann…

Provides algorithms for training and evaluating several types of Boltzmann Machines (BMs). BoltzmannMachines.jl is a Julia package that supports multiple cores: (i) learning of Restricted Boltzmann…

Combines the differential evolution (DE) algorithm with a classification based…

Combines the differential evolution (DE) algorithm with a classification based multifactor-dimensionality reduction (CMDR) to identify potential epistasis in genome-wide association studies (GWAS).…

Detects gene-gene interactions as a possible alternative to existing…

Detects gene-gene interactions as a possible alternative to existing algorithms, especially in situations where the number of involved determinants is high. KNN-MDR can be seen as an interesting…

Estimates and tests its marginal epistatic effect, the combined epistatic…

Estimates and tests its marginal epistatic effect, the combined epistatic effect between the examined variant and all other variants. By modeling and inferring the marginal epistatic effects, MAPIT…

Detects epistatic relationships between genes. MDR is a nonparametric and…

Detects epistatic relationships between genes. MDR is a nonparametric and genetic model-free data mining alternative to logistic regression for detecting and characterizing nonlinear interactions…

A generic epistasis model that provides a flexible solution for various…

A generic epistasis model that provides a flexible solution for various biological putative epistatic models in practice. eQTL epistasis enables one to efficiently characterize the functional…

A multi-objective heuristic optimization methodology for detecting genetic…

A multi-objective heuristic optimization methodology for detecting genetic interactions. In MACOED, we combine both logistical regression and Bayesian network methods, which are from opposing schools…

Discovers interactions from a real clinical breast cancer dataset.…

Discovers interactions from a real clinical breast cancer dataset. Exhaustive-IGain uses information gain and Bayesian Network (BN) scoring to learn interactions. It was used to learn interactions…

An R package for the detection and visualization of epistatic interactions of…

An R package for the detection and visualization of epistatic interactions of their orders from 1 to n (n ≥ 2). CINOEDV is composed of two stages, namely, detecting stage and visualizing stage.…

An efficient, scalable search algorithm that finds synergy between pairs of…

An efficient, scalable search algorithm that finds synergy between pairs of physically unlinked SNPs (genome-wide) in large case-control datasets. SIXPAC expects genotype and phenotype information as…

Detects gene-gene interactions in genome-wide case-control studies. For the…

Detects gene-gene interactions in genome-wide case-control studies. For the discovery of unknown gene-gene interactions that underlie complex diseases, BOOST allows examination of all pairwise…

Identifies susceptibility genes involved in epistatic interactions for…

Identifies susceptibility genes involved in epistatic interactions for case-control studies of candidate genes. In the FITF approach, likelihood-ratio tests are performed in stages that increase in…

A Bayesian partition computational method for detecting SNP interactions…

A Bayesian partition computational method for detecting SNP interactions (epistasis). The proposed approach builds a Bayesian model on both continuous data and discrete data to partition…

An approach based on ridge regression with polynomial kernels and model…

An approach based on ridge regression with polynomial kernels and model selection technique for determining the true degree of epistasis among single nucleotide polymorphisms (SNPs). KDSNP employs…

An efficient algorithm for detecting epistasis in quantitative GWAS, achieving…

An efficient algorithm for detecting epistasis in quantitative GWAS, achieving a substantial runtime speedup by avoiding the need to exhaustively test all SNP pairs using metric embedding and random…

An efficient algorithm which significantly speeds up epistasis detection for…

An efficient algorithm which significantly speeds up epistasis detection for human GWAS. TEAM is exhaustive, i.e. it does not ignore any epistatic interaction. Utilizing the minimum spanning tree…

Allows to identify epistatic interactions of single nucleotide polymorphisms…

Allows to identify epistatic interactions of single nucleotide polymorphisms (SNPs). eCEO is a model to find statistically significant epistatic interactions. The software is based on Google’s…

An ensemble learner for case-control studies when interactions of single…

An ensemble learner for case-control studies when interactions of single nucleotide polymorphisms (SNPs) are of particular interest. LogicFS uses bootstrap samples of the data and employs the Boolean…

Implements a two-stage epistasis detection procedure from genotype data. LIMEpi…

Implements a two-stage epistasis detection procedure from genotype data. LIMEpi is a selection method for polymorphic loci and can be used as the first stage of two-stage epistasis detection. It…

Reduces the multiple testing burden to one test per single nucleotide…

Reduces the multiple testing burden to one test per single nucleotide polymorphism (SNP) and allows interactions with unobserved factors. semisup is an R package able to move away from testing…

Filters a large, genomic dataset down to a subset of genetic variants, which…

Filters a large, genomic dataset down to a subset of genetic variants, which may be useful for interaction analysis. PLATO is a filter-based method bringing together many analytical methods…

Calculates the number of susceptibility single nucleotide polymorphisms (SNPs)…

Calculates the number of susceptibility single nucleotide polymorphisms (SNPs) and power of future studies. INPower uses the effect sizes for a set of known susceptibility SNPs and the power of…

A fast implementation of random forest or recursive partitioning, particularly…

A fast implementation of random forest or recursive partitioning, particularly suited for high dimensional data. Classification, regression, probability estimation and survival forests are supported.

Can render the search for epistasis universally viable in terms of hardware…

Can render the search for epistasis universally viable in terms of hardware availability, cost and computational time. epiGPU is limited to performing linear regression on quantitative traits, but…

An efficient parallel solution extending the PLINK epistasis module, designed…

An efficient parallel solution extending the PLINK epistasis module, designed to test for epistasis effects when analyzing continuous phenotypes. FastEpistasis is capable of analyzing several…

A non-linear methodology based on information theory for finding combinatorial…

A non-linear methodology based on information theory for finding combinatorial association between multi-SNPs and a given phenotype. This method has been applied as a relevance criterion of a…

A simple, fast and effective algorithm to detect genome-wide multi-locus…

A simple, fast and effective algorithm to detect genome-wide multi-locus epistatic interactions based on the clustering of relatively frequent items. Extensive experiments on simulated data show that…

An approach to epistasis detection by exhaustive testing of all possible SNP…

An approach to epistasis detection by exhaustive testing of all possible SNP pairs. The search strategy based on the Hilbert-Schmidt Independence Criterion can help delineate various forms of…

Detects two-locus associations allowing for interactions from GWAS.…

Detects two-locus associations allowing for interactions from GWAS. SNPAssociation displays many advantages over existing methods: 1) it can detect two-locus associations allowing for interactions…

A GPU-implementation of BOOST based on the CUDA technology by Nvidia. GBOOST…

A GPU-implementation of BOOST based on the CUDA technology by Nvidia. GBOOST achieves a 40-fold speedup compared with BOOST. It completes the analysis of Wellcome Trust Case Control Consortium Type 2…

An algorithm for learning maximum entropy probability models of disease risk…

An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions. Unlike neural networks and support vector…

Facilitates the rapid analysis of GWA data. Random Jungle yields valid results…

Facilitates the rapid analysis of GWA data. Random Jungle yields valid results and computes up to 159 times faster than the fastest alternative implementation, while still maintaining all options of…

Detects SNP-SNP interactions in GWA studies. SNPHarvester creates multiple…

Detects SNP-SNP interactions in GWA studies. SNPHarvester creates multiple paths in which the visited SNP groups tend to be statistically associated with diseases, and then harvests those significant…

A learning approach based on the predictive rule inference to find…

A learning approach based on the predictive rule inference to find disease-associated epistatic interactions. SNPRuler first uses the predictive rule learning to narrow down possible interactions…

A general approach for efficient large scale gene-gene interaction analysis,…

A general approach for efficient large scale gene-gene interaction analysis, which supports a wide range of tests. COE is especially efficient for large permutation test. Extensive experiments…

A three-stage method based on co-information theory. In screening stage,…

A three-stage method based on co-information theory. In screening stage, co-information index (CII) is employed to visualize and rank contributions of individual SNPs to the phenotype, with the…

A SNP interaction prioritization algorithm. iLOCi accounts for marker…

A SNP interaction prioritization algorithm. iLOCi accounts for marker dependencies separately in case and control groups. Disease-associated interactions are then prioritized according to a novel…

A multifactor dimensionality reduction method for epistasis detection in small…

A multifactor dimensionality reduction method for epistasis detection in small or extended pedigrees. FAM-MDR combines features of the Genome-wide Rapid Association using Mixed Model And Regression…

An efficient algorithm for performing ANOVA tests on SNP-pairs in a batch mode,…

An efficient algorithm for performing ANOVA tests on SNP-pairs in a batch mode, which also supports large permutation test. We derive an upper bound of SNP-pair ANOVA test, which can be expressed as…

Analyzes and visualizes epistatic interactions of both two-way and three-way.…

Analyzes and visualizes epistatic interactions of both two-way and three-way. ViSEN is a network-based analysis and visualization tool for epistasis studies. It not only identifies strong…

A hybrid method which is merging the strengths of MDR (multifactor…

A hybrid method which is merging the strengths of MDR (multifactor dimensionality reduction) and genotype-PDT (genotype pedigree disequilibrium test). One of the major strengths of MDR is the ability…

A visualization tool that is specifically designed to analyze and explore…

A visualization tool that is specifically designed to analyze and explore genetic interactions. EINVis displays interactions among genetic markers as a network. EINVis utilizes a circular layout…

A non-parametric method specifically designed to detect epistasis in lifetime…

A non-parametric method specifically designed to detect epistasis in lifetime datasets. The core of the SDR algorithm is the classification procedure used to label as “high-risk” or…

A learning algorithm to find high order SNP interactions in genome wide…

A learning algorithm to find high order SNP interactions in genome wide association studies. The goal of MegaSNPHunter is to find the remarkable multi-SNP interactions from large genome data to…

A method for jointly detecting disease-causing single-locus effects and…

A method for jointly detecting disease-causing single-locus effects and gene-gene interactions. randompat is suitable and powerful for detecting disease susceptibility variants with potentially small…

Maps phenotypes to pairs of genetic loci and systematically searches for the…

Maps phenotypes to pairs of genetic loci and systematically searches for the epistatic interactions expected to reveal part of this missing heritability. GLIDE makes use of the computational power of…

Implements a forest-based approach to accommodate the haplotype uncertainties…

Implements a forest-based approach to accommodate the haplotype uncertainties and variable importance to sort out significant haplotypes and their interactions in genomewide case-control association…

A two-stage ant colony optimization algorithm for detecting epistasis in a…

A two-stage ant colony optimization algorithm for detecting epistasis in a case-control design. Based on some practical epistatic models, AntEpiSeeker has performed very well. AntEpiSeeker is a…

An approach for detecting gene associations on traits by selecting the most…

An approach for detecting gene associations on traits by selecting the most significant functional category and then using single nucleotide polymorphisms (SNPs) within it to assess gene…

Takes advantage of a Bayesian model with a properly designed Gibbs sampling…

Takes advantage of a Bayesian model with a properly designed Gibbs sampling strategy to facilitate the detection of epistatic modules. It was confirmed via extensive simulation studies that epiMODE…