ArticleNucleic acids research2012
BiForce Toolbox: powerful high-throughput computational analysis of gene-gene interactions in genome-wide association studies.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Review on GPU accelerated methods for genome-wide SNP-SNP interactions.Molecular genetics and genomics : MGG · 2024Review
- Genome-Wide Association Study Reveals Candidate Genes for Root-Related Traits in Rice.Current issues in molecular biology · 2022Article
- A Large-Scale Genome-Wide Gene-Gene Interaction Study of Lung Cancer Susceptibility in Europeans With a Trans-Ethnic Validation in Asians.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2022Article
- Recessive/dominant model: Alternative choice in case-control-based genome-wide association studies.PloS one · 2021Article
- A parallelized strategy for epistasis analysis based on Empirical Bayesian Elastic Net models.Bioinformatics (Oxford, England) · 2020Article
- Clinical Implications of Single Nucleotide Polymorphisms in Diagnosis of Asthma and its Subtypes.Yonsei medical journal · 2019Review
- pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms.BMC bioinformatics · 2017Article
- CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies.BMC bioinformatics · 2016Article
- Detecting epistasis in human complex traits.Nature reviews. Genetics · 2014Review
- Abundant local interactions in the 4p16.1 region suggest functional mechanisms underlying SLC2A9 associations with human serum uric acid.Human molecular genetics · 2014Article
- A comparison study of succinct data structures for use in GWAS.BMC bioinformatics · 2013Article
- A whole-genome simulator capable of modeling high-order epistasis for complex disease.Genetic epidemiology · 2013Article
- Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives.BioData mining · 2013Article
- Properties of local interactions and their potential value in complementing genome-wide association studies.PloS one · 2013Article
- Approaching "phantom heritability" in psychiatry by hypothesis-driven gene-gene interactions.Frontiers in human neuroscience · 2013Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Genome-wide association studies (GWAS) have discovered many loci associated with common disease and quantitative traits. However, most GWAS have not studied the gene-gene interactions (epistasis) that could be important in complex trait genetics. A major challenge in analysing epistasis in GWAS is the enormous computational demands of analysing billions of SNP combinations. Several methods have been developed recently to address this, some using computers equipped with particular graphical processing units, most restricted to binary disease traits and all poorly suited to general usage on the most widely used operating systems. We have developed the BiForce Toolbox to address the demand for high-throughput analysis of pairwise epistasis in GWAS of quantitative and disease traits across all commonly used computer systems. BiForce Toolbox is a stand-alone Java program that integrates bitwise computing with multithreaded parallelization and thus allows rapid full pairwise genome scans via a graphical user interface or the command line. Furthermore, BiForce Toolbox incorporates additional tests of interactions involving SNPs with significant marginal effects, potentially increasing the power of detection of epistasis. BiForce Toolbox is easy to use and has been applied in multiple studies of epistasis in large GWAS data sets, identifying interesting interaction signals and pathways.
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Registered trials
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