ArticleBioinformatics (Oxford, England)2010
FastEpistasis: a high performance computing solution for quantitative trait epistasis.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers, 1 of them a synthesis that pooled it.
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Who cites it
63 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Ultrafast genome-wide scan for SNP-SNP interactions in common complex disease.Genome research · 2012Pooled it
- Sparse modeling of interactions enables fast detection of genome-wide epistasis in biobank-scale studies.American journal of human genetics · 2025Article
- Review on GPU accelerated methods for genome-wide SNP-SNP interactions.Molecular genetics and genomics : MGG · 2024Review
- Network medicine-based epistasis detection in complex diseases: ready for quantum computing.Nucleic acids research · 2024Article
- BridGE: a pathway-based analysis tool for detecting genetic interactions from GWAS.Nature protocols · 2024Review
- Interaction models matter: an efficient, flexible computational framework for model-specific investigation of epistasis.BioData mining · 2024Article
- Network medicine-based epistasis detection in complex diseases: ready for quantum computing.medRxiv : the preprint server for health sciences · 2023Article
- Leveraging the genetic correlation between traits improves the detection of epistasis in genome-wide association studies.G3 (Bethesda, Md.) · 2023Article
- Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets.American journal of human genetics · 2023Article
- Dissecting Complex Traits Using Omics Data: A Review on the Linear Mixed Models and Their Application in GWAS.Plants (Basel, Switzerland) · 2022Review
- Article
- Epi-MEIF: detecting higher order epistatic interactions for complex traits using mixed effect conditional inference forests.Nucleic acids research · 2022Article
- Genetic Dissection of Epistatic Interactions Contributing Yield-Related Agronomic Traits in Rice Using the Compressed Mixed Model.Plants (Basel, Switzerland) · 2022Article
- A Review of Feature Selection Methods for Machine Learning-Based Disease Risk Prediction.Frontiers in bioinformatics · 2022Review
- A parallelized strategy for epistasis analysis based on Empirical Bayesian Elastic Net models.Bioinformatics (Oxford, England) · 2020Article
- GenEpi: gene-based epistasis discovery using machine learning.BMC bioinformatics · 2020Article
- Deep mixed model for marginal epistasis detection and population stratification correction in genome-wide association studies.BMC bioinformatics · 2019Article
- A multi-omics digital research object for the genetics of sleep regulation.Scientific data · 2019Article
- HENA, heterogeneous network-based data set for Alzheimer's disease.Scientific data · 2019Article
- Article
3 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
motivationGenome-wide association studies have become widely used tools to study effects of genetic variants on complex diseases. While it is of great interest to extend existing analysis methods by considering interaction effects between pairs of loci, the large number of possible tests presents a significant computational challenge. The number of computations is further multiplied in the study of gene expression quantitative trait mapping, in which tests are performed for thousands of gene phenotypes simultaneously.
resultsWe present FastEpistasis, an efficient parallel solution extending the PLINK epistasis module, designed to test for epistasis effects when analyzing continuous phenotypes. Our results show that the algorithm scales with the number of processors and offers a reduction in computation time when several phenotypes are analyzed simultaneously. FastEpistasis is capable of testing the association of a continuous trait with all single nucleotide polymorphism (SNP) pairs from 500 000 SNPs, totaling 125 billion tests, in a population of 5000 individuals in 29, 4 or 0.5 days using 8, 64 or 512 processors. AVAILABILITY: FastEpistasis is open source and available free of charge only for non-commercial users from http://www.vital-it.ch/software/FastEpistasis.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.