2012
DOI: 10.1186/1471-2164-13-s7-s2
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iLOCi: a SNP interaction prioritization technique for detecting epistasis in genome-wide association studies

Abstract: BackgroundGenome-wide association studies (GWAS) do not provide a full account of the heritability of genetic diseases since gene-gene interactions, also known as epistasis are not considered in single locus GWAS. To address this problem, a considerable number of methods have been developed for identifying disease-associated gene-gene interactions. However, these methods typically fail to identify interacting markers explaining more of the disease heritability over single locus GWAS, since many of the interact… Show more

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Cited by 48 publications
(39 citation statements)
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“…The advantages of GPU were also successfully implemented in epiGPU Recently, another hardware technology, field-programmable gate array (FPGa), was used for problems related to bioinformatics. This technology was applied to outperform the iLOCi method (interaction prioritization algorithm based on LD differences between cases and controls) (Piriyapongsa et al 2012;wienbrandt et al 2014), but in principle it can be adapted to many existing methodologies for exhaustive association interaction analysis.…”
Section: Statistical Methods To Screen For Epistasis In Large-scale Gmentioning
confidence: 99%
“…The advantages of GPU were also successfully implemented in epiGPU Recently, another hardware technology, field-programmable gate array (FPGa), was used for problems related to bioinformatics. This technology was applied to outperform the iLOCi method (interaction prioritization algorithm based on LD differences between cases and controls) (Piriyapongsa et al 2012;wienbrandt et al 2014), but in principle it can be adapted to many existing methodologies for exhaustive association interaction analysis.…”
Section: Statistical Methods To Screen For Epistasis In Large-scale Gmentioning
confidence: 99%
“…iLOCi [16] is an algorithm that can be considered a prioritization algorithm. iLOCi accounts for marker dependencies separately in case and control groups.…”
Section: Comparison With Other Methodsmentioning
confidence: 99%
“…Some methods, instead of controlling type 1 error, try to prioritize the SNP pairs [16]. The benefit to prioritization is that it may enable identification of interactions with modest, yet potentially relevant statistical significance that becomes insignificant after correction for multiple testing.…”
Section: Introductionmentioning
confidence: 99%
“…However, it is able to reduce the dimensionality of any problem into one dimension categorizing into high-risk, low-risk and no evidence groups before calculating a chi-squared test statistic. Other tools defining different test statistics include BiForce [8], iLOCi [18] and EDCF [27]. The latter uses a clustering approach in order to reduce the computational burden.…”
Section: Introductionmentioning
confidence: 99%