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Exhaustive search of the SNP-sNP interactome identifies epistatic effects on brain volume in two cohorts

Derrek P Hibar, Jason L Stein, Neda Jahanshad, Omid Kohannim, Arthur W Toga, Katie L McMahon, Greig I de Zubicaray, Grant W Montgomery, Nicholas G Martin, Margaret J Wright, Michael W Weiner, Paul M Thompson
Using an implementation of the SIS algorithm (called EPISIS), we used exhaustive search of the genome-wide, SNP-SNP interactome to identify and prioritize SNPs for interaction analysis.  ...  We found that each additional loading in the epistatic effect was associated with approximately 5% greater brain regional brain volume (a protective effect) in both the ADNI and QTIM samples.  ...  A single exhaustive search of the genome-wide, SNP-SNP interactome with EPISIS was completed in 7 hours (using one NVIDIA Tesla C2050 GPU card).  ... 
pmid:24505811 pmcid:PMC4109883 fatcat:ttujrzd35neanmzufh6dr3elcy

Genome-wide interaction analysis reveals replicated epistatic effects on brain structure

Derrek P. Hibar, Jason L. Stein, Neda Jahanshad, Omid Kohannim, Xue Hua, Arthur W. Toga, Katie L. McMahon, Greig I. de Zubicaray, Nicholas G. Martin, Margaret J. Wright, Michael W. Weiner, Paul M. Thompson
2015 Neurobiology of Aging  
Each additional loading in the interaction effect was associated with ~5% greater brain regional brain volume (a protective effect) in both ADNI and QTIM samples.  ...  We mapped the whole-brain, voxelwise effects of the interaction in the ADNI dataset and separately in an independent replication dataset of healthy twins (QTIM).  ...  One of the authors, Michael Weiner, receives private funding unrelated to the content of this paper.  ... 
doi:10.1016/j.neurobiolaging.2014.02.033 pmid:25264344 pmcid:PMC4332874 fatcat:3cobzfxf6za7pmachyxu7gowsy

GWAS genetic variant data and their integration in the context of network biology

Mufassra Naz, Martin Hofmann-Apitius
2016 Journal of Systems and Integrative Neuroscience  
Regardless of the success of Genome Wide Association Studies (GWAS) to identify genetic variants associated with human diseases, investigating the molecular mechanisms and disease-associated genes linked  ...  Moreover, approaches like computational and bioinformatics predictions based on the variants location and its sequence attributes can assist to propose the candidate genes.  ...  EPIQ discovers SNPs with epistatic effect, without exhaustively testing all pairs of SNPs [194] .  ... 
doi:10.15761/jsin.1000135 fatcat:xhvcgelncne7tgywvom35mupny

The Genetics of Multiple Sclerosis [chapter]

2017 Multiple Sclerosis: Perspectives in Treatment and Pathogenesis  
To date, after a number of GWAS screenings, 110 MS risk variants have been discovered outside the MHC locus in European populations.  ...  In recent years, the advent of genome-wide association studies (GWAS) and collaborative efforts among international centers have fueled the characterization of several non-MHC loci associated with MS susceptibility  ...  effects in the MHC region: six HLA-DRB1 and one HLA-DPB1 alleles in the centromeric class II region of the locus; one HLA-A and two HLA-B alleles in the telomeric class I region; and one in the class  ... 
doi:10.15586/codon.multiplesclerosis.2017.ch1 fatcat:tgswhjasfrc2toc5sguzz3rwrq

Unraveling Gene Networks of Human Cholesterol Homeostasis and Their Roles in Cardiovascular Disease

Anthi Trasta
In parallel, in collaboration with Heiko Runz (Merck Research Laboratories), all lead SNPs of the genes tested with co-RNAi were examined for co-occurrence and SNP-SNP interactions in a cohort of more  ...  In summary, the study in hand identified combinatorial effects of genes on cholesterol homeostasis, through systematic identification of genetic interactions between GWAS-derived genes.  ...  where both SNPs are present (2 SNPs) versus individuals carrying 1 of the two SNPs (1 SNP) or no SNP for the three SNP pairs that were identified as having an additive effect in the Bioimage cohort and  ... 
doi:10.11588/heidok.00023205 fatcat:oi5l3girj5bnzgzr5c57db5hoy