Discovering SNP-disease relationships in genome-wide SNP data using an improved harmony search based on SNP locus and genetic inheritance patternsdoi:10.1371/journal.pone.0292266HEREDITYMETAHEURISTIC algorithmsHUMAN genomeSEARCH algorithmsNUCLEOTIDE sequencing...
at the genome-wide significant threshold (p < 5.0 × 10−8)23. The SNP effect sizes reported in the mbQTL GWAS summary statistics represent how the host genetic loci affect the relative abundance of each microbiome taxa (mbQTLs)23. In the present study, we limited our analyses ...
Genetic association between PRSs for Collinsella and APOE rs429358 genotype in the discovery sample. Individuals in the discovery sample were separated by their genotype at the APOE SNP rs429358. Those with the genotype of TC and CC had higher PRSs for genetically predicted Collinsella abundance than...
We successfully identified 41 significant SNPs relevant to RA, 25 associated genes and a number of important SNP-SNP interactions (SNP patterns). Many findings (loci, genes and interactions) have experimental support from previous studies while novel findings may define unknown genetic pathways for ...
This observation may be a reflection of stronger cis-eQTLs tending to have a smaller distance between SNP and gene42. In contrast, p-value estimates between two disease traits were comparable across the two window sizes. Partial correlations were computed where three-way relationships were observed...
Once more, no other SNP reached genome wide significance (Bertram et al., 2008). Beecham and colleagues analyzed ∼500 LOAD cases and ∼500 cognitive controls followed by a further > 200 cases and > 200 controls used as a validation dataset for SNPs that reached nominal, but not genome...
This is because genetic structures, such as linkage disequilibrium (LD) blocks, are different across populations and because the GWAS summary statistics used as a weight for each single-nucleotide polymorphism (SNP) to calculate the PRS are based primarily on people of European ancestry. Taking a ...
They genotyped 4 SNPs in Fcγ receptor-like gene 3 (FCRL3) and found a significant association between-110 SNP and AIP. Interestingly, serum IgG4 concentrations were found to be significantly correlated with the number of susceptible alleles. The same group [36] studied 5 CTLA-4 polymorphisms...
Hereβis ann-vector that contains the standardized effect size ofnindependent SNPs on the phenotype, derived from GWAS.γis a vector of lengthnthat contains the standardized effect size, intrans-, of each SNP on the gene expression.Cis the pair-wise LD matrix between thenSNPs. ...
be less prevalent in PD cases (n = 25,243 PD cases, 41,945 healthy, refer to “Methods”).dSingle nucleotide polymorphisms (SNPs) in over 44 genomic regions show significant (p < 5 x 10−8) association to PD. Each point presents an independent SNP hit associated with ...