The tests are compatible with chip-based genotypes for single-nucleotide polymorphismsDanielCenterShrinerCenterWileyGenetic EpidemiologyShriner D. Approximate and exact tests of Hardy-Weinberg equilibrium using uncer- tain genotypes. Genet Epidemiol 2011; 35: 632-637....
In a nutshell, HEELS uses variant-level statistics, including marginal association statistics and the LD matrix, to estimate SNP-heritability by iteratively solving the REML score equation17. Because the score equations solved by HEELS are identical to those solved by GREML1, HEELS yields heritability...
The human genetic factors that affect resistance to infectious disease are poorly understood. Here we report a genome-wide association study in 17,000 severe malaria cases and population controls from 11 countries, informed by sequencing of fam
different genetic loci within the same population, employing a threshold of 0.3. Hardy-Weinberg equilibrium (HWE) evaluates the relation between allele and genotype frequencies, with SNPs having ap-value< 1 \times 10^{-5}considered as outliers and subsequently excluded from the dataset. Given the ...
Moreover, SNPs were removed due to low call frequency (<95%), failure in the Hardy–Weinberg equilibrium test (<1e-06), and low minor allele frequency (<5%). After SNP quality control, the heterogeneity of chickens, falling outside the boundaries of ±3 standard deviations from the mean...
All but 147 SNPs included only in the overall SNP set were in Hardy-Weinberg equilibrium (pHWE > 0.001). Preparation and purification of equimolar DNA pools for the Allelotyping analysis For the allelotyping analysis, two disjunct DNA pools (Pool 1 and Pool 2), each consisting of ...
To calculate how much larger the stGWAS sample size would have to be to give the same mean χ2statistics than mtGWAS, the following equation was used [33]: $$ {\mathrm{N}}_{\mathrm{GWAS}\ \mathrm{equivalent}}={\mathrm{N}}_{\mathrm{GWAS}}\frac{\overline{\upchi_{\mathrm{mtGWAS...
All but 147 SNPs included only in the overall SNP set were in Hardy-Weinberg equilibrium (pHWE > 0.001). Preparation and purification of equimolar DNA pools for the Allelotyping analysis For the allelotyping analysis, two disjunct DNA pools (Pool 1 and Pool 2), each consisting of equimolar...
A simple calculation of the relative risk could be done through the following risk score (RS) equation: RS = 2.47(ERS-0.94) * 3.32FH * 2.05(GRS-6.98). This is how Fig. 3 was constructed: An individual with the average exposure in the population (i.e.: with no family history (...
7). Unlike the derivation of Yu and Meuwissen9, we did not calculate the multivariate likelihood but simplified the derivation using f(Y|g j , σ 2) to replace f(y −j |B j g j , I \({{\sigma }_{e}}^{2}\)). Thus, the equation (5) can be rewritten as: $$E({g}_...