The method reliably corrects for linkage disequilibrium in summary statistics of 5 million dense genome-wide markers and consistently improves prediction accuracy over state of the art techniques.
A bottleneck history fitted the S. cebifrons data significantly better than a model of constant N e, using the folded bSFS for n = 5 (Δ lnL = 110 after correcting for linkage).
Our analysis crudely corrected for linkage disequilibrium, which has confounded significance statistics in previous studies (Maurano et al., 2012), by taking broad 100 kbp regions (or most proximal gene body) surrounding regulatory elements to include disease-associated polymorphisms across the haplotype block.
To adjust for underestimation of rates using the linked datasets, and to correct for any linkage bias whereby the percentage of eligible cancer records linked varied by socio-demographic characteristics, we calculated weights for strata of age, sex, ethnicity, region, small area deprivation, and time since census.
The Bonferroni corrected test for linkage disequilibrium showed there were several spurious significant linkages between microsatellite loci that were not consistent across populations.
Using many SNPs from GWAS analysis that are not significantly associated with height, Yang et al. [ 17] estimated the proportion of variance in height explained by SNPs as 0.45 and even got close to the heritability estimate of 0.84 after correcting for incomplete linkage disequilibrium between SNPs genotyped and causal variants.
By bootstrapping on observed individuals and not on randomly created individuals generated via allelic frequencies, we might also expect to correct for biases due to linkage disequilibria or genotyping errors.
We compared three methods that correct for relatedness either implicitly or explicitly: linkage and linkage disequilibrium haplotype-based analysis (LDLA), efficient mixed-model association (EMMA) analysis, and Bayesian whole-genome regression (BayesC).
Methods that are optimized for computational speed that also correct for multiple tests appropriately given linkage disequilibrium and non-independent multilocus models under consideration are needed to effectively search the genome for gene-gene interactions.
To correct for founder effects and HLA linkage disequilibrium, we identified associations using the program PhyloD [4], which we ran on 5 trees selected from a set of trees for their high log likelihood scores.
