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Pair wise linkage (D') and haplotype analysis was carried out using the Polymorphism and Haplotype Analysis Suite [26].
The outcome of the family wise linkage analysis was the identification of one region reaching the threshold for significant linkage and four regions reaching the threshold for suggestive linkage (Table 1).
HAPLOVIEW 4.1 software was used to evaluate pair wise linkage disequilibrium (LD) and haplotype frequency between each tag SNP.
Hardy-Weinberg equilibrium, pair wise linkage disequilibrium (LD), genotype success rate and minor allele frequency were calculated using the statistical programme Haploview version 4.2 [ 41].
Hardy-Weinberg equilibrium, pair wise linkage disequilibrium (LD), genotype success rate and minor allele frequency were calculated using the statistical programme Haploview version 4.2 [ 37].
Pair wise linkage disequilibrium (LD; D') estimations between polymorphisms and haplotype reconstruction were performed with Haploview version 3 32 (Broad Institute of Massachusetts Institute of Technology and Harvard University; Cambridge; MA).
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Local pair-wise linkage disequilibrium (LD) in GWAS hits overlapping putative novel loci.
Low to moderate pair-wise linkage disequilibrium estimates were observed among the SNPs in the three ethnic groups (Fig. 7).
Pair-wise linkage disequilibrium analysis showed significant linkage disequilibrium (LD) among these five markers in both patient and control groups.
Pair-wise linkage disequilibrium was evaluated by two linkage disequilibrium parameters, Lewontin's D2 [24] and r2 [25], which were both calculated in haploview (http://www.broad.mit.edu/mpg/haploview/) [26].
ldSelect identified bins of SNPs with minor allele frequency (MAF) ≥0.05 using a pair-wise linkage disequilibrium (LD) threshold of r2≥0.8.
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