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For the data available at the time, it was not possible to select tagging SNPs for just a Caucasian population.
The software Haploview [18] was used to calculate linkage disequilibrium (LD) patterns and to select tagging SNPs (MAF 0.001, r2>0.8).
These SNPs were genotyped in 92 Swedish control samples to assess linkage disequilibrium patterns, to select tagging SNPs (tagSNPs) and to evaluate their coverage.
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With this purpose, we selected tagging SNPs.
Illumina selected tagging SNPs whereas Affymetrix selected SNPs based on assay availability and minor allele frequency.
We first selected tagging SNPs for the whole region (from CAMTA1 to ERRFI1).
We selected tagging SNPs in the SDF1 and CXCR4 genes from the HapMap database (data release in June 2005).
The METSIM cohort was genotyped for all four selected tagging SNPs to analyze SGK genetic variance for the endpoint diabetes (type 2) in a population-based cohort.
For 11 genes, we selected tagging SNPs every 5 kb, on average.
For each gene, we selected tagging SNPs from HapMap project using the criteria of: MAF >10%, R = 80% in Caucasian population (>70% of the patients are Caucasians).
We selected tagging SNPs according to HapMap phase III (release 28) Han Chinese database with a threshold of r > 0.8 by using Haploview (v 4.2).
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