Computational protocol: Evolutionary Signatures of Common Human Cis-Regulatory Haplotypes

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Protocol publication

[…] For each analyzed region, the LD plotting, haplotype block partitioning, and the delineation and population frequency estimation of major haplotypes were performed by the HAPLOVIEW program, version 3.32 (http://www.broad.mit.edu/mpg/haploview) . The haplotype block partitioning was generally determined with YRI data using one of the three methods (confidence intervals, four gamete rule, solid spine of LD) incorporated into the HAPLOVIEW program, depending on which covered the most extensive area containing the peak SNP. For some genes, we covered more extensive regions to increase informativeness. The haplotype frameworks were clustered based on YRI allele frequencies, as described in our previous publication . [...] LD-derived SNP bins were defined from SNPs within the block containing the originally reported peak SNPs using the TAGGER program (“tagger pairwise” option) incorporated into the HapMap graphical browser . For each bin (generally marking the branches in the genealogical analysis), a tagging SNP was selected based on the completeness of genotypes across the three populations for testing association. Association analysis between each tagging SNP and two sets of HapMap expression data, based on two (Affymetrix and Illumina) platforms and across three HapMap populations, (GEO accession number GSE2552 , GSE5859 , and GSE6536 ), was conducted by following the regression methods described in Cheung et al. (discussed in ). The nominal p-value of each tagging SNP was used for the determination of SNPs showing strongest association. The value of 0.05 was used as our cutoff for statistical significance. […]

Pipeline specifications

Software tools Haploview, Tagger
Application GWAS
Organisms Homo sapiens, Pan troglodytes