Mapping determinants of human gene expression by regional and genome-wide association

Abstract

To study the genetic basis of natural variation in gene expression, we previously carried out genome-wide linkage analysis and mapped the determinants of approximately 1,000 expression phenotypes. In the present study, we carried out association analysis with dense sets of single-nucleotide polymorphism (SNP) markers from the International HapMap Project. For 374 phenotypes, the association study was performed with markers only from regions with strong linkage evidence; these regions all mapped close to the expressed gene. For a subset of 27 phenotypes, analysis of genome-wide association was performed with >770,000 markers. The association analysis with markers under the linkage peaks confirmed the linkage results and narrowed the candidate regulatory regions for many phenotypes with strong linkage evidence. The genome-wide association analysis yielded highly significant results that point to the same locations as the genome scans for about 50% of the phenotypes. For one candidate determinant, we carried out functional analyses and confirmed the variation in cis-acting regulatory activity. Our findings suggest that association studies with dense SNP maps will identify susceptibility loci or other determinants for some complex traits or diseases.

Figure 1. Results of genome-wide association analysis for six representative phenotypes with cis regulators

The horizontal line in each panel corresponds to P = 0.05 after Šidák correction.

Figure 2. Results of genome-wide linkage analysis (dotted line) superimposed on those from genome-wide association (bars) for the chromosome where the expressed gene is located

The location of the expressed gene is indicated by an arrow. The dotted horizontal line is for data from linkage scans and corresponds to t = 4, P = 3.7 × 10⁻⁵. The solid horizontal line is for data from GWA and corresponds to P = 0.05 after Šidák correction. The x axis indicates chromosome location in megabases.

Figure 3. HaploChIP assay with RNA polymerase II antibody to estimate allele-specific binding

Open squares show fluorescence intensities (Vic/Fam ratios) of genomic DNA samples with experimentally varied proportions of allele Tat SNP rs755467. The linear regression line is shown. Solid triangles show mean fluorescence intensities of immunoprecipitated products from three individuals heterozygous at rs755467. In all three cases, the immunoprecipitated products contained more T than G in the DNA. Estimates greater than 100% for the T-allele imply that no G-allele-bearing DNA fragments were detected in the immunoprecipitated products. Standard deviation of triplicate measurements is shown.