Localization of a small genomic region associated with elevated ACE

Abstract

Defining the relationship between multiple polymorphisms in a small genomic region and an underlying quantitative trait locus (QTL) represents a major challenge in human genetics. Pedigree analyses have shown that angiotensin I-converting enzyme (ACE) levels are influenced by a QTL located within or close to the ACE gene and most likely resides in the 3' region of this locus. We genotyped seven polymorphisms spanning 13 kb in the 3' end of ACE in 159 Afro-Caribbean subjects to evaluate the linkage disequilibrium between these sites and to narrow the genomic region associated with an elevated ACE level using a cladistic analysis. The linkage disequilibrium measurement D' and a haplotype tree revealed three distinct haplotype segments, presumably because of recombination. The value of the linkage disequilibrium parameter p(excess) was highest for site 22982, which is located in the middle segment. A series of nested, cladistic analyses confirmed that the other two regions are unlikely to be the ACE-linked QTL and that the variant resides in the middle region. Analyses of the same polymorphisms in 98 unrelated Europeans in the Monitoring Trends and Determinants in Cardiovascular Diseases (MONICA) study resulted in fewer haplotypes than were observed among the Afro-Caribbean subjects, suggesting that populations with greater genetic diversity may be especially informative for fine-scale mapping.

Figures

Figure 1

Polymorphic markers genotyped in ACE. The genomic region of ACE covers ∼24 kb on chromosome 17 (Rieder et al. 1999). Six single-nucleotide polymorphisms, in addition to the Alu insertion/deletion, were typed in 159 Jamaicans. The shaded area in the 5′ region represents the promoter and 8-kb region excluded from containing a functional ACE variant (Keavney et al. 1998).

Figure 2

Site-specific ACE levels in Jamaicans (left bars) and Europeans (right bars). All site genotypes are plotted against ACE activity normalized to the lowest level (100%) at each site. Two sites showed a significant change in ACE levels on the basis of genotypes (20833 and 22982) for Jamaicans. All sites showed a significant change for Europeans. An asterisk (*) denotes that P<.05 versus the lowest homozygote (white bar).

Figure 3

The eight most frequent haplotypes were used to infer a maximum-parsimony tree. Haplotypes were then grouped with neighboring haplotypes into clades A, B, and C. The maximum-parsimony mutational connections among the haplotypes are indicated by solid lines, with the 0s representing all intermediate haplotypes that are missing from the sample. The number under the haplotypes corresponds to the haplotype, and the number under or beside the solid lines is the mutation site. The phenotypic effects attributed to these groups then were tested under different model assumptions against plasma ACE activity by use of a measured-haplotype analysis.

Figure 4

Maximum pexcess with error bars denoting one standard deviation for each site. Solid and dotted lines represent the pexcess values for the Jamaican and European samples, respectively. The offset for the two curves represents the higher average level of linkage disequilibrium among the Europeans.