A locus on chromosome 11p with multiple restriction site polymorphisms

Abstract

We have discovered and characterized a new polymorphic locus on chromosome 11p, D11S12, defined by an arbitrary genomic DNA segment cloned in the plasmid pADJ762. Four different polymorphic restriction sites with minor allele frequencies greater than 5% are revealed by Southern hybridization of this probe and its derivatives to digests of human DNAs. These include two MspI sites, a TaqI site, and a BclI site. The frequencies of the common haplotypes at this locus have been determined in a Utah population. Significant linkage disequilibrium has been demonstrated to exist between some pairs of polymorphic sites. A molecular map of this region has been determined, and the polymorphic sites have been localized. Comparison of physical separation with degree of linkage disequilibrium reveals an interesting case where an MspI site and a TaqI site that are separated by 6.8 kilobases (kb) show a greater degree of disequilibrium with each other than they do with two polymorphic sites located between them. One of the two interior sites is a BclI site that is approximately 0.2 kb away from the TaqI site but shows the same degree of disequilibrium with the TaqI site as with the MspI site 6.7 kb away. Although there is significant linkage disequilibrium at this locus, there are four major haplotypes with frequencies of 5% or greater, and the polymorphic information content (PIC) of this locus is .64.