High-resolution haplotype structure in the human genome

Linkage disequilibrium (LD) analysis is traditionally based on individual g enetic markers and often yields an erratic, nonmonotonic picture, because t he power to detect allelic associations depends on specific properties of e ach marker, such as frequency and population history. Ideally, LD analysis should be based directly on the underlying haplotype structure of the human genome, but this structure has remained poorly understood. Here we report a high-resolution analysis of the haplotype structure across 500 kilobases. on chromosome 5q31 using 103 single-nucleotide polymorphisms (SNPs) in a E uropean-derived population. The results show a picture of discrete haplotyp e blocks (of tens to hundreds of kilobases), each with limited diversity pu nctuated by apparent sites of recombination. In addition, we develop an ana lytical model for LID mapping based on such haplotype blocks. If our observ ed structure is general (and published data suggest that it may be), it off ers a coherent framework for creating a haplotype map of the human genome.