Blocks of Limited Haplotype Diversity

Abstract A haplotype block is a DNA sequence containing polymorphisms in strong linkage disequilibrium (LD) and with low haplotype diversity, separated from other blocks by steps of low LD with high haplotype diversity. Haplotype blocks may be as short as 2 kb or more than 150 kb, depending both on block definition and the spacing of LD cold spots, which tend to be shorter than blocks. Haplotype diversity measured by the effective number of haplotypes is said to be low if smaller than the number of polymorphisms defining the haplotype. To be useful in genetic analysis, the haplotype should be shorter than a typical block.