Blocks of Limited Haplotype Diversity


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.

Keywords: haplotype block; linkage disequilibrium; haplotype diversity; linkage disequilibrium map; selective sweep

Figure 1.

Graph of the linkage disequilibrium map in the TAP2 region oriented from pter to qter (a) and meiotic recombination (b). ?: signifies some uncertainty in location. (Data reported by Jeffreys et al. and LD map after Maniatis et al. .)



Jeffreys AJ, Kauppi L and Neumann R (2001) Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nature Genetics 29: 217–222.

Maniatis N, Collins A, Xu C‐F et al. (2002) The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. Proceedings of the National Academy of Sciences of the USA 99: 2228–2233.

Further Reading

Daly MJ, Rioux JD, Schaffner SF, Hudson TJ and Lander ES (2001) High‐resolution haplotype structure in the human genome. Nature Genetics 29: 229–232.

Goldstein DB (2001) Islands of linkage disequilibrium. Nature Genetics 29: 109–111.

Helmuth L (2001) Map of human genome 3.0. Science 293: 583–585.

Johnson GCL, Esposito L, Barratt BJ et al. (2001) Haplotype tagging for the identification of common disease genes. Nature Genetics 29: 233–237.

McVean G, Spencer CC and Chaix R (2005) Perspectives on human genetic variation from the HapMap Project. PLoS Genetics 1: e54.

Patil N, Berno AJ, Hinds DA et al. (2001) Blocks of limited haplotype diversity revealed by high‐resolution scanning of human chromosome 21. Science 294: 1719–1723.

Stephens JC, Schneider JA, Tanguay DA et al. (2001) Haplotype variation and linkage disequilibrium in 313 human genes. Science 293: 489–493.

Sun X, Stephens JC and Zhao H (2004) The impact of sample size and marker selection on the study of haplotype structures. Human Genomics 1: 179–193.

Taillon‐Miller P, Bauer‐Sardina I, Saccone NL et al. (2000) Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28. Nature Genetics 25: 324–328.

Verhoeven KJ and Simonsen KL (2005) Genomic haplotype blocks may not accurately reflect spatial variation in historic recombination intensity. Molecular Biology and Evolution 22: 735–740.

Weiss KM and Clark AR (2002) Linkage disequilibrium and the mapping of complex human traits. Trends in Genetics 18: 19–24.

Zhang K, Calabrese P, Nordborg M and Sun F (2002) Haplotype block structure and its applications to association studies: power and study designs. American Journal of Human Genetics 71: 1386–1394.

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Morton, Newton E(Dec 2007) Blocks of Limited Haplotype Diversity. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0006251.pub2]