Haplotype block

In genetics, a haplotype block is a region of an organism's genome in which there is little evidence of a history of genetic recombination, and which contain only a small number of distinct haplotypes.[1] According to the haplotype-block model, such blocks should show high levels of linkage disequilibrium and be separated from one another by numerous recombination events.[2] The boundaries of haplotype blocks cannot be directly observed; they must instead be inferred indirectly through the use of algorithms. However, some evidence suggests that different algorithms for identifying haplotype blocks give very different results when used on the same data,[3] though another study suggests that their results are generally consistent.[4] The National Institutes of Health funded the HapMap project to catalog haplotype blocks throughout the human genome.[5]

Definition

There are two main ways that the term "haplotype block" is defined: one based on whether a given genomic sequence displays higher linkage disequilibrium than a predetermined threshold, and one based on whether the sequence consists of a minimum number of single nucleotide polymorphisms (SNPs) that explain a majority of the common haplotypes in the sequence (or a lower-than-usual number of unique haplotypes).[6] In 2001, Patil et al.[7] proposed the following definition of the term: "Suppose we have a number of haplotypes consisting of a set of consecutive SNPs. A segment of consecutive SNPs is a block if at least α percent of haplotypes are represented more than once".[8]

References

  1. ^ Gabriel, S. B.; Daly, Mark J.; Lander, Eric S.; Ward, Ryk; Cooper, Richard; Adeyemo, Adebowale; Rotimi, Charles; Liu-Cordero, Shau Neen; Faggart, Maura (2002-06-21). "The Structure of Haplotype Blocks in the Human Genome". Science. 296 (5576): 2225–2229. Bibcode:2002Sci...296.2225G. doi:10.1126/science.1069424. ISSN 0036-8075. PMID 12029063. S2CID 10069634.
  2. ^ Wall, Jeffrey D.; Pritchard, Jonathan K. (1 August 2003). "Haplotype blocks and linkage disequilibrium in the human genome". Nature Reviews Genetics. 4 (8): 587–597. doi:10.1038/nrg1123. PMID 12897771. S2CID 15478115.
  3. ^ Schulze, Thomas G.; Zhang, Kui; Chen, Yu-Sheng; Akula, Nirmala; Sun, Fengzhu; McMahon, Francis J. (1 February 2004). "Defining haplotype blocks and tag single-nucleotide polymorphisms in the human genome". Human Molecular Genetics. 13 (3): 335–342. doi:10.1093/hmg/ddh035. PMID 14681300.
  4. ^ Indap, Amit R; Marth, Gabor T; Struble, Craig A; Tonellato, Peter; Olivier, Michael (2005). "Analysis of concordance of different haplotype block partitioning algorithms". BMC Bioinformatics. 6 (1): 303. doi:10.1186/1471-2105-6-303. PMC 1343594. PMID 16356172.
  5. ^ Cardon, Lon R.; Abecasis, Gonçalo R. (March 2003). "Using haplotype blocks to map human complex trait loci". Trends in Genetics. 19 (3): 135–140. CiteSeerX 10.1.1.398.8937. doi:10.1016/S0168-9525(03)00022-2. PMID 12615007. {{cite journal}}: Cite uses deprecated parameter |citeseerx= (help)
  6. ^ Wang, Ning; Akey, Joshua M.; Zhang, Kun; Chakraborty, Ranajit; Jin, Li (November 2002). "Distribution of Recombination Crossovers and the Origin of Haplotype Blocks: The Interplay of Population History, Recombination, and Mutation". The American Journal of Human Genetics. 71 (5): 1227–1234. doi:10.1086/344398. PMC 385104. PMID 12384857.
  7. ^ Patil, N; Berno, AJ; Hinds, DA; Barrett, WA; Doshi, JM; Hacker, CR; Kautzer, CR; Lee, DH; Marjoribanks, C; McDonough, DP; Nguyen, BT; Norris, MC; Sheehan, JB; Shen, N; Stern, D; Stokowski, RP; Thomas, DJ; Trulson, MO; Vyas, KR; Frazer, KA; Fodor, SP; Cox, DR (23 November 2001). "Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21". Science. 294 (5547): 1719–23. Bibcode:2001Sci...294.1719P. doi:10.1126/science.1065573. PMID 11721056. S2CID 14168219.
  8. ^ Zhang, Kui; Calabrese, Peter; Nordborg, Magnus; Sun, Fengzhu (December 2002). "Haplotype Block Structure and Its Applications to Association Studies: Power and Study Designs". The American Journal of Human Genetics. 71 (6): 1386–1394. doi:10.1086/344780. PMC 378580. PMID 12439824.
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