A first-generation linkage disequilibrium map of human chromosome 22 - PubMed (original) (raw)
. 2002 Aug 1;418(6897):544-8.
doi: 10.1038/nature00864. Epub 2002 Jul 10.
Gonçalo R Abecasis, Suzannah Bumpstead, Yuan Chen, Sarah Hunt, David M Beare, Jagjit Pabial, Thomas Dibling, Emma Tinsley, Susan Kirby, David Carter, Marianna Papaspyridonos, Simon Livingstone, Rocky Ganske, Elin Lõhmussaar, Jana Zernant, Neeme Tõnisson, Maido Remm, Reedik Mägi, Tarmo Puurand, Jaak Vilo, Ants Kurg, Kate Rice, Panos Deloukas, Richard Mott, Andres Metspalu, David R Bentley, Lon R Cardon, Ian Dunham
Affiliations
- PMID: 12110843
- DOI: 10.1038/nature00864
Free article
A first-generation linkage disequilibrium map of human chromosome 22
Elisabeth Dawson et al. Nature. 2002.
Free article
Abstract
DNA sequence variants in specific genes or regions of the human genome are responsible for a variety of phenotypes such as disease risk or variable drug response. These variants can be investigated directly, or through their non-random associations with neighbouring markers (called linkage disequilibrium (LD)). Here we report measurement of LD along the complete sequence of human chromosome 22. Duplicate genotyping and analysis of 1,504 markers in Centre d'Etude du Polymorphisme Humain (CEPH) reference families at a median spacing of 15 kilobases (kb) reveals a highly variable pattern of LD along the chromosome, in which extensive regions of nearly complete LD up to 804 kb in length are interspersed with regions of little or no detectable LD. The LD patterns are replicated in a panel of unrelated UK Caucasians. There is a strong correlation between high LD and low recombination frequency in the extant genetic map, suggesting that historical and contemporary recombination rates are similar. This study demonstrates the feasibility of developing genome-wide maps of LD.
Similar articles
- Recombination hotspots and block structure of linkage disequilibrium in the human genome exemplified by detailed analysis of PGM1 on 1p31.
Rana NA, Ebenezer ND, Webster AR, Linares AR, Whitehouse DB, Povey S, Hardcastle AJ. Rana NA, et al. Hum Mol Genet. 2004 Dec 15;13(24):3089-102. doi: 10.1093/hmg/ddh337. Epub 2004 Oct 27. Hum Mol Genet. 2004. PMID: 15509594 - The extent of linkage disequilibrium in Arabidopsis thaliana.
Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D. Nordborg M, et al. Nat Genet. 2002 Feb;30(2):190-3. doi: 10.1038/ng813. Epub 2002 Jan 7. Nat Genet. 2002. PMID: 11780140 - Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC.
Ahmad T, Neville M, Marshall SE, Armuzzi A, Mulcahy-Hawes K, Crawshaw J, Sato H, Ling KL, Barnardo M, Goldthorpe S, Walton R, Bunce M, Jewell DP, Welsh KI. Ahmad T, et al. Hum Mol Genet. 2003 Mar 15;12(6):647-56. Hum Mol Genet. 2003. PMID: 12620970 - Characterization of LD structures and the utility of HapMap in genetic association studies.
Gu CC, Yu K, Rao DC. Gu CC, et al. Adv Genet. 2008;60:407-35. doi: 10.1016/S0065-2660(07)00415-4. Adv Genet. 2008. PMID: 18358328 Review. - On selecting markers for association studies: patterns of linkage disequilibrium between two and three diallelic loci.
Garner C, Slatkin M. Garner C, et al. Genet Epidemiol. 2003 Jan;24(1):57-67. doi: 10.1002/gepi.10217. Genet Epidemiol. 2003. PMID: 12508256 Review.
Cited by
- Genome-wide association mapping of quantitative traits in outbred mice.
Zhang W, Korstanje R, Thaisz J, Staedtler F, Harttman N, Xu L, Feng M, Yanas L, Yang H, Valdar W, Churchill GA, Dipetrillo K. Zhang W, et al. G3 (Bethesda). 2012 Feb;2(2):167-74. doi: 10.1534/g3.111.001792. Epub 2012 Feb 1. G3 (Bethesda). 2012. PMID: 22384395 Free PMC article. - A survey of haplotype variants at several disease candidate genes: the importance of rare variants for complex diseases.
Liu PY, Zhang YY, Lu Y, Long JR, Shen H, Zhao LJ, Xu FH, Xiao P, Xiong DH, Liu YJ, Recker RR, Deng HW. Liu PY, et al. J Med Genet. 2005 Mar;42(3):221-7. doi: 10.1136/jmg.2004.024752. J Med Genet. 2005. PMID: 15744035 Free PMC article. - Evidence of a large-scale functional organization of mammalian chromosomes.
Petkov PM, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen K. Petkov PM, et al. PLoS Genet. 2005 Sep;1(3):e33. doi: 10.1371/journal.pgen.0010033. PLoS Genet. 2005. PMID: 16163395 Free PMC article. - Haplotypes, "hyplotypes," and complex genetic disease.
Luft FC. Luft FC. J Mol Med (Berl). 2003 Apr;81(4):215-7. doi: 10.1007/s00109-003-0429-8. J Mol Med (Berl). 2003. PMID: 12785323 No abstract available. - Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data.
Zhang K, Sun F, Waterman MS, Chen T. Zhang K, et al. Am J Hum Genet. 2003 Jul;73(1):63-73. doi: 10.1086/376437. Epub 2003 Jun 10. Am J Hum Genet. 2003. PMID: 12802783 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials