Patterns of linkage disequilibrium in the MHC region on human chromosome 6p - PubMed (original) (raw)

Comparative Study

. 2004 Mar;114(4):377-85.

doi: 10.1007/s00439-003-1075-5. Epub 2004 Jan 22.

Affiliations

• PMID: 14740295
• DOI: 10.1007/s00439-003-1075-5

Comparative Study

Patterns of linkage disequilibrium in the MHC region on human chromosome 6p

Annette Stenzel et al. Hum Genet. 2004 Mar.

Abstract

Single nucleotide polymorphisms (SNPs) in the human genome are thought to be organised into blocks of high internal linkage disequilibrium (LD), separated by intermittent recombination hotspots. Since understanding haplotype structure is critical for an accurate assessment of inter-individual genetic differences, we investigated up to 968 SNPs from a 10-Mb region on chromosome 6p21, including the human major histocompatibility complex (MHC), in five different population samples (45-550 individuals). Regions of well-defined block structure were found to coexist alongside large areas lacking any clear structure; occasional long-range LD was observed in all five samples. The four white populations analysed were remarkably similar in terms of the extend and spatial distribution of local LD. In US African Americans, the distribution of LD was similar to that in the white populations but the observed haplotype diversity was higher. The existence of large regions without any clear block structure renders the systematic and thorough construction of SNP haplotype maps a crucial prerequisite for disease-association studies.

PubMed Disclaimer

Similar articles

• Evaluating linkage disequilibrium and recombination provides a haplotype-tagging SNP panel of the major histocompatibility complex in African Americans.
  Kelley JM, Hughes LB, Feng R, Liu N, Padilla MA, Vaughan LK, Bridges SL Jr. Kelley JM, et al. Genes Immun. 2008 Apr;9(3):271-3. doi: 10.1038/gene.2008.6. Epub 2008 Feb 28. Genes Immun. 2008. PMID: 18305489
• The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern.
  De La Vega FM, Isaac H, Collins A, Scafe CR, Halldórsson BV, Su X, Lippert RA, Wang Y, Laig-Webster M, Koehler RT, Ziegle JS, Wogan LT, Stevens JF, Leinen KM, Olson SJ, Guegler KJ, You X, Xu LH, Hemken HG, Kalush F, Itakura M, Zheng Y, de Thé G, O'Brien SJ, Clark AG, Istrail S, Hunkapiller MW, Spier EG, Gilbert DA. De La Vega FM, et al. Genome Res. 2005 Apr;15(4):454-62. doi: 10.1101/gr.3241705. Epub 2005 Mar 21. Genome Res. 2005. PMID: 15781572 Free PMC article.
• A comparison of linkage disequilibrium patterns and estimated population recombination rates across multiple populations.
  Evans DM, Cardon LR. Evans DM, et al. Am J Hum Genet. 2005 Apr;76(4):681-7. doi: 10.1086/429274. Epub 2005 Feb 17. Am J Hum Genet. 2005. PMID: 15719321 Free PMC article.
• Patterns of genetic variation in the hypertension candidate gene GRK4: ethnic variation and haplotype structure.
  Lohmueller KE, Wong LJ, Mauney MM, Jiang L, Felder RA, Jose PA, Williams SM. Lohmueller KE, et al. Ann Hum Genet. 2006 Jan;70(Pt 1):27-41. doi: 10.1111/j.1529-8817.2005.00197.x. Ann Hum Genet. 2006. PMID: 16441255
• The impact of SNP density on fine-scale patterns of linkage disequilibrium.
  Ke X, Hunt S, Tapper W, Lawrence R, Stavrides G, Ghori J, Whittaker P, Collins A, Morris AP, Bentley D, Cardon LR, Deloukas P. Ke X, et al. Hum Mol Genet. 2004 Mar 15;13(6):577-88. doi: 10.1093/hmg/ddh060. Epub 2004 Jan 20. Hum Mol Genet. 2004. PMID: 14734624

Cited by

• Genome-wide association study of behavioural and psychiatric features in human prion disease.
  Thompson AG, Uphill J, Lowe J, Porter MC, Lukic A, Carswell C, Rudge P, MacKay A, Collinge J, Mead S. Thompson AG, et al. Transl Psychiatry. 2015 Apr 21;5(4):e552. doi: 10.1038/tp.2015.42. Transl Psychiatry. 2015. PMID: 25897833 Free PMC article.
• Functional gene polymorphism to reveal species history: the case of the CRTISO gene in cultivated carrots.
  Soufflet-Freslon V, Jourdan M, Clotault J, Huet S, Briard M, Peltier D, Geoffriau E. Soufflet-Freslon V, et al. PLoS One. 2013 Aug 5;8(8):e70801. doi: 10.1371/journal.pone.0070801. Print 2013. PLoS One. 2013. PMID: 23940644 Free PMC article.
• Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype.
  Tragante V, Gho JMIH, Felix JF, Vasan RS, Smith NL, Voight BF; CHARGE Heart Failure Working Group; Palmer C, van der Harst P, Moore JH, Asselbergs FW. Tragante V, et al. BioData Min. 2017 May 26;10:18. doi: 10.1186/s13040-017-0137-5. eCollection 2017. BioData Min. 2017. PMID: 28559929 Free PMC article.
• Very long haplotype tracts characterized at high resolution from HLA homozygous cell lines.
  Norman PJ, Norberg SJ, Nemat-Gorgani N, Royce T, Hollenbach JA, Shults Won M, Guethlein LA, Gunderson KL, Ronaghi M, Parham P. Norman PJ, et al. Immunogenetics. 2015 Sep;67(9):479-85. doi: 10.1007/s00251-015-0857-y. Epub 2015 Jul 22. Immunogenetics. 2015. PMID: 26198775 Free PMC article.
• A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphisms.
  Miretti MM, Walsh EC, Ke X, Delgado M, Griffiths M, Hunt S, Morrison J, Whittaker P, Lander ES, Cardon LR, Bentley DR, Rioux JD, Beck S, Deloukas P. Miretti MM, et al. Am J Hum Genet. 2005 Apr;76(4):634-46. doi: 10.1086/429393. Epub 2005 Mar 1. Am J Hum Genet. 2005. PMID: 15747258 Free PMC article.

References

1. 1. Hum Mol Genet. 2003 Dec 1;12(23):3145-9 - PubMed
2. 1. Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2228-33 - PubMed
3. 1. Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):22-5 - PubMed
4. 1. Immunogenetics. 1999 Jul;49(7-8):660-5 - PubMed
5. 1. Mol Cell. 1998 Aug;2(2):267-73 - PubMed

Publication types

MeSH terms

LinkOut - more resources

• Full Text Sources

  • Springer

• Other Literature Sources

  • The Lens - Patent Citations Database

• Research Materials

  • Coriell Cell Repositories
  • NCI CPTC Antibody Characterization Program

• Miscellaneous

  • NCI CPTAC Assay Portal