Patterns of linkage disequilibrium in the MHC region on human chromosome 6p (original) (raw)
References
Ahmad T, Neville M, Marshall SE, Armuzzi A, Mulcahy-Hawes K, Crawshaw J, Sato H, Ling KL, Barnardo M, Goldthorpe S, et al (2003) Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC. Hum Mol Genet 12:647–656 ArticleCASPubMed Google Scholar
Allcock RJ, Christiansen FT, Price P (1999) The central MHC gene IKBL carries a structural polymorphism that is associated with HLA-A3,B7,DR15. Immunogenetics 49:660–665 ArticleCASPubMed Google Scholar
Barbujani G, Bertorelle G (2001) Genetics and the population history of Europe. Proc Natl Acad Sci USA 98:22–25 CASPubMed Google Scholar
Becker KG, Simon RM, Bailey-Wilson JE, Freidlin B, Biddison WE, McFarland HF, Trent JM (1998) Clustering of non-major histocompatibility complex susceptibility candidate loci in human autoimmune diseases. Proc Natl Acad Sci USA 95:9979–9984 CASPubMed Google Scholar
Cereb N, Hughes AL, Yang SY (1997) Locus-specific conservation of the HLA class I introns by intra-locus homogenization. Immunogenetics 47:30–36 ArticleCASPubMed Google Scholar
Cullen M, Perfetto SP, Klitz W, Nelson G, Carrington M (2002) High-resolution patterns of meiotic recombination across the human major histocompatibility complex. Am J Hum Genet 71:759–776 ArticlePubMed Google Scholar
D’Alfonso S, Bolognesi E, Mazzola G, Dall’Omo A, Richiardi PM (1999) Historical recombinant sites in extended HLA haplotypes. J Biol Regul Homeost Agents 13:8–13 CASPubMed Google Scholar
Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES (2001) High-resolution haplotype structure in the human genome. Nat Genet 29:229–232 CASPubMed Google Scholar
Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, et al (2002) A first-generation linkage disequilibrium map of human chromosome 22. Nature 418:544–548 CASPubMed Google Scholar
De La Vega FM, Dailey D, Ziegle J, Williams J, Madden D, Gilbert DA (2002) New generation pharmacogenomic tools: a SNP linkage disequilibrium map, validated SNP assay resource, and high-throughput instrumentation system for large-scale genetic studies. Biotechniques Suppl:48–54 Google Scholar
De La Vega FM, Su X, Avi-Itzhak HI, Halldorson BV, Gordon D, Collins A, Lippert R, Schwartz R, Scafe CR, Wang Y, et al (2003) Patterns of linkage disequilibrium across human chromosomes 6, 21, and 22 in African-American and Caucasian populations. Nat Genet (in press)
Frisse L, Hudson RR, Bartoszewicz A, Wall JD, Donfack J, Di Rienzo A (2001) Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am J Hum Genet 69:831–843 ArticleCASPubMed Google Scholar
Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, et al (2002) The structure of haplotype blocks in the human genome. Science 296:2225–2229 CASPubMed Google Scholar
Gaudieri S, Leelayuwat C, Tay GK, Townend DC, Dawkins RL (1997) The major histocompatability complex (MHC) contains conserved polymorphic genomic sequences that are shuffled by recombination to form ethnic-specific haplotypes. J Mol Evol 45:17–23 CASPubMed Google Scholar
Goldstein DB (2001) Islands of linkage disequilibrium. Nat Genet 29:109–111 CASPubMed Google Scholar
Guillon H, Massy B de (2002) An initiation site for meiotic crossing-over and gene conversion in the mouse. Nat Genet 32:296–299 ArticleCASPubMed Google Scholar
Hampe J, Wollstein A, Lu T, Frevel HJ, Will M, Manaster C, Schreiber S (2001) An integrated system for high throughput TaqMan based SNP genotyping. Bioinformatics 17:654–655 ArticleCASPubMed Google Scholar
Jeffreys AJ, Neumann R (2002) Reciprocal crossover asymmetry and meiotic drive in a human recombination hot spot. Nat Genet 31:267–271 ArticleCASPubMed Google Scholar
Jeffreys AJ, Murray J, Neumann R (1998) High-resolution mapping of crossovers in human sperm defines a minisatellite-associated recombination hotspot. Mol Cell 2:267–273 CASPubMed Google Scholar
Jeffreys AJ, Kauppi L, Neumann R (2001) Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat Genet 29:217–222 CASPubMed Google Scholar
Johnson GC, Esposito L, Barratt BJ, Smith AN, Heward J, Di Genova G, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, et al (2001) Haplotype tagging for the identification of common disease genes. Nat Genet 29:233–237 CASPubMed Google Scholar
Kauppi L, Sajantila A, Jeffreys AJ (2003) Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region. Hum Mol Genet 12:33–40 ArticleCASPubMed Google Scholar
Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, New York
Lercher MJ, Hurst LD (2002) Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet 18:337–340 ArticleCASPubMed Google Scholar
Lewontin RC (1988) On measures of gametic disequilibrium. Genetics 120:849–852 CASPubMed Google Scholar
Lonjou C, Zhang W, Collins A, Tapper WJ, Elahi E, Maniatis N, Morton NE (2003) Linkage disequilibrium in human populations. Proc Natl Acad Sci USA 29:29 Google Scholar
Maniatis N, Collins A, Xu CF, McCarthy LC, Hewett DR, Tapper W, Ennis S, Ke X, Morton NE (2002) The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. Proc Natl Acad Sci USA 99:2228–2233 CASPubMed Google Scholar
May CA, Shone AC, Kalaydjieva L, Sajantila A, Jeffreys AJ (2002) Crossover clustering and rapid decay of linkage disequilibrium in the Xp/Yp pseudoautosomal gene SHOX. Nat Genet 31:272–275 ArticleCASPubMed Google Scholar
Meyer D, Thomson G (2001) How selection shapes variation of the human major histocompatibility complex: a review. Ann Hum Genet 65:1–26 ArticleCASPubMed Google Scholar
Morton NE, Zhang W, Taillon-Miller P, Ennis S, Kwok PY, Collins A (2001) The optimal measure of allelic association. Proc Natl Acad Sci USA 98:5217–5221 ArticleCASPubMed Google Scholar
Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA, Studebaker JF, Ankener WM, Alfisi SV, Kuo FS, et al (2003) Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat Genet 33:382–387 CASPubMed Google Scholar
Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, et al (2001) Linkage disequilibrium in the human genome. Nature 411:199–204 ArticlePubMed Google Scholar
Reich DE, Schaffner SF, Daly MJ, McVean G, Mullikin JC, Higgins JM, Richter DJ, Lander ES, Altshuler D (2002) Human genome sequence variation and the influence of gene history, mutation and recombination. Nat Genet 32:135–142 ArticleCASPubMed Google Scholar
Sanchez-Mazas A, Djoulah S, Busson M, Le Monnier de Gouville I, Poirier JC, Dehay C, Charron D, Excoffier L, Schneider S, Langaney A, et al (2000) A linkage disequilibrium map of the MHC region based on the analysis of 14 loci haplotypes in 50 French families. Eur J Hum Genet 8:33–41 ArticleCASPubMed Google Scholar
Schneider S, Roessli D, Excoffier L (2000) Arlequin: a software for population genetics data analysis, ver 2.000. Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva
Simoni L, Calafell F, Pettener D, Bertranpetit J, Barbujani G (2000) Geographic patterns of mtDNA diversity in Europe. Am J Hum Genet 66:262–278 CASPubMed Google Scholar
Stephens JC, Reich DE, Goldstein DB, Shin HD, Smith MW, Carrington M, Winkler C, Huttley GA, Allikmets R, Schriml L, et al (1998) Dating the origin of the CCR5-Delta32 AIDS-resistance allele by the coalescence of haplotypes. Am J Hum Genet 62:1507–1515 CASPubMed Google Scholar
Tapper WJ, Ke X, Morton NE, Collins A (2002) Recombination, interference and sequence: comparison of chromosomes 21 and 22. Ann Hum Genet 66:75–86 ArticleCASPubMed Google Scholar
Teare MD, Dunning AM, Durocher F, Rennart G, Easton DF (2002) Sampling distribution of summary linkage disequilibrium measures. Ann Hum Genet 66:223–233 Google Scholar
Walsh EC, Mather KA, Schaffner SF, Farwell L, Daly MJ, Patterson N, Cullen M, Carrington M, Bugawan TL, Erlich H, Campbell J, Barrett J, Miller K, Thomson G, Lander ES, Rioux JD (2003) An integrated haplotype map of the human major histocompatibility complex. Am J Hum Genet 73:580–590 ArticleCASPubMed Google Scholar
Wang WY, Todd JA (2003) The usefulness of different density SNP maps for disease association studies of common variants. Hum Mol Genet 12:3145–3149 ArticleCASPubMed Google Scholar
Zavattari P, Deidda E, Whalen M, Lampis R, Mulargia A, Loddo M, Eaves I, Mastio G, Todd JA, Cucca F (2000) Major factors influencing linkage disequilibrium by analysis of different chromosome regions in distinct populations: demography, chromosome recombination frequency and selection. Hum Mol Genet 9:2947–2957 CASPubMed Google Scholar
Zhang K, Akey JM, Wang N, Xiong M, Chakraborty R, Jin L (2003) Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: an act of genetic drift. Hum Genet 113:51–59 PubMed Google Scholar