Linkage disequilibrium patterns and tagSNP transferability among European populations

American Journal of Human Genetics

Volumn 76, Issue 3, 2005, Pages 387-398

  Mueller, Jakob C ^a   Lõhmussaar, Elin ^a,b   Mägi, Reedik ^b   Remm, Maido ^b   Bettecken, Thomas ^a   Lichtner, Peter ^a   Biskup, Saskia ^a   Illig, Thomas ^a   Pfeufer, Arne ^c   Luedemann, Jan ^d   Schreiber, Stefan ^e   Pramstaller, Peter ^f   Pichler, Irene ^f   Romeo, Giovanni ^g   Gaddi, Anthony ^g   Testa, Alessandra ^h   Wichmann, Heinz Erich ^a   Metspalu, Andres ^b   Meitinger, Thomas ^a,c  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b UNIVERSITY OF TARTU   (Estonia)

^c TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^d UNIVERSITY OF GREIFSWALD   (Germany)

^e UNIVERSITY HOSPITAL SCHLESWIG HOLSTEIN   (Germany)

^f INSTITUTE FOR RENEWABLE ENERGY   (Italy)

^g UNIVERSITY OF BOLOGNA   (Italy)

^h Ctr Clin Physiol Cons Naz D   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT;

ALLELISM; ARTICLE; EUROPE; GENE LINKAGE DISEQUILIBRIUM; GENE TRANSFER; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC POLYMORPHISM; GENETIC TRAIT; GENETIC VARIABILITY; GENOTYPE; HAPMAP PROJECT; HUMAN; NATURAL POPULATION; POPULATION DENSITY; POPULATION GENETIC PARAMETERS; POPULATION GENETIC STRUCTURE; POPULATION GENETICS; PREDICTION; PRIORITY JOURNAL; SAMPLING; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; TAGGING SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 13844253254     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/427925     Document Type: Article

References (25)

1. Barbujani G, Sokal RR (1990) Zones of sharp genetic change in Europe are also linguistic boundaries. Proc Natl Acad Sci USA 87:1816-1819
2. Cardon LR, Abecasis GR (2003) Using haplotype blocks to map human complex trait loci. Trends Genet 19:135-140
3. Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA (2004) Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74:106-120
4. Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The history and geography of human genes. Princeton University Press, Princeton, NJ
5. Chapman JM, Cooper JD, Todd JA, Clayton DG (2003) Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power. Hum Hered 56:18-31
6. Dausset J, Cann H, Cohen D, Lathrop M, Lalouel JM, White R (1990) Centre d'etude du polymorphisme humain (CEPH): collaborative genetic mapping of the human genome. Genomics 6:575-577
7. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D (2002) The structure of haplotype blocks in the human genome. Science 296:2225-2229
8. Hoggart CJ, Shriver MD, Kittles RA, Clayton DG, McKeigue PM (2004) Design and analysis of admixture mapping studies. Am J Hum Genet 74:965-978
9. International HapMap Consortium (2003) The International HapMap Project. Nature 426:789-796
10. Ke X, Hunt S, Tapper W, Lawrence R, Stavrides G, Ghori J, Whittaker P, Collins A, Morris AP, Bentley D, Cardon LR, Deloukas P (2004) The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum Mol Genet 13:577-588
11. Lao O, Andres AM, Mateu E, Bertranpetit J, Calafell F (2003) Spatial patterns of cystic fibrosis mutation spectra in European populations. Eur J Hum Genet 11:385-394
12. Mannila H, Koivisto M, Perola M, Varilo T, Hennah W, Ekelund J, Lukk M, Peltonen L, Ukkonen E (2003) Minimum description length block finder, a method to identify haplotype blocks and to compare the strength of block boundaries. Am J Hum Genet 73:86-94
13. Marchini J, Cardon LR, Phillips MS, Donnelly P (2004) The effects of human population structure on large genetic association studies. Nat Genet 36:512-517
14. Nei M (1972) Genetic distance between populations. Am Nat 106:283-292
15. Nejentsev S, Godfrey L, Snook H, Rance H, Nutland S, Walker NM, Lam AC, Guja C, Ionescu-Tirgoviste C, Undlien DE, Ronningen KS, Tuomilehto-Wolf E, Tuomilehto J, Newport MJ, Clayton DG, Todd JA (2004) Comparative high-resolution analysis of linkage disequilibrium and tag single nucieotide polymorphisms between populations in the vitamin D receptor gene. Hum Mol Genet 13:1633-1639
16. Ng MCY, Wang Y, So WY, Cheng S, Visvikis S, Zee RYL, Fernandez-Cruz A, Lindpaintner K, Chan JCN (2004) Ethnic differences in the linkage disequilibrium and distribution of single-nucleotide polymorphisms in 35 candidate genes for cardiovascular diseases. Genomics 83:559-565
17. Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA, Studebaker JF, et al (2003) Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat Genet 33:382-387
18. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW (2002) Genetic structure of human populations. Science 298:2381-2385
19. Schwartz R, Halldorsson BV, Bafna V, Clark AG, Istrail S (2003) Robustness of inference of haplotype block structure. J Comput Biol 10:13-19
20. Stenzel A, Lu T, Koch WA, Hampe J, Guenther SM, De La Vega FM, Krawczak M, Schreiber S (2004) Patterns of linkage disequilibrium in the MHC region on human chromosome 6p. Hum Genet 114:377-385
21. Thompson D, Stram D, Goldgar D, Witte JS (2003) Haplotype tagging single nucleotide polymorphisms and association studies. Hum Hered 56:48-55
22. Wall JD, Pritchard JK (2003) Haplotype blocks and linkage disequilibrium in the human genome. Nat Rev Genet 4:587-597
23. Wang WYS, Todd JA (2003) The usefulness of different density SNP maps for disease association studies of common variants. Hum Mol Genet 12:3145-3149
24. Weale ME, Depondt C, Macdonald SJ, Smith A, Lai PS, Shorvon SD, Wood NW, Goldstein DB (2003) Selection and evaluation of tagging SNPs in the neuronal-sodium-channel gene SCN1A: implications for linkage-disequilibrium gene mapping. Am J Hum Genet 73:551-565
25. Zhang K, Jin L (2003) HaploBlockFinder: haplotype block analyses. Bioinformatics 19:1300-1301