Global similarity with local differences in linkage disequilibrium between the Dutch and HapMap-CEU populations

European Journal of Human Genetics

Volumn 17, Issue 6, 2009, Pages 802-810

  Pardo, Luba ^a   Bochdanovits, Zoltán ^a   de Geus, Eco ^b   Hottenga, Jouke J ^b   Sullivan, Patrick ^c   Posthuma, Danielle ^a,b   Penninx, Brenda W J H ^d,e,f   Boomsma, Dorret ^b   Heutink, Peter ^a  

^a VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^b VU UNIVERSITY AMSTERDAM   (Netherlands)

^c UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^d VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^e LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^f UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOSOME; CONTROLLED STUDY; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC VARIABILITY; HAPLOTYPE MAP; HUMAN; NETHERLANDS; NORMAL HUMAN; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED STATES;

EUROPEAN CONTINENTAL ANCESTRY GROUP; GENE FREQUENCY; GENETICS, POPULATION; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; NETHERLANDS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 67349166489     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2008.248     Document Type: Article

References (39)

1. Zeggini E, Weedon MN, Lindgren CM et al: Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science 2007; 316: 1336-1341.
2. Hinds DA, Stuve LL, Nilsen GB et al: Whole-genome patterns of common DNA variation in three human populations. Science 2005; 307: 1072-1079.
3. Gabriel SB, Schaffner SF, Nguyen H et al: The structure of haplotype blocks in the human genome. Science 2002; 296: 2225-2229.
4. International HapMap Consortium: A haplotype map of the human genome. Nature 2005; 437: 1299-1320.
5. Collins FS, GuyerCMS, Chakravarti A: Variations on a theme: cataloging human DNA sequence variation. Science 1997; 278: 1580-1581.
6. Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES: High-resolution haplotype structure in the human genome. Nat Genet 2001; 29: 229-232.
7. The International HapMap Consortium: The International HapMap Project. Nature 2003; 426: 789-796.
8. Xing J, Witherspoon DJ, Watkins WS, Zhang Y, Tolpinrud W, Jorde LB: HapMap tagSNP transferability in multiple populations: General guidelines. Genomics 2008; 92: 41-51.
9. Ribas G, Gonzalez-Neira A, Salas A et al: Evaluating HapMap SNP data transferability in a large-scale genotyping project involving 175 cancer-associated genes. Hum Genet 2006; 118: 669-679.
10. Mueller JC, Lohmussaar E, Magi R et al: Linkage disequilibrium patterns and tagSNP transferability among European populations. Am J Hum Genet 2005; 76: 387-398.
11. de Bakker PI, Yelensky R, Pe'er I, Gabriel SB, Daly MJ, Altshuler D: Efficiency and power in genetic association studies. Nat Genet 2005; 37: 1217-1223.
12. Gonzalez-Neira A, Ke X, Lao O et al: The portability of tagSNPs across populations: A worldwide survey. Genome Res 2006; 16: 323-330.
13. Conrad DF, Jakobsson M, Coop G et al: A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet 2006; 38: 1251-1260.
14. Montpetit A, Nelis M, Laflamme P et al: An evaluation of the performance of tag SNPs derived from HapMap in a caucasian population. PLoS Genet 2006; 2: E27.
15. Liu N, Sawyer SL, Mukherjee N et al: Haplotype block structures show significant variation among populations. Genet Epidemiol 2004; 27: 385-400.
16. Gu S, Pakstis AJ, Li H, Speed WC, Kidd JR, Kidd KK: Significant variation in haplotype block structure but conservation in tagSNP patterns among global populations. Eur J Hum Genet 2007; 15: 302-312.
17. Greenwood TA, Rana BK, Schork NJ: Human haplotype block sizes are negatively correlated with recombination rates. Genome Res 2004; 14: 1358-1361.
18. Osabe D, Tanahashi T, Nomura K et al: Evaluation of sample size effect on the identification of haplotype blocks. BMC Bioinformatics 2007; 8: 200.
19. Kayser M, Liu F, Janssens ACJW et al: Three genome-wide association studies and a linkage analysis identify HERC2 as a human iris color gene. Am J Hum Genet 2008; 82: 411-423.
20. van Es MA, van Vught PWJ, Blauw HM et al: Genetic variation in DPP6 is associated with susceptibility to amyotrophic lateral sclerosis. Nat Genet 2008; 40: 29-31.
21. Sulem. P, Gudbjartsson DF, Stacey SN et al: Genetic determinants of hair, eye and skin pigmentation in Europeans. Nat Genet 2007; 39: 1443-1452.
22. GAIN Collaborative Research GroupManolio TA, Rodriguez LL, Brooks L et al: New models of collaboration in genome-wide association studies: The Genetic Association Information Network. Nat Genet 2007; 39: 1045-1051.
23. Boomsma DI, Willemsen G, Sullivan PF et al: Genome-wide association of major depression: Description of samples for the GAIN Major Depressive Disorder Study: NTR and NESDA biobank projects. Eur J Hum Genet 2008; 16: 335-342.
24. HAmminger BM, Saelim. B, Sullivan PF: TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits. Bioinformatics 2006; 22: 626-627.
25. International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR et al: A second generation human haplotype map of over 3.1 million SNPs. Nature 2007; 449: 851-861.
26. Wheeler DL, Barrett T, Benson DA et al: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2008; 36: D13-D21.
27. BarreAt JC, Fry B, Mailer J, Daly MJ: Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005; 21 263-265.
28. Sokal R, Rohlf F: Correlation; in Company WHFa (ed):: Biometry. NewYork, 2003, pp 555-608.
29. PArcell S, Neale B, Todd-Brown K et al: PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559-575.
30. Marchini J, Cutler D, Patterson N et al: A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet 2006; 78: 437-450.
31. Terwilliger JD, Hiekkalinna T: An utter refutation of the 'Fundamental Theorem of the HapMap'. Eur J Hum Genet 2006; 14: 426-437.
32. Gu CC, Yu K, Rao DC: Characterization of LD structures and the utility of HapMap in genetic association studies. AdvGenet 2008; 60: 407-435.
33. Pardo LM, MacKay I, Oostra B, van Duijn CM, Aulchenko YS: The effect of genetic drift in a young genetically isolated population. Ann Hum Genet 2005; 69: 288-295.
34. Gu CC, Yu K, Boerwinkle E: Measuring market information content by the ambiguity of block boundaries observed in dense SNP data. Ann Hum Genet 2007; 71: 127-140.
35. Teare MD, Dunning AM, Durocher F, Rennart G, Easton DF: Sampling distribution of summary linkage disequilibrium. measures. Ann Hum Genet 2002, 66: 223-233.
36. Weiss KM, Clark AG: Linkage disequilibrium and the mapping of complex human traits. Rends Genet 2002; 18: 19-24.
37. Zeggini E, Rayner W, Morris AP et al: An evaluation of HapMap sample size and tagging SNP performance in large-scale empirical and simulated data sets. Nat Genet 2005; 37: 1320-1322.
38. Ioannidis JPA: Non-replication and inconsistency in the genome-wide association setting. Hum Hered 2007; 64: 203-213.
39. McCarthy MI, Abecasis GR, Cardon LR et al: Genome-wide association studies for complex traits: Consensus, uncertainty and challenges. Nat Rev Genet 2008; 9: 356-369.