Haplotype block structures show significant variation among populations

Genetic Epidemiology

Volumn 27, Issue 4, 2004, Pages 385-400

  Liu, Nianjun ^a   Sawyer, Sarah L ^b   Mukherjee, Namita ^a   Pakstis, Andrew J ^a   Kidd, Judith R ^a   Kidd, Kenneth K ^a   Brookes, Anthony J ^b   Zhao, Hongyu ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b KAROLINSKA INSTITUTE   (Sweden)

Author keywords

Haplotype; Haplotype block; Similarity; Single nucleotide polymorphisms; Tagging SNP

Indexed keywords

AFRICA; ARTICLE; CHROMOSOME 10; COMPARATIVE STUDY; CONTROLLED STUDY; EUROPE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; HAPLOTYPE; HUMAN; HUMAN GENOME; INTERMETHOD COMPARISON; POPULATION GENETICS; POPULATION RESEARCH; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 10; GENETIC PREDISPOSITION TO DISEASE; GENETICS, POPULATION; GENOME, HUMAN; HAPLOTYPES; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; VARIATION (GENETICS);

EID: 10044238869     PISSN: 07410395     EISSN: None     Source Type: Journal    
DOI: 10.1002/gepi.20026     Document Type: Article

References (26)

1. Abecasis GR, Cookson WO. 2000. GOLD - graphical overview of linkage disequilibrium. Bioinformatics 16:182-183.
2. Avi-Itzhak HI, Su X, De La Vega FM. 2003. Selection of minimum subsets of single nucleotide polymorphisms to capture haplotype block diversity. Pacific Symp Biocomput 8:466-477.
3. Bafna V, Halldorsson BV, Schwartz R, Clark AG, Istrail S. 2003. Haplotypes and informative SNP selection algorithms: don't block out information. In: Vingron M, Istrail S, Pevzner P, Waterman M, editors. Proceedings of the Seventh Annual International Conference on Computational Molecular Biology. New York: ACM Press. p 19-27.
4. Clayton D. 2001. http://www.nature.com/ng/journal/v29/n2/extref/ng1001- 233-S10.pdf.
5. Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES. 2001. High-resolution haplotype structure in the human genome. Nat Genet 29:229-232.
6. Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, Carter D, Papaspyridonos M, Livingstone S, Ganske R, Lohmussaar E, Zernant J, Tonisson N, Remm M, Magi R, Purrand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR, Dunham I. 2002. A first-generation linkage disequilibrium map of human chromosome 22. Nature 418:544-548.
7. De La Vega FM, Su X, Avi-itzhak H, Scafe C, Spier E. 2002. The architecture of linkage disequilibrium blocks across human chromosomes 6, 21, and 22. Am J Hum Genet [Suppl] 71:205.
8. 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. 2002a. The structure of haplotype blocks in the human genome. Science 296:2225-2229.
9. Gabriel SB, Schaffner SF, Reich DE, Sabeti P, Freedman M, Daly MJ, Altshuler D. 2002b. An extended analysis of haplotype structure in the human genome. Am J Hum Genet [Suppl] 71:205.
10. Goldstein DB. 2001. Islands of linkage disequilibrium. Nature Genet 29:109-111.
11. Gordon AD. 1999. Classification, 2nd ed. Boca Raton: Chapman & Hall/CRC Press LLC.
12. Hudson RR, Kaplan NL. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147-164.
13. Johnson G, Esposito L, Barratt BJ, Smith AN, Heward J, Genova GD, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, Twells R, Payne F, Hughes W, Nutland S, Stevens H, Carr P, Tuomilehto-Wolf E, Tuomilehto J, Gough S, Clayton DG, Todd JA. 2001. Haplotype tagging for the identification of common disease genes. Nat Genet 29:233-237.
14. Lin D. 1998. An information-theoretic definition of similarity. In: Shavlik JW, editor. Proceedings of Fifteenth International Conference on Machine Learning, San Francisco: Morgan Kaufmann Publishers Inc. p 296-304.
15. Niu T, Qin ZS, Xu X, Liu JS. 2002. Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet 70:157-169.
16. Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR, Lee DH, Marjoribanks C, McDonough D, Nguyen B, Norris MC, Sheehan JB, Shen N, Stern D, Stokowski RP, Thomas DJ, Trulson MO, Vyas KR, Frazer KA, Fodor S, Cox DR. 2001. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294:1719-1723.
17. Perola M, Koivisto M, Varilo T, Hennah W, Ekelund J, Lugg M, Peltonen L, Ukkonen E, Mannila H. 2002. A method to find and compare the strength of haplotype block boundaries and its application in populations with different settlement histories. Am J Hum Genet [Suppl] 71:219.
18. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES. 2001. Linkage disequilibrium in the human genome. Nature 411:199-204.
19. Reich DE, Gabriel SB, Goldstein DB, McDonald GM, Wilson JF, Sabeti PC, Thomas MG, Bradman N, Ward R, Ferrell R, Linares AR, Pearce L, Henderson B, Jorde LB, Altshuler D, Lander ES. 2002. Haplotype structure and linkage disequilibrium in 26 worldwide populations. Am J Hum Genet [Suppl] 71:205.
20. Sim DG, Kwon OK, Park RH. 1999. Object matching algorithms using robust Hausdorff distance measures. IEEE Trans Image Process 8:425-429.
21. Sun X, Stephens JC, Zhao H. 2004. The impact of sample size and marker selection on the study of haplotype structures. Hum Genom 1:179-193.
22. Wang N, Akey JM, Zhang K, Chakraborty R, Jin L. 2002. Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation. Am J Hum Genet 71:1227-1234.
23. Weiss KM, Clark AG. 2002. Linkage disequilibrium and the mapping of complex human traits. Trends Genet 18:19-24.
24. Zhang K, Li J. 2003. HaploBlockFinder: an efficient program for haplotype block identification. Bioinformatics 19:1-3.
25. Zhang K, Deng M, Chen T, Waterman M, Sun F. 2002. A dynamic programming algorithm for haplotype block partitioning. Proc Natl Acad Sci USA 99:7335-7339.
26. Zhang K, Sun F, Waterman M, Chen T. 2003. Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data. In: Vingron M, Istrail S, Pevzner P, Waterman M, editors. Proceedings of the Seventh Annual International Conference on Computational Molecular Biology. New York: ACM Press. p 332-340.