Large-scale single-nucleotide polymorphism (SNP) and haplotype analyses, using dense SNP maps, of 199 drug-related genes in 752 subjects: The analysis of the association between uncommon SNPs within haplotype blocks and the haplotypes constructed with haplotype-tagging SNPs

American Journal of Human Genetics

Volumn 75, Issue 2, 2004, Pages 190-203

  Kamatani, Naoyuki ^a   Sekine, Akihiro ^b   Kitamoto, Takuya ^b   Iida, Aritoshi ^b   Saito, Susumu ^b   Kogame, Akifumi ^a   Inoue, Eisuke ^a   Kawamoto, Manabu ^a   Harigai, Masayoshi ^a   Nakamura, Yusuke ^b  

^a TOKYO WOMEN'S MEDICAL UNIVERSITY   (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ADULT; ARTICLE; CONTROLLED STUDY; CORRELATION COEFFICIENT; DRUG METABOLISM; DRUG RESPONSE; FEMALE; GENE FREQUENCY; HAPLOTYPE; HUMAN; JAPAN; MALE; MONTE CARLO METHOD; NORMAL HUMAN; PHARMACOGENETICS; PHENOTYPE; PRIORITY JOURNAL; PROBABILITY; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 3242694120     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/422853     Document Type: Article

References (40)

1. Avi-Itzhak HI, Su X, De La Vega FM (2003) Selection of minimum subsets of single nucleotide polymorphisms to capture haplotype block diversity. Pac Symp Biocomput 2003:466-477
2. Clark AG, Weiss KM, Nickerson DA, Taylor SL, Buchanan A, Stengard J, Salomaa V, Vartiainen E, Perola M, Boerwinkle E, Sing CF (1998) Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am J Hum Genet 63:595-612
3. Collins A, Lonjou C, Morton NE (1999) Genetic epidemiology of single-nucleotide polymorphisms. Proc Natl Acad Sci USA 96:15173-15177
4. Couzin J (2002) Human genome: HapMap launched with pledges of $100 million. Science 298:941-942
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. Drysdale CM, McGraw DW, Stack CB, Stephens JC, Judson RS, Nandabalan K, Arnold K, Ruano G, Liggett SB (2000) Complex promoter and coding region beta 2-adrenergic receptor haplotypes alter receptor expression and predict in vivo responsiveness. Proc Natl Acad Sci USA 97:10483-10488
7. Evans WE, McLeod HL (2003) Pharmacogenomics-drug disposition, drug targets, and side effects. N Engl J Med 348:538-549
8. Evans WE, Relling MV (1999) Pharmacogenomics: translating functional genomics into rational therapeutics. Science 286:487-491
9. Excoffier L, Slatkin M (1995) Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12:921-927
10. 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
11. Hirakawa M, Tanaka T, Hashimoto Y, Kuroda M, Takagi T, Nakamura Y (2002) JSNP: a database of common gene variations in the Japanese population. Nucleic Acids Res 30:158-162
12. Horikawa Y, Oda N, Cox NJ, Li X, Orho-Melander M, Hara M, Hinokio Y, Lindner TH, Mashima H, Schwarz PE, del Bosque-Plata L, Horikawa Y, Oda Y, Yoshiuchi I, Colilla S, Polonsky KS, Wei S, Concannon P, Iwasaki N, Schulze J, Baier LJ, Bogardus C, Groop L, Boerwinkle E, Hanis CL, Bell GI (2000) Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus. Nat Genet 26:163-175
13. Hugot JP, Chamaillard M, Zouali H, Lesage S, Cezard JP, Belaiche J, Almer S, Tysk C, O'Morain CA, Gassull M, Binder V, Finkel Y, Cortot A, Modigliani R, Laurent-Puig P, Gower-Rousseau C, Macry J, Colombel JF, Sahbatou M, Thomas G (2001) Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature 411:599-603
14. Iida A, Saito S, Sekine A, Mishima C, Kitamura Y, Kondo K, Harigae S, Osawa S, Nakamura Y (2002a) Catalog of 605 single-nucleotide polymorphisms (SNPs) among 13 genes encoding human ATP-binding cassette transporters:ABCA4, ABCA7, ABCA8, ABCD1, ABCD3, ABCD4, ABCE1, ABCF1, ABCG1, ABCG2, ABCG4, ABCG5, and ABCG8. J Hum Genet 47:285-310
15. - (2002b) Catalog of 86 single-nucleotide polymorphisms (SNPs) in three uridine diphosphate glycosyltransferase genes: UGT2A1, UGT2B15, and UGT8. J Hum Genet 47:505-510
16. - (2003) Catalog of 668 SNPs detected among 31 genes encoding potential drug targets on the cell surface. J Hum Genet 48:23-46
17. Iida A, Saito S, Sekine A, Mishima C, Kondo K, Kitamura Y, Harigae S, Osawa S, Nakamura Y (2001a) Catalog of 258 single-nucleotide polymorphisms (SNPs) in genes encoding three organic anion transporters, three organic anion-transporting polypeptides, and three NADH:ubiquinone oxido-reductase flavoproteins. J Hum Genet 46:668-683
18. Iida A, Sekine A, Saito S, Kitamura Y, Kitamoto T, Osawa S, Mishima C, Nakamura Y (2001b) Catalog of 320 single nucleotide polymorphisms (SNPs) in 20 quinone oxido-reductase and sulfotransferase genes. J Hum Genet 46:225-240
19. Johnson GC, Esposito L, Barratt BJ, Smith AN, Heward J, Di Genova G, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, Twells RC, Payne F, Hughes W, Nutland S, Stevens H, Carr P, Tuomilehto-Wolf E, Tuomilehto J, Gough SC, Clayton DG, Todd JA (2001) Haplotype tagging for the identification of common disease genes. Nat Genet 29:233-237
20. Judson R, Stephens JC (2001) Notes from the SNP vs. haplotype front. Pharmacogenomics 2:7-10
21. Jurinke C, van den Boom D, Cantor CR, Koster H (2002) The use of MassARRAY technology for high throughput genotyping. Adv Biochem Eng Biotechnol 77:57-74
22. 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
23. Kitamura Y, Moriguchi M, Kaneko H, Morisaki H, Morisaki T, Toyama K, Kamatani N (2002) Determination of probability distribution of diplotype configuration (diplotype distribution) for each subject from genotypic data using the EM algorithm. Ann Hum Genet 66:183-193
24. Kruglyak L (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 22:139-144
25. Kruglyak L, Nickerson DA (2001) Variation is the spice of life. Nat Genet 27:234-236
26. Kwiatkowski RW, Lyamichev V, de Arruda M, Neri B (1999) Clinical, genetic, and pharmacogenetic applications of the Invader assay. Mol Diagn 4:353-364
27. Lazarou J, Pomeranz BH, Corey PN (1998) Incidence of adverse drug reactions in hospitalized patients: a meta-analysis of prospective studies. JAMA 279:1200-1205
28. Long JC, Williams RC, Urbanek M (1995) An E-M algorithm and testing strategy for multiple locus haplotypes. Am J Hum Genet 56:799-810
29. Meyer UA (2000) Pharmacogenetics and adverse drug reactions. Lancet 356:1667-1671
30. Ogura Y, Bonen DK, Inohara N, Nicolae DL, Chen FF, Ramos R, Britton H, Moran T, Karaliuskas R, Duerr RH, Achkar JP, Brant SR, Bayless TM, Kirschner BS, Hanauer SB, Nunez G, Cho JH (2001) A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature 411:603-606
31. Ohnishi Y, Tanaka T, Ozaki K, Yamada R, Suzuki H, Nakamura Y (2001) A high-throughput SNP typing system for genome-wide association studies. J Hum Genet 46:471-477
32. Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR, Lee DH, Marjoribanks C, McDonough DP, Nguyen BT, Norris MC, Sheehan JB, Shen N, Stern D, Stokowski RP, Thomas DJ, Trulson MO, Vyas KR, Frazer KA, Fodor SP, Cox DR (2001) Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294:1719-1723
33. Qin ZS, Niu T, Liu JS (2002) Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet 71:1242-1247
34. Rioux JD, Daly MJ, Silverberg MS, Lindblad K, Steinhart H, Cohen Z, Delmonte T, et al (2001) Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease. Nat Genet 29:223-228
35. Saito S, Iida A, Sekine A, Ogawa C, Kawauchi S, Higuchi S, Nakamura Y (2002) Catalog of 238 variations among six human genes encoding solute carriers (hSLCs) in the Japanese population. J Hum Genet 47:576-584
36. Smigielski EM, Sirotkin K, Ward M, Sherry ST (2000) dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res 28:352-355
37. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978-989
38. Tanaka E, Taniguchi A, Urano W, Nakajima H, Matsuda Y, Kitamura Y, Saito M, Yamanaka H, Saito T, Kamatani N (2002) Adverse effects of sulfasalazine in patients with rheumatoid arthritis are associated with diplotype configuration at the N-acetyltransferase 2 gene. J Rheumatol 29:2492-2499
39. Urano W, Taniguchi A, Yamanaka H, Tanaka E, Nakajima H, Matsuda Y, Akama H, Kitamura Y, Kamatani N (2002) Polymorphisms in the methylenetetrahydrofolate reductase gene were associated with both the efficacy and the toxicity of methotrexate used for the treatment of rheumatoid arthritis, as evidenced by single locus and haplotype analyses. Pharmacogenetics 12:183-190
40. Zhu X, Yan D, Cooper RS, Luke A, Ikeda MA, Chang YP, Weder A, Chakravarti A (2003) Linkage disequilibrium and haplotype diversity in the genes of the renin-angiotensin system: findings from the family blood pressure program. Genome Res 13:173-181