Evaluation of resequencing on number of tag SNPs of 13 atherosclerosis- related genes in Thai population

Journal of Human Genetics

Volumn 53, Issue 1, 2008, Pages 74-86

  Tocharoentanaphol, Chintana ^a,b   Promso, Somying ^c,f   Zelenika, Dianna ^a   Lowhnoo, Tassanee ^a,c   Tongsima, Sissades ^d   Sura, Thanyachai ^c   Chantratita, Wasun ^c   Matsuda, Fumihiko ^a   Mooney, Sean ^f   Sakuntabhai, Anavaj ^c,e  

^a CENTRE NATIONAL DE GÉNOTYPAGE   (France)

^b Chulabhorn Cancer Research Centre   (Thailand)

^c MAHIDOL UNIVERSITY   (Thailand)

^d NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

^e INSTITUT PASTEUR   (France)

^f INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Atherosclerosis; Novel SNP; Resequencing; SNP; Tag SNP; Thai

Indexed keywords

ADULT; ARTICLE; ATHEROSCLEROSIS; COMPARATIVE STUDY; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA FLANKING REGION; GENE FREQUENCY; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC POLYMORPHISM; GENOTYPE; HAPLOTYPE; HUMAN; NORMAL HUMAN; NUCLEOTIDE SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

AFRICAN CONTINENTAL ANCESTRY GROUP; ATHEROSCLEROSIS; GENE FREQUENCY; GENETICS, POPULATION; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SEQUENCE TAGGED SITES; THAILAND; VARIATION (GENETICS);

EID: 37549035912     PISSN: 14345161     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10038-007-0220-8     Document Type: Article

References (39)

1. Asztalos BF (2004) High-density lipoprotein metabolism and progression of atherosclerosis: new insights from the HDL Atherosclerosis Treatment Study. Curr Opin Cardiol 19:385-391
2. Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263-265
3. Brown CM, Rea TJ, Hamon SC, Hixson JE, Boerwinkle E, Clark AG, Sing CF (2006) The contribution of individual and pairwise combinations of SNPs in the APOA1 and APOC3 genes to interindividual HDL-C variability. J Mol Med V84:561-572
4. Carlson CS, Eberle MA, Rieder MJ, Smith JD, Kruglyak L, Nickerson DA (2003) Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat Genet 33:518-521
5. Cha PC, Yamada R, Sekine A, Nakamura Y, Koh CL (2004) Inference from the relationships between linkage disequilibrium and allele frequency distributions of 240 candidate SNPs in 109 drug-related genes in four Asian populations. J Hum Genet 49:558-572
6. de Bakker PI, Yelensky R, Pe'er I, Gabriel SB, Daly MJ, Altshuler D (2005) Efficiency and power in genetic association studies. Nat Genet 37:1217-1223
7. Department of Medical Service Thailand G (2006a) Statistical report. ( http://www.dms.moph.go.th/statreport/index.html )
8. Department of Medical Service Thailand G (2006b) Statistical report of cardiovascular disease in Thai population. ( http://www.dms.moph.go.th/ statreport/2547/table0647.htm )
9. Disabella E, Grasso M, Marziliano N, Ansaldi S, Lucchelli C, Porcu E, Tagliani M, Pilotto A, Diegoli M, Lanzarini L, Malattia C, Pelliccia A, Ficcadenti A, Gabrielli O, Arbustini E (2006) Two novel and one known mutation of the TGFBR2 gene in Marfan syndrome not associated with FBN1 gene defects. Eur J Hum Genet 14:34-38
10. Do H, Vasilescu A, Diop G, Hirtzig T, Coulonges C, Labib T, Heath SC, Spadoni JL, Therwath A, Lathrop M, Matsuda F, Zagury JF (2006) Associations of the IL2Ralpha, IL4Ralpha, IL10Ralpha, and IFN (gamma) R1 cytokine receptor genes with AIDS progression in a French AIDS cohort. Immunogenetics 58:89-98
11. Fuki IV, Blanchard N, Jin W, Marchadier DH, Millar JS, Glick JM, Rader DJ (2003) Endogenously produced endothelial lipase enhances binding and cellular processing of plasma lipoproteins via heparan sulfate proteoglycan-mediated pathway. J Biol Chem 278:34331-34338
12. 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
13. Hoh J, Matsuda F, Peng X, Markovic D, Lathrop MG, Ott J (2003) SNP haplotype tagging from DNA pools of two individuals. BMC Bioinform 4:14
14. Ishida T, Choi SY, Kundu RK, Spin J, Yamashita T, Hirata K, Kojima Y, Yokoyama M, Cooper AD, Quertermous T (2004) Endothelial lipase modulates susceptibility to atherosclerosis in apolipoprotein-E-deficient mice. J Biol Chem 279:45085-45092
15. Jaye M, Lynch KJ, Krawiec J, Marchadier D, Maugeais C, Doan K, South V, Amin D, Perrone M, Rader DJ (1999) A novel endothelial-derived lipase that modulates HDL metabolism. Nat Genet 21:424-428
16. Kim JY, Moon SM, Ryu HJ, Kim JJ, Kim HT, Park C, Kimm K, Oh B, Lee JK (2005) Identification of regulatory polymorphisms in the TNF-TNF receptor superfamily. Immunogenetics 57:297-303
17. Laukkanen J, Yla-Herttuala S (2002) Genes involved in atherosclerosis. Exp Nephrol 10:150-163
18. Maglott D, Ostell J, Pruitt KD, Tatusova T (2005) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 33:D54-D58
19. Mahasirimongkol S, Chantratita W, Promso S, Pasomsab E, Jinawath N, Jongjaroenprasert W, Lulitanond V, Krittayapoositpot P, Tongsima S, Sawanpanyalert P, Kamatani N, Nakamura Y, Sura T (2006) Similarity of the allele frequency and linkage disequilibrium pattern of single nucleotide polymorphisms in drug-related gene loci between Thai and northern East Asian populations: implications for tagging SNP selection in Thais. J Hum Genet 51:896-904
20. Matyas G, Arnold E, Carrel T, Baumgartner D, Boileau C, Berger W, Steinmann B (2006) Identification and in silico analyses of novel TGFBR1 and TGFBR2 mutations in Marfan syndrome-related disorders. Hum Mutat 27:760-769
21. McCarthy JJ, Lehner T, Reeves C, Moliterno DJ, Newby LK, Rogers WJ, Topol EJ (2003) Association of genetic variants in the HDL receptor, SR-B1, with abnormal lipids in women with coronary artery disease. J Med Genet 40:453-458
22. McDermott DH, Yang Q, Kathiresan S, Cupples LA, Massaro JM, Keaney JF Jr, Larson MG, Vasan RS, Hirschhorn JN, O'Donnell CJ, Murphy PM, Benjamin EJ (2005) CCL2 polymorphisms are associated with serum monocyte chemoattractant Protein-1 levels and myocardial infarction in the Framingham Heart Study. Circulation 112:1113-1120
23. Michiels S, Danoy P, Dessen P, Bera A, Boulet T, Bouchardy C, Lathrop M, Sarasin A, Benhamou S (2007) Polymorphism discovery in 62 DNA repair genes and haplotype-associations with risks for lung, and head and neck cancers. Carcinogenesis (in press)
24. Mizuguchi T, Collod-Beroud G, Akiyama T, Abifadel M, Harada N, Morisaki T, Allard D, Varret M, Claustres M, Morisaki H, Ihara M, Kinoshita A, Yoshiura K, Junien C, Kajii T, Jondeau G, Ohta T, Kishino T, Furukawa Y, Nakamura Y, Niikawa N, Boileau C, Matsumoto N (2004) Heterozygous TGFBR2 mutations in Marfan syndrome. Nat Genet 36:855-860
25. Ng PC, Henikoff S (2002) Accounting for human polymorphisms predicted to affect protein function. Genome Res 12:436-446
26. R Development Core Team G (2006) R: a language and environment for statistical computing
27. Ramensky V, Bork P, Sunyaev S (2002) Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30:3894-900
28. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365-386
29. Ruano G, Seip RL, Windemuth A, Zollner S, Tsongalis GJ, Ordovas J, Otvos J, Bilbie C, Miles M, Zoeller R, Visich P, Gordon P, Angelopoulos TJ, Pescatello L, Moyna N, Thompson PD (2006) Apolipoprotein A1 genotype affects the change in high density lipoprotein cholesterol subfractions with exercise training. Atherosclerosis 185:65-69
30. Schneider M, Tognolli M, Bairoch A (2004) The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools. Plant Physiol Biochem 42:1013-1021
31. Simon DI, Chen Z, Seifert P, Edelman ER, Ballantyne CM, Rogers C (2000) Decreased neointimal formation in Mac-1-/- mice reveals a role for inflammation in vascular repair after angioplasty. J Clin Invest 105:293-300
32. Singh NN, Ramji DP (2006) The role of transforming growth factor-beta in atherosclerosis. Cytokine Growth Factor Rev 17:487-499
33. Tabara Y, Kohara K, Yamamoto Y, Igase M, Nakura J, Kondo I, Miki T (2003) Polymorphism of the monocyte chemoattractant Protein (MCP-1) gene is associated with the plasma level of MCP-1 but not with carotid intima-media thickness. Hypertens Res 26:677-683
34. Tabibiazar R, Wagner RA, Ashley EA, King JY, Ferrara R, Spin JM, Sanan DA, Narasimhan B, Tibshirani R, Tsao PS, Efron B, Quertermous T (2005) Signature patterns of gene expression in mouse atherosclerosis and their correlation to human coronary disease. Physiol Genom 22:213-226
35. Takahashi M, Matsuda F, Margetic N, Lathrop M (2002) Automated identification of single nucleotide polymorphisms from sequencing data. Proc IEEE Comput Soc Bioinform Conf 1:87-93
36. The Innate Immunity PGA P (2000) IIPGA genetic data: ITGAM allele frequencies. ( https://innateimmunity.net/IIPGA2/PGAs/InnateImmunity/ITGAM/ allele_freqs?flavor=masked )
37. The International HapMap C (2005) A haplotype map of the human genome. Nature 437:1299-1320
38. Wang X, Le Roy I, Nicodeme E, Li R, Wagner R, Petros C, Churchill GA, Harris S, Darvasi A, Kirilovsky J, Roubertoux PL, Paigen B (2003) Using advanced intercross lines for high-resolution mapping of HDL cholesterol quantitative trait loci. Genome Res 13:1654-1664
39. Yue P, Melamud E, Moult J (2006) SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinform 7:166