A graphical assessment of p-values from sliding window haplotype tests of association to identify asthma susceptibility loci on chromosome 11q

BMC Genetics

Volumn 7, Issue , 2006, Pages

  Mathias, Rasika A ^a   Gao, Peisong ^b   Goldstein, Janet L ^c   Wilson, Alexander F ^a   Pugh, Elizabeth W ^c   Furbert Harris, Paulette ^d   Dunston, Georgia M ^d   Malveaux, Floyd J ^d   Togias, Alkis ^b   Barnes, Kathleen C ^b   Beaty, Terri H ^e   Huang, Shau Ku ^b  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b JOHNS HOPKINS ASTHMA AND ALLERGY CENTER   (United States)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d HOWARD UNIVERSITY COLLEGE OF MEDICINE   (United States)

^e JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASTHMA; CHROMOSOME 11Q; CONTROLLED STUDY; DATA ANALYSIS; GENE LOCATION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC SUSCEPTIBILITY; HAPLOTYPE; HUMAN; NUCLEOTIDE SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; UNINDEXED SEQUENCE;

AFRICAN AMERICANS; ASTHMA; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 11; COMPUTER GRAPHICS; GENETIC LINKAGE; GENETIC PREDISPOSITION TO DISEASE; HAPLOTYPES; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 33746816031     PISSN: 14712156     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-7-38     Document Type: Article

References (50)

1. Hellmig S, Mascheretti S, Renz J, Frenzel H, Jelschen F, Rehbein JK, Folsch U, Hampe J, Schreiber S: Haplotype analysis of the CDII gene cluster in patients with chronic Helicobacter pylori infection and gastric ulcer disease. Tissue Antigens 2005, 65:271-274.
2. Gibson F, Froguel P: Genetics of the APMI locus and its contribution to type 2 diabetes susceptibility in French Caucasians. Diabetes 2004, 53:2977-2983.
3. Skipper L, Wilkes K, Toft M, Baker M, Lincoln S, Hulihan M, Ross OA, Hutton M, Aasly J, Farrer M: Linkage disequilibrium and association of MAPT HI in Parkinson disease. Am J Hum Genet 2004, 75:669-677.
4. Nakajima T, Wooding S, Sakagami T, Emi M, Tokunaga K, Tamiya G, Ishigami T, Umemura S, Munkhbat B, Jin F, Guan-Jun J, Hayasaka I, Ishida T, Saitou N, Pavelka K, Lalouel JM, Jorde LB, Inoue I: Natural selection and population history in the human angiotensinogen gene (AGT): 736 complete AGT sequences in chromosomes from around the world. Am J Hum Genet 2004, 74:898-916.
5. Innan H, Padhukasahasram B, Nordborg M: The pattern of polymorphism on human chromosome 21. Genome Res 2003, 13:1158-1168.
6. Paschou P, Feng Y, Pakstis AJ, Speed WC, DeMille MM, Kidd JR, Jaghori B, Kurlan R, Pauls DL, Sandor P, Barr CL, Kidd KK: Indications of linkage and association of Gilles de la Tourette syndrome in two independent family samples: 17q25 Is a putative susceptibility region. Am J Hum Genet 2004, 75:545-560.
7. Åberg N: Familial occurrence of atopic disease: genetic versus environmental factors. Clin Exp Allergy 1993, 23:829-34.
8. Cooke RA, Jr AVV: Human Sensitization. J Immunol 1916, 1:210-305.
9. Gerrard JW, Ko CG, Vickers P, Gerrard CD: The familial incidence of allergic disease. Annals of Allergy 1976, 36:10-15.
10. Barnes KC: Atopy and asthma genes - where do we stand? Allergy 2000, 55(9):803-17.
11. Ober C, Moffatt MF: Contributing factors to the pathobiology. The genetics of asthma. Clin Chest Med 2000, 21:245-61.
12. Zhang Y, Leaves NI, Anderson GG, Ponting CP, Broxholme J, Holt R, Edser P, Bhattacharyya S, Dunham A, Adcock IM, Pulleyn L, Barnes PJ, Harper JI, Abecasis G, Cardon L, White M, Burton J, Matthews L, Mott R, Ross M, Cox R, Moffatt MF, Cookson WO: Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma. Nat Genet 2003, 34:181-186.
13. Allen M, Heinzmann A, Noguchi E, Abecasis G, Broxholme J, Ponting CP, Bhattacharyya S, Tinsley J, Zhang Y, Holt R, Jones EY, Lench N, Carey A, Jones H, Dickens NJ, Dimon C, Nicholls R, Baker C, Xue L, Townsend E, Kabesch M, Weiland SK, Carr D, Von Mutius E, Adcock IM, Barnes PJ, Lathrop GM, Edwards M, Moffatt MF, Cookson WO: Positional cloning of a novel gene influencing asthma from chromosome 2q14. Nat Genet 2003, 35:258-263.
14. Van Eerdewegh P, Little RD, Dupuis J, Del Mastro RG, Falls K, Simon J, Torrey D, Pandit S, McKenny J, Braunschweiger K, Walsh A, Liu Z, Hayward B, Folz C, Manning SP, Bawa A, Saracino L, Thackston M, Benchekroun Y, Capparell N, Wang M, Adair R, Feng Y, Dubois J, FitzGerald MG, Huang H, Gibson R, Allen KM, Pedan A, Danzig MR, Umland SP, Egan RW, Cuss FM, Rorke S, Clough JB, Holloway JW, Holgate ST, Keith TP: Association of the ADAM33 gene with asthma and bronchial hyperresponsiveness. Nature 2002, 418:426-430.
15. Laitinen T, Polvi A, Rydman P, Vendelin J, Pulkkinen V, Salmikangas P, Makela S, Rehn M, Pirskanen A, Rautanen A, Zucchelli M, Gullsten H, Leino M, Alenius H, Petays T, Haahtela T, Laitinen A, Laprise C, Hudson T-J, Laitinen LA, Kere J: Characterization of a common susceptibility locus for asthma-related traits. Science 2004, 304:300-304.
16. Xu J, Meyers DA, Ober C, Blumenthal MN, Mellen B, Barnes KC, King RA, Lester LA, Howard TD, Solway J, Langefeld CD, Beaty TH, Rich SS, Bleecker ER, Cox NJ: Genomewide Screen and Identification of Gene-Gene Interactions for Asthma-Susceptibility Loci in Three U.S. Populations: Collaborative Study on the Genetics of Asthma. Am J Hum Genet 2001, 68:1437-1446.
17. Huang SK, Mathias RA, Ehrlich E, Plunkett B, Liu X, Cutting GR, Wang XJ, Li XD, Togias A, Barnes KC, Malveaux F, Rich S, Mellen B, Lange E, Beaty TH: Evidence for asthma susceptibility genes on chromosome II in an African-American population. Hum Genet 2003, 113:71-75.
18. Hirai H, Tanaka K, Yoshie O, Ogawa K, Kenmotsu K, Takamori Y, Ichimasa M, Sugamura K, Nakamura M, Takano S, Nagata K: Prostaglandin D2 selectively induces chemotaxis in T helper type 2 cells, eosinophils, and basophils via seven-transmembrane receptor CRTH2. J Exp Med 2001, 193:255-261.
19. Hizawa N, Yamaguchi E, Jinushi E, Konno S, Kawakami Y, Nishimura M: Increased total serum IgE levels in patients with asthma and promoter polymorphisms at CTLA4 and FCERIB. J Allergy Clin Immunol 2001, 108:74-9.
20. Chen LC, Zhang Z, Myers AC, Huang SK: Cutting edge: altered pulmonary eosinophilic inflammation in mice deficient for Clara cell secretory 10-kDa protein. J Immunol 2001, 167:3025-3028.
21. Huang JL, Gao PS, Mathias RA, Yao TC, Chen LC, Kuo ML, Hsu SC, Plunkett B, Togias A, Barnes KC, Stellato C, Beaty TH, Huang SK: Sequence variants of the gene encoding chemoattractant receptor expressed on Th2 cells (CRTH2) are associated with asthma and differentially influence mRNA stability. Hum Mol Genet 2004, 13:2691-2697.
22. Fan JB, Oliphant A, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, McBride C, Bibikova M, Rubano T, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS: Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol 2003, 68:69-78.
23. 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: The structure of haplotype blocks in the human genome. Science 2002, 296:2225-2229.
24. Zhao H, Pfeiffer R, Gail MH: Haplotype analysis in population genetics and association studies. Pharmacogenomics 2003, 4:171-178.
25. Beckman L, Fischer C, Obreiter M, Rabes M, Chang-Claude J: Haplotype sharing analysis using Mantel statistics for combined genetic effects. BMC Genet 2005, 6:S70.
26. Durrant C, Morris A: Linkage disequilibrium mapping via cladistic analysis of phase-unknown genotypes and inferred haplotypes in the Genetic Analysis Workshop 14 simulated data. BMC Genet 2005, 6:S100.
27. Meng Z, Zaykin DV, Xu CF, Wagner M, Ehm MG: Selection of genetic markers for association analyses, using linkage disequilibrium and haplotypes. Am J Hum Genet 2003, 73:115-130.
28. Lin S, Chakravarti A, Cutler DJ: Exhaustive allelic transmission disequilibrium tests as a new approach to genome-wide association studies. Nat Genet 2004, 36:1181-1188.
29. Cheng R, Ma JZ, Wright FA, Lin S, Gao X, Wang D, Elston RC, Li MD: Nonparametric disequilibrium mapping of functional sites using haplotypes of multiple tightly linked single-nucleotide polymorphism markers. Genetics 2003, 164:1175-1187.
30. Chiu YF, Liu X, Tsai YY: A comparison in association and linkage genome-wide scans for alcoholism susceptibility genes using single-nucleatide polymorphisms. BMC Genet 2005, 6:S89.
31. Pugh EW, Mandal DM, Wilson AF: A graphical approach for presenting linkage results from a genomic screen. Genet Epidemiol 1995, 12:807-812.
32. Abecasis GR, Cookson WO: GOLD - graphical overview of linkage disequilibrium. Bioinformatics 2000, 16:182-3.
33. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 1998, 95:14863-14868.
34. Yi Y, Mirosevich J, Shyr Y, Matusik R, George ALJ: Coupled analysis of gene expression and chromosomal location. Genomics 2005, 85:401-412.
35. Lingjaerde OC, Baumbusch LO, Liestol K, Glad IK, Borresen-Dale AL: CGH-Explorer: a program for analysis of array-CGH data. Bioinformatics 2005, 21:821-822.
36. Awad IA, Rees CA, Hernandez-Boussard T, Ball CA, Sherlock G: Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. BMC Bioinformatics 2004, 5:151.
37. Chi B, DeLeeuw RJ, Coe BP, MacAulay C, Lam WL: SeeGH - a software tool for visualization of whole genome array comparative genomic hybridization data. BMC Bioinformatics 2004, 5:13.
38. Dresen IM, Husing J, Kruse E, Boes T, Jockel KH: Software packages for quantitative microarray-based gene expression analysis. Curr Pharm Biotechnol 2003, 4:417-437.
39. Sharrocks AD, Brown AL, Ling Y, Yates PR: The ETS-domain transcription factor family. Int J Biochem Cell Biol 1997, 29:1371-1387.
40. Slutsky AS, Zamel N: Genetics of asthma: the University of Toronto Program. University of Toronto Genetics of Asthma Research Group. Am J Respir Crit Care Med 1997, 156:S130-S132.
41. Sreekumar GP, Binnie CG, Carden EG, Sharma S, Sprankle CS, Sherman PA, Xue ZY, Fling ME, Reisman M, Blumenthal M, Vestbo J, Sundy J, Pericak-Vance MA, Brewster S, Ehm MG, Burns DK, Wagner MJ: Association of asthma and related phenotypes with ASTH-1/J genes on chromosome 11p in Caucasians. Am J Hum Genet 2000.
42. Baron RM, Palmer LJ, Tantisira K, Gabriel S, Sonna LA, Le L, Hallock A, Libermann TA, Drazen JM, Weiss ST, Silverman ES: DNA sequence variants in epithelium-specific ETS-2 and ETS-3 are not associated with asthma. Am J Respir Crit Care Med 2002, 166:927-932.
43. Silverman ES, Baron RM, Palmer LJ, Le L, Hallock A, Subramaniam V, Riese RJ, McKenna MD, Gu X, Libermann TA, Tugores A, Haley KJ, Shore S, Drazen JM, Weiss ST: Constitutive and cytokine-induced expression of the ETS transcription factor ESE-3 in the lung. Am J Respir Cell Mol Biol 2002, 27:697-704.
44. http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=603506. 2006.
45. Utku N, Heinemann T, Tullius SG, Bulwin GC, Beinke S, Blumberg RS, Beato F, Randall J, Kojima R, Busconi L, Robertson ES, Schulein R, Volk HD, Milford EL, Gullans SR: Prevention of acute allograft rejection by antibody targeting of TIRC7, a novel T cell membrane protein. Immunity 1998, 9:509-518.
46. Barker DL, Hansen MS, Faruqi AF, Giannola D, Irsula OR, Lasken RS, Latterich M, Makarov V, Oliphant A, Pinter JH, Shen R, Sleptsova. I, Ziehler W, Lai E: Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel. Genome Res 2004, 14:901-907.
47. http://www.molecularstaging.com. 2006.
48. Rabinowitz D, Laird N: A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information. Hum Hered 2000, 50:211-23.
49. Horvath S, Xu X, Lake SL, Silverman EK, Weiss ST, Laird NM: Family-based tests for associating haplotypes with general phenotype data: application to asthma genetics. Genet Epidemiol 2004, 26:61-69.
50. Fallin D, Schork NJ: Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. Am J Hum Genet 2000, 67:947-959.