Single nucleotide polymorphism screening and association analysis - Exclusion of integrin β7 and vitamin D receptor (chromosome 12q) as candidate genes for asthma

Clinical and Experimental Allergy

Volumn 34, Issue 12, 2004, Pages 1841-1850

  Vollmert, Caren ^a   Illig, T ^a   Altmuller J ^a,c   Klugbauer, S ^a,d   Loesgen, S ^a,e   Dumitrescu, L ^a   Wjst, M ^a,b  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

^c MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^d Sweden Diagnostics   (Germany)

^e Sweden Diagnostics ^*  (Switzerland)

Author keywords

Association analysis; Asthma; Complex disease; ITGB7; MALDI TOF mass spectrometry; SNP; VDR

Indexed keywords

BETA7 INTEGRIN; IMMUNOGLOBULIN E; VITAMIN D RECEPTOR;

ADOLESCENT; AMINO ACID SUBSTITUTION; ARTICLE; ASTHMA; CHROMOSOME 12Q; DOSE RESPONSE; EXON; FAMILIAL DISEASE; FEMALE; GENE; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC POLYMORPHISM; GENETIC SCREENING; GENETIC VARIABILITY; HUMAN; INTRON; ITGB7 GENE; MAJOR CLINICAL STUDY; MALE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PATHOGENESIS; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION; SCHOOL CHILD; SINGLE NUCLEOTIDE POLYMORPHISM;

ADOLESCENT; ADULT; ASTHMA; CHILD; CHROMOSOMES, HUMAN, PAIR 12; FEMALE; GENE EXPRESSION PROFILING; GENOTYPE; HUMANS; INTEGRIN BETA CHAINS; LINKAGE DISEQUILIBRIUM; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; RECEPTORS, CALCITRIOL; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 11144261794     PISSN: 09547894     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2222.2004.02047.x     Document Type: Article

References (59)

1. Asher MI, Keil U, Anderson HR et al. International Study of Asthma and Allergies in Childhood (ISAAC): rationale and methods. Eur Respir J 1995; 8:483-91.
2. Palmer LJ, Cookson WO. Genomic approaches to understanding asthma. Genome Res 2000; 10:1280-7.
3. Barnes KC, Neely JD, Duffy DL et al. Linkage of asthma and total serum IgE concentration to markers on chromosome 12q: evidence from Afro-Caribbean and Caucasian populations. Genomics 1996; 37:41-50.
4. Nickel R, Wahn U, Hizawa N et al. Evidence for linkage of chromosome 12q15-q24.1 markers to high total serum IgE concentrations in children of the German Multicenter Allergy Study. Genomics 1997; 46:159-62.
5. The Collaborative Study on the Genetics of Asthma. A genome-wide search for asthma susceptibility loci in ethnically diverse populations. Nat Genet 1997; 15:389-92.
6. Wilkinson J, Grimley S, Collins A, Thomas NS, Holgate ST, Morton N. Linkage of asthma to markers on chromosome 12 in a sample of 240 families using quantitative phenotype scores. Genomics 1998; 53:251-9.
7. Ober C, Cox NJ, Abney M et al. Genome-wide search for asthma susceptibility loci in a founder population. The Collaborative Study on the Genetics of Asthma. Hum Mol Genet 1998; 7:1393-8.
8. Wjst M, Fischer G, Immervoll T et al. A genome-wide search for linkage to asthma. German Asthma Genetics Group. Genomics 1999; 58:1-8.
9. Dizier MH, Besse-Schmittler C, Guilloud-Bataille M et al. Genome screen for asthma and related phenotypes in the French EGEA study. Am J Respir Crit Care Med 2000; 162:1812-8.
10. Immervoll T, Loesgen S, Dutsch G et al. Fine mapping and single nucleotide polymorphism association results of candidate genes for asthma and related phenotypes. Hum Mutat 2001; 18:327-36.
11. Malerba G, Lauciello MC, Scherpbier T et al. Linkage analysis of chromosome 12 markers in Italian families with atopic asthmatic children. Am J Respir Crit Care Med 2000; 162:1587-90.
12. Hayden C, Pereira E, Rye P et al. Mutation screening of interferon-gamma (IFNgamma) as a candidate gene for asthma. Clin Exp Allergy 1997; 27:1412-6.
13. Barnes KC, Freidhoff LR, Nickel R et al. Dense mapping of chromosome 12q13.12-q23.3 and linkage to asthma and atopy. J Allergy Clin Immunol 1999; 104:485-91.
14. Thomas NS, Wilkinson J, Holgate ST. The candidate region approach to the genetics of asthma and allergy. Am J Respir Crit Care Med 1997; 156:8144-51.
15. Mathew S, Murty VV, Hunziker W, Chaganti RS. Subregional mapping of 13 single-copy genes on the long arm of chromosome 12 by fluorescence in situ hybridization. Genomics 1992; 14:775-9.
16. Mancini JA, Evans JF. Cloning and characterization of the human leukotriene A4 hydrolase gene. Eur J Biochem 1995; 231:65-71.
17. Duetsch G, Illig T, Loesgen S et al. STAT6 as an asthma candidate gene: polymorphism-screening, association and haplotype analysis in a Caucasian sib-pair study. Hum Mol Genet 2002; 11:613-21.
18. Grasemann H, Yandava CN, Drazen JM. Neuronal NO synthase (NOS1) is a major candidate gene for asthma. Clin Exp Allergy 1999; 29:39-41.
19. Krissansen GW, Yuan Q, Jenkins D et al. Chromosomal locations of the genes coding for the integrin beta 6 and beta 7 subunits. Immunogenetics 1992; 35:58-61.
20. Baker E, Sutherland GR, Jiang WM et al. Mapping of the human integrin beta 7 gene (ITG beta 7) to 12q13.13 by non-isotopic in situ hybridization. Mamm Genome 1992; 2:272-3.
21. Labuda M, Ross MV, Fujiwara TM et al. Two hereditary defects related to vitamin D metabolism map to the same region of human chromosome 12q.II. J Bone Miner Res 1992; 7:1447-53.
22. Popper HH, Pailer S, Wurzinger G, Feldner H, Hesse C, Eber E. Expression of adhesion molecules in allergic lung diseases. Virchows Arch 2002; 440:172-80.
23. Erle DJ, Sheppard D, Breuss J, Ruegg C, Pytela R. Novel integrin alpha and beta subunit cDNAs identified in airway epithelial cells and lung leukocytes using the polymerase chain reaction. Am J Respir Cell Mol Biol 1991; 5:170-7.
24. Erle DJ, Ruegg C, Sheppard D, Pytela R. Complete amino acid sequence of an integrin beta subunit (beta 7) identified in leukocytes. J Biol Chem 1991; 266:11009-16.
25. Parker CM, Cepek KL, Russell GJ et al. A family of beta 7 integrins on human mucosal lymphocytes. Proc Natl Acad Sci USA 1992; 89:1924-8.
26. Berlin C, Berg EL, Briskin MJ et al. Alpha 4 beta 7 integrin mediates lymphocyte binding to the mucosal vascular addressin MAdCAM-1. Cell 1993; 74:185-5.
27. Tidswell M, Pachynski R, Wu SW et al. Structure-function analysis of the integrin beta 7 subunit: identification of domains involved in adhesion to MAdCAM-1. J Immunol 1997; 159:1497-505.
28. Ruegg C, Postigo AA, Sikorski EE, Butcher EC, Pytela R, Erle DJ. Role of integrin alpha 4 beta 7/alpha 4 beta P in lymphocyte adherence to fibronectin and VCAM-1 and in homotypic cell clustering. J Cell Biol 1992; 117:179-89.
29. Cepek KL, Shaw SK, Parker CM et al. Adhesion between epithelial cells and T lymphocytes mediated by E-cadherin and the alpha E beta 7 integrin. Nature 1994; 372:190-3.
30. Van Heel DA, Carey AH, Jewell DP. Identification of novel polymorphisms in the β7 integrin gene: family-based association studies in inflammatory bowel disease. Genes and Immunity 2001; 2:455-60.
31. Elewaut D, Van Damme N, De Keyser F et al. Altered expression of alpha E beta 7 integrin on intra-epithelial and lamina propria lymphocytes in patients with Crohn's disease. Acta Gastroenterol Belg 1998; 61:288-94.
32. Elewaut D, De Keyset F, Van Den Bosch F et al. Enrichment of T cells carrying beta7 integrins in inflamed synovial tissue from patients with early spondyloarthropathy, compared to rheumatoid arthritis. J Rheumatol 1998; 25:1932-7.
33. Rogge L, Bianchi E, Biffi M et al. Transcript imaging of the development of human T helper cells using oligonucleotide arrays. Nat Genet 2000; 25:96-101.
34. Romagnani S. Lymphokine production by human T cells in disease states. Annu Rev Immunol 1994; 12:227-57.
35. O'Garra A. Cytokines induce the development of functionally heterogenous T helper subsets. Immunity 1998; 8:275-83.
36. Seder RA, Paul WE. Acquisition of lymphokine-producing phenotype by CD4+ T cells. Annu Rev Immunol 1994; 12: 635-73.
37. Lemire JM, Archer DC, Beck L, Spiegelberg HL. Immunosuppressive actions of 1,25-dihydroxyvitamin D3: preferential inhibition of Th1 functions. J Nutr 1995; 125:1704S-8S.
38. Wjst M, Dold S. Genes, factor X, and allergen: what causes allergic diseases? Allergy 1999; 54:757-9.
39. Heinrich J, Nowak D, Wassmer G et al. Age-dependent differences in the prevalence of allergic rhinitis and atopic sensitization between an eastern and a western German city. Allergy 1998; 53:89-93.
40. Chiu KC, Chuang LM, Yoon C. The vitamin D receptor polymorphism in the translation initiation codon is a risk factor for insulin resistance in glucose tolerant Caucasians. BMC Med Genet 2001; 2:2.
41. Ban Y, Taniyama M, Yanagawa T et al. Vitamin D receptor initiation codon polymorphism influences genetic susceptibility to type 1 diabetes mellitus in the Japanese population. BMC Med Genet 2001; 2:7.
42. Yokoyama K, Shigematsu T, Kagami S et al. Vitamin D receptor gene polymorphism detected by digestion with Apa I influences the parathyroid response to extracellular calcium in Japanese chronic dialysis patients. Nephron 2001; 89:315-20.
43. Okita H, Ohtsuka T, Yamakage A, Yamazaki S. Polymorphism of the vitamin D(3) receptor in patients with psoriasis. Arch Dermatol Res 2002; 294:159-62.
44. Price DK, Franks ME, Figg WD. Genetic variations in the vitamin D receptor, androgen receptor and enzymes that regulate androgen metabolism. J Urol 2004; 171:45-9; discussion S49.
45. NCBI data bases: OMIM, Locus Link http://www.ncbi.nlm.nih.gov/entrez/ dispomim.cgi?id=601769 http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?locusId=7421.
46. Arai H, Miyamoto K, Taketani Y et al. A vitamin D receptor gene polymorphism in the translation initiation codon: effect on protein activity and relation to bone mineral density in Japanese women. J Bone Miner Res 1997; 12:915-21.
47. Nagpal S, Lu J, Boehm MF. Vitamin D analogs: mechanism of action and therapeutic applications. Curr Med Chem 2001; 8:1661-79.
48. Wjst M, Wichmann HE. Collaborative study on the genetics of asthma in Germany. Clin Exp Allergy 1995; 25 S2:23-5.
49. Buetow KH, Edmonson M, MacDonald R et al. High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc Natl Acad Sci USA 2001; 98:581-4.
50. Knapp M. The transmission/disequilibrium test and parental-genotype reconstruction: the reconstruction-combined transmission/disequilibrium test. Am J Hum Genet 1999; 64:861-70.
51. Abecasis GR, Cardon LR, Cookson WO. A general test of association for quantitative traits in nuclear families. Am J Hum Genet 2000; 66:279-92.
52. Abecasis GR, Cookson WO. GOLD - Graphical overview of linkage disequilibrium. Bioinformatics 2000; 16:182-3.
53. Chen W-M, Deng H-W. A general and accurate approach for computing the statistical power of the transmission disequilibrium test for complex disease genes. Genet Epidemiol 2001; 21:53-67.
54. Cavalli-Sforza LL, Menozzi P, Piazza A. The history and geography of human genes. Princeton, NJ: Princeton University Press, 1994.
55. Wall JD, Pritchard JK. Haplotype blocks and linkage disequilibrium in the human genome. Nat Rev Genet 2003; 4:587-97.
56. Risch N. Implications of multilocus inheritance for gene-disease association studies. Theor Popul Biol 2001; 60:215-20.
57. McGhinnis R, Shifman S, Darvasi A. Power and efficiency of the TDT and case-control design for association scans. Behav Genet 2002; 32:135-14.
58. Guo SW. Gene-environment interactions and the affected-sib-pair designs. Hum Hered 2000; 50:271-85.
59. Deng HW, Li J. The effects of selected sampling on the transmission disequilibrium test of a quantitative trait locus. Genet Res 2002; 79:161-74.