High resolution MIC genotyping: Design and application to the investigation of inflammatory bowel disease susceptibility

Tissue Antigens

Volumn 60, Issue 2, 2002, Pages 164-179

  Ahmad, T ^a   Marshall, S E ^b   Mulcahy Hawes, K ^a   Orchard, T ^a   Crawshaw, J ^a   Armuzzi, A ^a   Neville, M ^a   Van Heel, D ^a   Barnardo, M ^a   Welsh, K I ^c   Jewell, D P ^a   Bunce, M ^d  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c NATIONAL HEART AND LUNG INSTITUTE   (United Kingdom)

^d Dynal Biotech Ltd   (United Kingdom)

Author keywords

Crohn's disease; Inflammatory bowel diseases; MIC gene; PCR SSP; Polymorphism; Ulcerative colitis

Indexed keywords

MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; MICROSATELLITE DNA; HLA ANTIGEN CLASS 1; HLA B ANTIGEN; MHC CLASS I RELATED CHAIN A; MHC CLASS I-RELATED CHAIN A; MICB ANTIGEN;

ALLELE; ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; CROHN DISEASE; DISEASE ASSOCIATION; ENTERITIS; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC POLYMORPHISM; GENETIC SUSCEPTIBILITY; GENOTYPE; HAPLOTYPE; HLA SYSTEM; HUMAN; LIGAND BINDING; LYMPHOCYTE ACTIVATION; MACROPHAGE ACTIVATION; MAJOR CLINICAL STUDY; MAJOR HISTOCOMPATIBILITY COMPLEX; NATURAL KILLER CELL; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RECEPTOR BINDING; SINGLE STRAND CONFORMATION POLYMORPHISM; T LYMPHOCYTE SUBPOPULATION; ULCERATIVE COLITIS; VARIABLE NUMBER OF TANDEM REPEAT; CAUCASIAN; COHORT ANALYSIS; ETHNOLOGY; EVALUATION; FEMALE; GENETIC PREDISPOSITION; GENETICS; METHODOLOGY; SENSITIVITY AND SPECIFICITY;

ALLELES; COHORT STUDIES; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HISTOCOMPATIBILITY ANTIGENS CLASS I; HLA-B ANTIGENS; HUMANS; INFLAMMATORY BOWEL DISEASES; LINKAGE DISEQUILIBRIUM; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; SENSITIVITY AND SPECIFICITY;

EID: 18644374191     PISSN: 00012815     EISSN: None     Source Type: Journal    
DOI: 10.1034/j.1399-0039.2002.600207.x     Document Type: Article

References (57)

1. Ahmad T, Satsangi J, McGovern D, Bunce M, Jewell D. The genetics of inflammatory bowel disease. Aliment Pharmacol Ther 2001: 15: 731-48.
2. Ioannidis J, Ntzani E, Trikalinos T, Contopoulos-Ioannidis D. Replication validity of genetic association studies. Nature Genet 2001: 29: 306-9.
3. Silverberg M, Daly M, Moskovitz D et al. Diagnostic misclassification reduces the ability to detect linkage in inflammatory bowel disease genetic studies. Gut 2001: 49: 773-6.
4. Satsangi J, Welsh KI, Bunce M et al. Contribution of genes of the major histocompatibility complex to susceptibility and disease phenotype in inflammatory bowel disease. Lancet 1996: 347: 1212-7.
5. Yang H, Plevy S, Taylor K. Linkage of Crohn's disease to the major histocompatibility complex region is detected by multiple non-parametric analyses. Gut 1999: 44: 519-26.
6. Hampe J, Schreiber S, Shaw S et al. A genome-wide analysis provides evidence for novel linkages in inflammatory bowel disease in a large European cohort. Am J Hum Genet 1999: 64: 808-16.
7. Hampe J, Shaw S, Saiz R et al. Linkage of inflammatory bowel disease to human chromosome 6p. Am J Hum Genet 1999: 65: 1647-55.
8. Rioux J, Silverberg M, Daly M et al. Genome-wide search in Canadian families with inflammatory bowel disease reveals two novel susceptibility loci. Am J Hum Genet 2000: 66: 1863-70.
9. Roussomoustakaki M, Satsangi J, Welsh K et al. Genetic markers may predict disease behaviour in patients with ulcerative colitis. Gastroenterology 1997: 112: 1845-53.
10. Reinshagen M, Loeliger C, Kuehni P et al. HLA Class II gene frequencies in Crohn's disease: A population based analysis in Germany. Gut 1996: 38: 538-42.
11. Danze P-M, Colombel J-F, Jacquot S et al. Association of HLA class II genes with susceptibility to Crohn's disease. Gut 1996: 39: 69-72.
12. Yoshitake S, Kimura A, Okada M, Yao T, Sasazuki T. HLA class II alleles in Japanese patients with inflammatory bowel disease. Tissue Antigens 1999: 53: 350-8.
13. Orchard T, Thiyagaraja S, Welsh K, Wordsworth B, Gaston J, Jewell D. Clinical phenotype is related to HLA genotype in the peripheral arthropathies of inflammatory bowel disease. Gastroenterology 2000: 118: 274-8.
14. Trachtenberg E, Yang H, Hayes E et al. HLA class II haplotype associations with inflammatory bowel disease in Jewish (Ashkenazi) and non-Jewish Caucasian populations. Hum Immunol 2000: 61: 326-33.
15. Bahram S, Bresnaha M, Geraghty D, Spies T. A second lineage of mammalian major histocompatibility complex class I gene. Proc Natl Acad Sci U S A 1994: 91: 6259-63.
16. Bahram S, Spies T. The MIC gene family. Non-polymorphic antigen presentation molecules. Res Immunol 1996: 147: 328-33.
17. Bahram S, Spies T. Nucleotide sequence of a human MHC class I MICB cDNA. Immunogenetics 1996: 43: 230-3.
18. Bahram S, Mizuki N, Inoko H, Spies T. Nucleotide sequence of the human MHC class I MICA gene. Immunogenetics 1996: 44: 80-1.
19. Li P, Bauer S, Morris D, Spies T, Strong R. Crystal structure of the class I homolog MICA, a Yd T cell ligand. Immunity 1999: 10: 1-20.
20. Groh V, Bahram S, Bauer S, Herman A, Beauchamp M, Spies T. Cell stress-regulated human major histocompatibility complex class I gene expressed in gastrointestinal epithelium. Proc Natl Acad Sci U S A 1996: 93: 12445-50.
21. Groh V, Steinle A, Bauer S, Spies T. Recognition of stress-induced MHC molecules by intestinal epithelial gamma delta T cells. Science 1998: 279: 1737-40.
22. Groh V, Rhinehart R, Randolph-Habecker J, Topp M, Riddell S, Spies T. Costimulation of CD8 αB T cells by NKG2D via engagement by MIC induced on virus-infected cells. Nature Immunol 2001: 2: 255-60.
23. Das H, Groh V, Kuijl C et al. MICA engagement by human Vλ2Vd2 T cells enhances their antigen-dependant effector function. Immunity 2001: 15: 83-93.
24. Wu J, Song Y, Bakker A et al. An activating immunoreceptor complex formed by NKG2D and DAP10. Science 1999: 285: 730-1.
25. Marsh S. http://www.anthonynolan.com/HIG/index.html, 2001.
26. Mizuki N, Ota M, Katsyama Y et al. Triplet repeat polymorphism in the transmembrane portion of the MICA gene. A strong association of six GCT repetitions with Behçet's disease. Proc Natl Acad Sci U S A 1997: 94: 1298-303.
27. Yao Z, Volgger A, Helmberg W et al. Definition of new alleles of MIC-A using sequencing-based typing. E J Immunogenetics 1999: 26: 225-32.
28. Steinle A, Li P, Morris D et al. Interactions of human NKG2D with its ligands MICA, MICB and homologs of the mouse RAE-1 protein family. Immunogenetics 2001: 53: 279-87.
29. Ota M, Bahram S, Katsuyama Y et al. On the MICA deleted-MICB null, HLA-B*4801 haplotype. Tissue Antigens 2000: 56: 268-71.
30. Sugimura K, Ota M, Matsuzama J et al. A close relationship of triplet repeat polymorphisms in MHC class I chain-related gene A (MICA) to the disease susceptibility and behaviour in ulcerative colitis. Tissue Antigens 2001: 57: 9-14.
31. Seki S, Sugimura K, Ota M et al. Stratification of MICA triplet repeat polymorphisms and HLA antigens associated with ulcerative colitis in Japanese. Tissue Antigens 2001: 58: 71-6.
32. Glas J, Martin K, Brunnler G et al. MICA, MICB and C1-4-1 polymorphism in Crohn's disease and ulcerative colitis. Tissue Antigens 2001: 58: 243-9.
33. Stephens HA, Vaughan RW, Collins R, Kondeatis E, Theron J, Payne A. Towards a molecular phototyping system for allelic variants of MICA, encoded by polymorphisms in exons 2, 3 and 4 of MHC class I chain- related genes (in process citation). Tissue Antigens 1999: 53: 167-74.
34. Orchard T, Dhar A, Simmons J, Vaughan R, Welsh K, Jewell D. MHC class I chain-like gene A (MICA) and its associations with inflammatory bowel disease and peripheral arthropathy. Clin Exp Immunol 2001: 126: 437-40.
35. Zhang Y, Lazaro A, Lavingia B, Stastny P. Typing for all known MICA alleles by group-specific PCR and SSOP. Hum Immunol 2000: 62: 620-31.
36. Fischer G, Arguello J, Perez-Rodriguez M et al. Sequence-specific oligonucleotide probing (SSOP) for MICB alleles reveals associations with MICA and HLA-B. Immunogenetics 2000: 51: 591-9.
37. Tsuchiya N, Shiota M, Moriyama S. MICA allele typing of HLA-B27 positive Japanese patients with seronegative spondylarthropathies and healthy individuals: Differential linkage disequilibrium with HLA-B27 subtypes. Arthritis Rheum 1998: 41: 68-73.
38. Visser C, Tilanus M, Tatari Z et al. Sequencing-based typing of MICA reveals 33 alleles: A study on linkage with classical HLA genes. Immunogenetics 1999: 49: 561-6.
39. Visser C, Tilanus M, Schaeffer V et al. Sequencing-based typing reveals six novel MHC class I chain-related gene B (MICB) alleles. Tissue Antigens 1998: 51: 649-52.
40. Bunce M, Barnardo M, Welsh K. The PCR-SSP Manager computer program: A tool for maintaining sequence alignments and automatically updating the specificities of PCR-SSP primers and primer mixes. Tissue Antigens 1998: 52: 159-75.
41. Ando H, Mizuki N, Ota M et al. Allelic variants of the human MHC class I chain-related B gene (MICB). Immunogenetics 1997: 46: 499-508.
42. Petersdorf E, Shuler K, Longton G, Spies T, Hansen J. Population study of allelic diversity in the human MHC class I-related MIC-A gene. Immunogenetics 1999: 49: 605-12.
43. Fischer G, Arguello J, Perez-Rodriguez M et al. Novel intronic variants of MICB (MHC class I chain-related gene B). European J Immunogenetics 1999: 26: 399-404.
44. Katsuyama Y, Ota M, Ando H et al. Sequencing-based typing for genetic polymorphisms in exons 2, 3 and 4 of the MICA gene. Tissue Antigens 1999: 54: 178-84.
45. Fischer G, Perez-Rodriguez M, Arguello J et al. Three novel MICB alleles. Tissue Antigens 2000: 55: 166-70.
46. Bunce M, O'Neill CM, Barnardo MC et al. Phototyping: Comprehensive DNA typing for HLA-A, B, C, DRB1, DRB3, DRB4, DRB5 and DQB1 by PCR with 144 primer mixes utilizing sequence-specific primers (PCR-SSP). Tissue Antigens 1995: 46: 355-67.
47. Welsh K, Bunce M. Molecular typing for the MHC with PCR-SSP. Rev Immunogenetics 1999: 1: 157-76.
48. Lennard-Jones J. Classification of inflammatory bowel disease. Scand J Gastroenterol 1989: 24: 2-6.
49. Schneider S, Roessli D, Excoffier L. Arlequin: A Software for Population Genetics Data Analysis. 2.000 Edn. Geneva, Switzerland: Genetics and Biometry Laboratory, University of Geneva, 2000.
50. Fanning G, Bunce M, Black C, Welsh K. Polymerase chain reaction haplotyping using-3′ mismatches in the forward and reverse primers: Application to the bi-allelic polymorphisms of tumour necrosis factor and lymphotoxin alpha. Tissue Antigens 1997: 50: 23-31.
51. Mullighan C, Marshall S, Bunce M, Welsh K. Variation in immunoregulatory genes determines the clinical phenotype of common variable immunodeficiency. Genes Immunity 1999: 1: 137-48.
52. Rompphruk A, Naruse T, Romphruk A et al. Diversity of MICA (PERB11.1) and HLA haplotypes in North-eastern Thais. Tissue Antigens 2001: 58: 83-9.
53. Ahmad T, Armuzzi A, Bunce M et al. Towards a molecular classification of the clinical manifestations of Crohn's disease. Gastroenterology 2002: 122: 854-66.
54. Cuthbert A, Fisher S, Mirza M et al. The contribution of N0D2 gene mutations to the risk and site of disease in inflammatory bowel disease. Gastroenterology 2002: 122: 867-74.
55. Liu Z, Geboes K, D'Haens SC, Rutgeerts P, Ceuppens J. IL-15 is highly expressed in inflammatory bowel disease and regulates local T cell-dependent cytokine production. J Immunol 2000: 164: 3608-15.
56. Roberts A, Lee L, Schwarz E et al. NKG2D receptors induced by IL-15 costimulate CD28-negative effector CTL in the tissue microenvironment. J Immunol 2001: 167: 5527-30.
57. Pellet P, Renaud M, Fodil N et al. Allelic repertoire of the human MICB gene. Immunogenetics 1997: 46: 434-6.