Comparison study for genotyping of a single-nucleotide polymorphism in the tumor necrosis factor promoter gene

Diagnostic Molecular Pathology

Volumn 11, Issue 4, 2002, Pages 228-233

  Juszczynski, Przemysław ^a   Woszczek, Grzegorz ^a   Borowiec, Maciej ^a   Kowalski, Marek ^a   Robak, Tadeusz ^a   Biliński, Przemysław ^a   Salles, Gilles ^a   Warzocha, Krzysztof ^a  

^a MEDICAL UNIVERSITY OF LODZ   (Poland)

Author keywords

Genotyping; Sensitivity; Single nucleotide polymorphism; Specificity; TNF

Indexed keywords

TUMOR NECROSIS FACTOR; TUMOR NECROSIS FACTOR ALPHA;

ACCURACY; ANALYTIC METHOD; ARTICLE; BASE MISPAIRING; GENOTYPE; HUMAN; PRIORITY JOURNAL; PROMOTER REGION; QUALITY CONTROL; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARD; AUTOMATION; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; METHODOLOGY; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY;

AUTOMATION; GENOTYPE; HUMANS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS (GENETICS); SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; TUMOR NECROSIS FACTOR-ALPHA;

EID: 0036891608     PISSN: 10529551     EISSN: None     Source Type: Journal    
DOI: 10.1097/00019606-200212000-00006     Document Type: Article

References (35)

1. Agarwal P, Oldenburg MC, Czarneski JE, et al. Comparison study for identifying promoter allelic polymorphism in interleukin 10 and tumor necrosis factor genes. Diagn Mol Pathol 2000;9:158-64.
2. Awad MR, Webber S, Boyle G, et al. The effect of cytokine gene polymorphisms on pediatric heart allograft outcome. J Heart Lung Transplant 2001;20:625-30.
3. Botstein D, White RL, Skolnick M, et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 1980;32:314-31.
4. Bouma G, Crusius JB, Oudkerk Pool M, et al. Secretion of tumour necrosis factor alpha and lymphotoxin alpha in relation to polymorphism in the TNF genes and HLA-DR alleles. Relevance for inflammatory bowel disease. Scand J Immunol 1996;43:456-63.
5. Brinkmann BMN, Huizinga TWJ, Kurban SS, et al. Tumour necrosis factor alpha gene polymorphisms in rheumatoid arthritis: Association with susceptibility to, or severity of, disease? Br J Rheumatol 1997;36:516-21.
6. Carlson CS, Newman TL, Nickerson DA. SNPing in the human genome. Cur Opin Chem Biol 2001;5:78-85.
7. Chen X, Kwok PY. Homogeneous genotyping assays for single nucleotide polymorphisms with fluorescence resonance energy transfer detection. Genet Anal 1999;14:157-63.
8. Cox A, Gonzalez AM, Wilson AG, et al. Comparative analysis of the genetic associations of HLA-DR3 and tumour necrosis factor alpha with human IDDM. Diabetologia 1994;37:500-3.
9. Garcia-Merino A, Alper CA, Usuku K, et al. Tumor necrosis factor (TNF) microsatellite haplotypes in relation to extended haplotypes, susceptibility to disease associated with the major histocompatibility complex and TNF secretion. Hum Immunol 1996;50:11-21.
10. Gravestein LA, Borst J. Tumor necrosis factor receptor family members in the immune system. Semin Immunol 1998;10:423-34.
11. Jacob CO, Fronek Z, Lewis GD, et al. Heritable major histocompatibility complex class II-associated differences in production of tumor necrosis factor alpha: Relevance to genetic predisposition to systemic lupus erythematosus. Proc Natl Acad Sci USA 1990;87:1233-37.
12. Juszczynski P, Kalinka E, Bienvenu J, et al. Human leukocyte antigens class II (HLA DRB1) and tumor necrosis factor genetic polymorphisms are independent predictors of non-Hodgkin's lymphoma outcome. Blood 2002;100:3037-40.
13. Kwok S, Kellogg DE, McKinney N, et al. Effects of primer-template mismatches on the polymerase chain reaction: Human immunodeficiency virus type-1 model studies. Nucleic Acids Res 1990;18:999-1005.
14. Lech-Maranda E, Baseggio L, Bienvenu J, et al. A single nucleotide polymorphism in the IL-10 gene promoter is associated with an adverse outcome of diffuse large B-cell lymphoma patients. Ann Oncol 2002;13[Suppl. 2]:18.
15. Livak KJ. Allelic discrimination using fluorogenic probes and the 5'nuclease assay. Genet Anal 1999;14:143-49.
16. Lyamichev V, Mast AL, Hall JG, et al. Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat Biotechnol 1999;17:292-96.
17. McGuire W, Hill AV, Allsopp CE, et al. Variation in the TNF-alpha promoter region associated with susceptibility to cerebral malaria. Nature 1994;371:508-11.
18. Middleton PG, Taylor PRA, Jackson G, et al. Cytokine gene polymorphisms associating with severe acute graft-versus-host disease in HLA-identical sibling transplants. Blood 1998;92:3943-48.
19. Newton CR, Graham A, Heptinstall LE, et al. Analysis of any point mutation in DNA: The amplification refractory mutation system (ARMS). Nucleic Acids Res 1989;17:2503-16.
20. Nikiforov TT, Rendle RB, Goelet P, et al. Genetic bit analysis: A solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Res 1994;22:4167-75.
21. Okayama H, Curiel DT, Brantly ML, et al. Rapid nonradioactive detection of mutations in the human genome by allele-specific amplification. J Lab Clin Med 1989;11:105-13.
22. Ortolani C, Ispano M, Pastorello EA, et al. Comparison of results of skin prick tests (with fresh foods and commercial food extracts) and RAST in 100 patients with oral allergy syndrome. Allergy Clin Immunol 1989;83:683-90.
23. Parsons BL, Heflich RH. Genotypic selection methods for the direct analysis of point mutations. Mutation Res 1997;387:97-121.
24. Pociot F, Briant L, Jongeneel CV, et al. Association of tumor necrosis factor (TNF) and class II major histocompatibility complex alleles with the secretion of TNF-alpha and TNF-beta by human mononuclear cells: A possible link to insulin-dependent diabetes mellitus. Eur J Immunol 1993;23:224-31.
25. Saiki RK, Bugawan TL, Horn GT, et al. Analysis of enzymatically amplified beta-globin and HLA-DQ alpha DNA with allele-specific oligonucleotide probes. Nature 1986;324:163-66.
26. Seidemann K, Zimmermann M, Book M, et al. TNF and lymphotoxin-α genetic polymorphisms are associated with outcome in pediatric patients with Burkitt's lymphoma/B-ALL and high tumor load - Results from 221 patients trial NHL-BFM 95. Ann Oncol 2002;13[Suppl. 2]:31.
27. Sommer SS, Groszbach AR, Bottema CDK. PCR amplification of specific alleles (PASA) is a general method for rapidly detecting known single-base changes. BioTechniques 1992;12:82-87.
28. Syvanen AC. From gels to chips: 'Minisequencing' primer extension for analysis of point mutations and single nucleotide polymorphisms. Hum Mutat 1999;13:1-10.
29. Verjans GM, Brinkman BM, Van Doornik CE, et al. Polymorphism of tumor necrosis factor-alpha (TNFα) at position -308 in relation to ankylosing spondylitis. Clin Exp Immunol 1994;97:45-7.
30. Warzocha K, Ribeiro P, Bienvenu J, et al. Genetic polymorphisms in the tumor necrosis factor locus influence non-Hodgkin's lymphoma outcome. Blood 1998;91:3574-81.
31. Warzocha K, Salles G, Bienvenu J, et al. Tumor necrosis factor ligand receptor system can predict treatment outcome in lymphoma patients. J Clin Oncol 1997;15:499-508.
32. Westendorp RG, Langermans JA, Huizinga TW, et al. Genetic influence on cytokine production and fatal meningococcal disease. Lancet 1997;349:170-73.
33. Wilson AG, de Vries N, Pociot F, et al. An allelic polymorphism within the human tumor necrosis factor α promoter region is strongly associated with HLA A1, B8 and DR3 alleles. J Exp Med 1993;177:557-60.
34. Wilson AG, Symons JA, McDowell TL, et al. Effects of a polymorphism in the human tumor necrosis factor alpha promoter on transcriptional activation. Proc Natl Acad Sci USA 1997;94:3195-99.
35. Zhu KY, Clark JM. Addition of a competitive primer can dramatically improve the specificity of PCR amplification of specific alleles. BioTechniques 1996;21:586-90.