Assembly of inflammation-related genes for pathway-focused genetic analysis

PLoS ONE

Volumn 2, Issue 10, 2007, Pages

  Loza, Matthew J ^a   McCall, Charles E ^a   Li, Liwu ^b   Isaacs, William B ^c   Xu, Jianfeng ^a   Chang, Bao Li ^a  

^a WAKE FOREST SCHOOL OF MEDICINE   (United States)

^b VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTOR PROTEIN; B7 ANTIGEN; CASPASE 8; CASPASE RECRUITMENT DOMAIN PROTEIN 15; CASPASE RECRUITMENT DOMAIN PROTEIN 4; COMPLEMENT FACTOR H; CYTOTOXIC T LYMPHOCYTE ANTIGEN 4; G PROTEIN COUPLED RECEPTOR; GLUTATHIONE; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERFERON REGULATORY FACTOR 5; INTERLEUKIN 4 RECEPTOR ALPHA; JANUS KINASE; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; MITOGEN ACTIVATED PROTEIN KINASE; MITOGEN ACTIVATED PROTEIN KINASE 1; MITOGEN ACTIVATED PROTEIN KINASE 3; NITRIC OXIDE; PHOSPHATIDYLINOSITOL 3 KINASE; PROTEIN FOS; PROTEIN KINASE B; REACTIVE OXYGEN METABOLITE; STRESS ACTIVATED PROTEIN KINASE; SUPPRESSOR OF CYTOKINE SIGNALING; TOLL LIKE RECEPTOR 4; TRANSCRIPTION FACTOR FOXP3; TRANSCRIPTION FACTOR NFAT; TRANSFORMING GROWTH FACTOR BETA1; TUMOR NECROSIS FACTOR ALPHA;

ALLERGIC ASTHMA; ARTICLE; BREAST CANCER; CROHN DISEASE; DNA MICROARRAY; ENTERITIS; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE INTERACTION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; GRAVES DISEASE; HUMAN; IMMUNE RESPONSE; IMMUNOCOMPETENT CELL; INFLAMMATION; INSULIN DEPENDENT DIABETES MELLITUS; MOLECULAR PHYLOGENY; PATHOGENESIS; PSORIATIC ARTHRITIS; RETINA MACULA AGE RELATED DEGENERATION; RHEUMATOID ARTHRITIS; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEMIC LUPUS ERYTHEMATOSUS; ALLELE; GENE EXPRESSION PROFILING; GENE LINKAGE DISEQUILIBRIUM; GENETIC LINKAGE; GENETIC PREDISPOSITION; GENETIC PROCEDURES; GENOME; HAPLOTYPE;

ALLELES; GENE EXPRESSION PROFILING; GENETIC PREDISPOSITION TO DISEASE; GENETIC TECHNIQUES; GENOME, HUMAN; GENOTYPE; HAPLOTYPES; HUMANS; INFLAMMATION; LINKAGE (GENETICS); LINKAGE DISEQUILIBRIUM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 42049106907     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0001035     Document Type: Article

References (52)

1. Lawrence T, Gilroy DW (2007) Chronic inflammation: a failure of resolution? Int J Exp Pathol 88: 85-94.
2. Han J, Ulevitch RJ (2005) Limiting inflammatory responses during activation of innate immunity. Nat Immunol 6: 1198-1205.
3. Forrester JS, Bick-Forrester J (2005) Persistence of inflammatory cytokines cause a spectrum of chronic progressive diseases: implications for therapy. Med Hypotheses 65: 227-231.
4. Goronzy JJ, Weyand CM (2005) Rheumatoid arthritis. Immunol Rev 204: 55-73.
5. Ross R (1999) Atherosclerosis - an inflammatory disease. N Engl J Med 340: 115-126.
6. Willerson JT, Ridker PM (2004) Inflammation as a cardiovascular risk factor. Circulation 109: II2-10.
7. Ridker PM, Cushman M, Stampfer MJ, Tracy RP, Hennekens CH (1997) Inflammation, aspirin, and the risk of cardiovascular disease in apparently healthy men. N Engl J Med 336: 973-979.
8. Neuman MG (2007) Immune dysfunction in inflammatory bowel disease. Transl Res 149: 173-186.
9. James SP (2005) Prototypic disorders of gastrointestinal mucosal immune function: Celiac disease and Crohn's disease. J Allergy Clin Immunol 115: 25-30.
10. Coussens LM, Werb Z (2002) Inflammation and cancer. Nature 420: 860-867.
11. Ernst PB, Gold BD (2000) The disease spectrum of Helicobacter pylori: the immunopathogenesis of gastroduodenal ulcer and gastric cancer. Annu Rev Microbiol 54: 615-640.
12. Karin M, Cao Y, Greten FR, Li ZW (2002) NF-kappaB in cancer: from innocent bystander to major culprit. Nat Rev Cancer 2: 301-310.
13. Kuper H, Adami HO, Trichopoulos D (2000) Infections as a major preventable cause of human cancer. J Intern Med 248: 171-183.
14. Shacter E, Weitzman SA (2002) Chronic inflammation and cancer. Oncology (Williston Park) 16: 217-26, 229.
15. Ulrich CM, Bigler J, Potter JD (2006) Non-steroidal anti-inflammatory drugs for cancer prevention: promise, perils and pharmacogenetics. Nat Rev Cancer 6: 130-140.
16. Calder PC (2006) Polyunsaturated fatty acids and inflammation. Prostaglandins Leukot Essent Fatty Acids 75: 197-202.
17. Aganna E, Martinon F, Hawkins PN, Ross JB, Swan DC, et al. (2002) Association of mutations in the NALP3/CIAS1/PYPAF1 gene with a broad phenotype including recurrent fever, cold sensitivity, sensorineural deafness, and AA amyloidosis. Arthritis Rheum 446: 2445-2452.
18. Dode C, Le Du N, Cuisset L, Letourneur F, Berthelot JM, et al. (2002) New mutations of CIAS1 that are responsible for Muckle-Wells syndrome and familial cold urticaria: a novel mutation underlies both syndromes. Am J Hum Genet 70: 1498-1506.
19. Hoffman HM, Mueller JL, Broide DH, Wanderer AA, Kolodner RD (2001) Mutation of a new gene encoding a putative pyrin-like protein causes familial cold autoinflammatory syndrome and Muckle-Wells syndrome. Nat Genet 29: 301-305.
20. Touitou I (2001) The spectrum of Familial Mediterranean Fever (FMF) mutations. Eur J Hum Genet 9: 473-483.
21. Aoki T, Hirota T, Tamari M, Ichikawa Y, Takeda K, et al. (2006) An association between asthma and TNF-308G/A polymorphism: meta-analysis. J Hum Genet 51: 677-685.
22. Lee YH, Harley JB, Nath SK (2006) Meta-analysis of TNF-alpha promoter -308 A/G polymorphism and SLE susceptibility. Eur J Hum Genet 14: 364-371.
23. Rahman P, Siannis F, Butt C, Farewell V, Peddle L, et al. (2006) TNFalpha polymorphisms and risk of psoriatic arthritis. Ann Rheum Dis 65: 919-923.
24. Lee YH, Rho YH, Choi SJ, Ji JD, Song GG, et al. (2007) The PTPN22 C1858T functional polymorphism and autoimmune disease -a meta-analysis. Rheumatology (Oxford) 46: 49-56.
25. Graham RR, Kozyrev SV, Bacchler EC, Reddy MV, Plenge RM, et al. (2006) A common haplotype of interferon regulatory factor 5 (IRF5) regulates splicing and expression and is associated with increased risk of systemic lupus erythematosus. Nat Genet 38: 550-555.
26. Smyth DJ, Cooper JD, Bailey R, Field S, Burren O, et al. (2006) A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nat Genet 38: 617-619.
27. Howson JM, Dunger DB, Nutland S, Stevens H, Wicker LS, et al. (2007) A type 1 diabetes subgroup with a female bias is characteriscd by failure in tolerance to thyroid peroxidase at an early age and a strong association with the cytotoxic T-lymphocyte-associated antigen-4 gene. Diabetologia 50: 741-746.
28. Payne F, Cooper JD, Walker NM, Lam AC, Smink LJ, et al. (2007) Interaction analysis of the CBLB and CTLA4 genes in type 1 diabetes. J Leukoc Biol 81: 581-583.
29. Ueda H, Howson JM, Esposito L, Heward J, Snook H, et al. (2003) Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease. Nature 423: 506-511.
30. Oostenbrug LE, Nolte IM, Oosterom E, van der SG, te Meerman GJ, et al. (2006) CARD 15 in inflammatory bowel disease and Crohn's disease phenotypes: an association study and pooled analysis. Dig Liver Dis 38: 834-845.
31. Duerr RE, Taylor KD, Brant SR, Rioux JD, Silverberg MS, et al. (2006) A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 314: 1461-1463.
32. Loza MJ, Chang B (2007) Association between Q551R IL4R genetic variants and atopic asthma risk demonstrated by meta-analysis. J Allergy Clin Immunol In press.
33. Breast Cancer Association Consortium (2006) Commonly studied single-nucleotide polymorphisms and breast cancer: results from the Breast Cancer Association Consortium. J Natl Cancer Inst 98: 1382-1396.
34. Gaudet MM, Egan KM, Lissowska J, Newcomb PA, Brinton LA, et al. (2007) Genetic variation in tumor necrosis factor and lymphotoxin-alpha (TNF-LTA) and breast cancer risk. Hum Genet.
35. Cox DG, Pontes C, Guino E, Navarro M, Osorio A, et al. (2004) Polymorphisms in prostaglandin synthase 2/cyclooxygenase 2 (PTGS2/COX2) and risk of colorectal cancer. Br J Cancer 91: 339-343.
36. Koh WP, Yuan JM, van den BD, Lee HP, Yu MC (2004) Interaction between cyclooxygenase-2 gene polymorphism and dietary n-6 polyunsaturated fatty acids on colon cancer risk: the Singapore Chinese Health Study. Br J Cancer 90: 1760-1764.
37. Lin HJ, Lakkides KM, Keku TO, Reddy ST, Louie AD, et al. (2002) Prostaglandin H synthase 2 variant (Val5l 1Ala) in African Americans may reduce the risk for colorectal neoplasia. Cancer Epidemiol Biomarkers Prev 11: 1305-1315.
38. Siezen CL, van Leeuwen AI, Kram NR, Luken ME, van Kranen HJ, et al. (2005) Colorectal adenoma risk is modified by the interplay between polymorphisms in arachidonic acid pathway genes and fish consumption. Carcinogenesis 26: 449-457.
39. Siczen CL, Bueno-de-Mesquita HB, Pecters PH, Krain NR, van Doeselaar M, et al. (2006) Polymorphisms in the genes involved in the arachidonic acid-pathway, fish consumption and the risk of colorectal cancer. Int J Cancer 119: 297-303.
40. Shahedi K, Lindstrom S, Zheng SL, Wiklund F, Adolfsson J, et al. (2006) Genetic variation in the COX-2 gene and the association with prostate cancer risk. Int J Cancer 119: 668-672.
41. Hedelin M, Chang ET, Wiklund F, Bellocco R, Klint A, et al. (2007) Assoctation of frequent consumption of fatty fish with prostate cancer risk is modified by COX-2 polymorphism. Int J Cancer 120: 398-405.
42. Zheng SL, Liu W, Wiklund F, Dimitrov L, Balter K, et al. (2006) A comprehensive association study for genes in inflammation pathway provides support for their roles in prostate cancer risk in the CAPS study. Prostate 66: 1556-1564.
43. Dinu V, Miller PL, Zhao H (2007) Evidence for association between multiple complement pathway genes and AMD. Genet Epidemiol.
44. Conley YP, Jakobsdottir J, Mah T, Weeks DE, Klein R, et al. (2006) CFH, ELOVL4, PLEKHA1 and LOC387715 genes and susceptibility to age-related maculopathy: AREDS and CHS cohorts and meta-analyses. Hum Mol Genet 15: 3206-3218.
45. Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, et al. (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308: 385-389.
46. Willer CJ, Scott LJ, Bonnycastle LL, Jackson AU, Chines P, et al. (2006) Tag SNP selection for Finnish individuals based on the CEPH Utah HapMap database. Genet Epidemiol 30: 180-190.
47. De Bakker PI, Graham RR, Altshuler D, Henderson BE, Haiman CA (2006) Transferability of tag SNPs to capture common genetic variation in DNA repair genes across multiple populations. Pac Symp Biocomput. pp 478-486.
48. Montpetit A, Nelis M, Laflamme P, Magi R, Ke X, et al. (2006) An evaluation of the performance of tag SNPs derived from HapMap in a Caucasian population. PLoS Genet 2: c27.
49. Tenesa A, Dunlop MG (2006) Validity of tagging SNPs across populations for association studies. Eur J Hum Genet 14: 357-363.
50. Xu Z, Kaplan NL, Taylor JA (2007) Tag SNP selection for candidate gene association studies using HapMap and gene resequencing data. Eur J Hum Genet.
51. Mueller JC, Lohmussaar E, Magi R, Remm M, Bettecken T, et al. (2005) Linkage disequilibrium patterns and tagSNP transferability among European populations. Am J Hum Genet 76: 387-398.
52. Johansson A, Vavruch-Nilsson V, Cox DR, Frazer KA, Gyllensten U (2007) Evaluation of the SNP tagging approach in an independent population sample-array-based SNP discovery in Sami. Hum Genet 122: 141-150.