GWAS signals across the HLA regions: Revealing a clue for common etiology underlying infectious tumors and other immunity diseases

Chinese Journal of Cancer

Volumn 30, Issue 4, 2011, Pages 231-239

  Shugarf, Yin Yao ^a   Wang, Ying ^b   Jia, Wei Hua ^c   Zeng, Yi Xin ^c  

^a NATIONAL INSTITUTE OF MENTAL HEALTH   (United States)

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

^c SUN YAT SEN UNIVERSITY CANCER CENTER   (China)

Author keywords

[No Author keywords available]

Indexed keywords

HLA ANTIGEN;

ALLELE; ARTICLE; CARCINOGENESIS; CELIAC DISEASE; CHRONIC LYMPHATIC LEUKEMIA; DISEASE ASSOCIATION; EPSTEIN BARR VIRUS; FOLLICULAR LYMPHOMA; GENE; GENETIC ASSOCIATION; GENETIC VARIABILITY; HAPLOTYPE; HLA GENE; HODGKIN DISEASE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNE DEFICIENCY; IMMUNOPATHOGENESIS; INFECTION; INFLAMMATORY DISEASE; INSULIN DEPENDENT DIABETES MELLITUS; LEPROSY; MULTIPLE SCLEROSIS; NASOPHARYNX CARCINOMA; NONHODGKIN LYMPHOMA; NONHUMAN; RHEUMATOID ARTHRITIS; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEMIC LUPUS ERYTHEMATOSUS; GENETIC PREDISPOSITION; GENETICS; IMMUNOLOGY; IMMUNOPATHOLOGY; ISOLATION AND PURIFICATION; METABOLISM; NASOPHARYNX TUMOR; REVIEW; VIROLOGY;

GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HERPESVIRUS 4, HUMAN; HLA ANTIGENS; HUMANS; IMMUNE SYSTEM DISEASES; LYMPHOMA, NON-HODGKIN; NASOPHARYNGEAL NEOPLASMS;

EID: 79954547355     PISSN: 1000467X     EISSN: 1944446X     Source Type: Journal    
DOI: None     Document Type: Article

References (55)

1. Tse KP, Su WH, Chang KP, et al. Genome-wide association study reveals multiple nasopharyngeal carcinoma-associated loci within the HLA region at chromosome 6p21.3 [J]. Am J Hum Genet, 2009,85(2): 194-203.
2. Bei JX, Li Y, Jia WH, et al. A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci [J]. Nat Genet, 2010,42(7):599-603.
3. Clancy RM, Marion MC, Kaufman KM, et al. Identification of candidate loci at 6p21 and 21q22 in a genome-wide association study of cardiac manifestations of neonatal lupus [J]. Arthritis Rheum, 2010,62(11):3415-3424.
4. Harley JB, Alarcon-Riquelme ME, Criswell LA, et al. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci [J]. Nat Genet, 2008,40(2):204-210.
5. Horn G, Graham RR, Modrek B, et al. Association of systemic lupus erythematosus with c8orf13-blk and itgam-itgax [J]. N Engl J Med, 2008,358(9):900-909.
6. Han JW, Zheng HF, Cui Y, et al. Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus [J]. Nat Genet, 2009,41(11):1234-1237.
7. Kamatani Y, Wattanapokayakit S, Ochi H, et al. A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians [J]. Nat Genet, 2009,41 (5):591-595.
8. Hirschfield GM, Liu X, Xu C, et al. Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants [J]. N Engl J Med, 2009,360(24):2544-2555.
9. Ferreira RC, Pan - Hammarstrom Q, Graham RR, et al. Association of IFIH1 and other autoimmunity risk alleles with selective iga deficiency [J]. Nat Genet, 2010,42(9):777-780.
10. Pereyra F, Jia X, McLaren PJ, et al. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation [J]. Science, 2010,330(6010):1551-1557.
11. Pelak K, Goldstein DB, Walley NM, et al. Host determinants of HIV-1 control in African Americans [J]. J Infect Dis, 2010,201 (8):1141-1149.
12. Fellay J, Ge D, Shianna KV, et al. Common genetic variation and the control of HIV-1 in humans [J]. PLoS Genet, 2009,5 (12):e1000791.
13. Franke A, Balschun T, Sina C, et al. Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL) [J]. Nat Genet, 2010,42(4):292-294.
14. Asano K, Matsushita T, Umeno J, et al. A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population [J]. Nat Genet, 2009,41 (12): 1325-1329.
15. Barrett JC, Lee JC, Lees CW, et al. Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region [J]. Nat Genet, 2009,41 (12): 1330-1334.
16. Silverberg MS, Cho JH, Rioux JD, et al. Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study [J]. Nat Genet, 2009,41 (2):216-220.
17. Franke A, Balschun T, Karlsen TH, et al. Sequence variants in IL10, arpc2 and multiple other loci contribute to ulcerative colitis susceptibility [J]. Nat Genet, 2008,40(11):1319-1323.
18. Kugathasan S, Baldassano RN, Bradfield JP, et al. Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease [J]. Nat Genet, 2008,40(10):1211-1215.
19. Radstake TR, Gorlova O, Rueda B, et al. Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus [J]. Nat Genet, 2010,42(5):426-429.
20. Nischwitz S, Cepok S, Kroner A, et al. Evidence for VAV2 and ZNF433 as susceptibility genes for multiple sclerosis [J]. J Neuroimmunol, 2010,227(1-2): 162-166.
21. Sanna S, Pitzalis M, Zoledziewska M, et al. Variants within the immunoregulatory cblb gene are associated with multiple sclerosis [J]. Nat Genet, 2010,42(6):495-497.
22. Jakkula E, Leppa V, Sulonen AM, et al. Genome-wide association study in a high-risk isolate for multiple sclerosis reveals associated variants in STAT3 gene [J]. Am J Hum Genet, 2010,86(2):285-291.
23. Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20 [J]. Nat Genet, 2009,41 (7):824-828.
24. De Jager PL, Jia X, Wang J, et al. Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci [J]. Nat Genet, 2009,41 (7):776-782.
25. Comabella M, Craig DW, Camina-Tato M, et al. Identification of a novel risk locus for multiple sclerosis at 13q31.3 by a pooled genome-wide scan of 500,000 single nucleotide polymorphisms [J]. PLoS One, 2008,3(10):e3490.
26. Hafler DA, Compston A, Sawcer S, et al. Risk alleles for multiple sclerosis identified by a genomewide study [J]. N Engl J Med, 2007,357(9):851-862.
27. Kochi Y, Okada Y, Suzuki A, et al. A regulatory variant in CCR6 is associated with rheumatoid arthritis susceptibility [J]. Nat Genet, 2010,42(6):515-519.
28. Genome-wide association study of 14,000 cases of seven common diseases and 3000 shared controls [J]. Nature, 2007,447(7145):661-678.
29. Julia A, Ballina J, Canete JD, et al. Genome-wide association study of rheumatoid arthritis in the Spanish population: KIF12 as a risk locus for rheumatoid arthritis susceptibility [J]. Arthritis Rheum, 2008,58(8):2275-2286.
30. Plenge RM, Seielstad M, Padyukov L, et al. TRAF1-C5 as a risk locus for rheumatoid arthritis-a genome-wide study [J]. N Engl J Med, 2007,357(12):1199-1209.
31. Raychaudhuri S, Remmers EF, Lee AT, et al. Common variants at CD40 and other loci confer risk of rheumatoid arthritis [J]. Nat Genet, 2008,40(10):1216-1223.
32. Stahl EA, Raychaudhuri S, Remmers EF, et al. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci [J]. Nat Genet, 2010,42(6):508-514.
33. Ellinghaus E, Ellinghaus D, Stuart PE, et al. Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2 [J]. Nat Genet, 2010,42(11):991-995.
34. Strange A, Capon F, Spencer CC, et al. A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1 [J]. Nat Genet, 2010,42(11):985-990.
35. Barrett JC, Clayton DG, Concannon P, et al. Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes [J]. Nat Genet, 2009,41 (6):703-707.
36. Capon F, Bijlmakers MJ, Wolf N, et al. Identification of ZNF313/ RNF114 as a novel psoriasis susceptibility gene [J]. Hum Mol Genet, 2008,17(13):1938-1945.
37. Cooper JD, Smyth DJ, Smiles AM, et al. Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci [J]. Nat Genet, 2008,40(12):1399-1401.
38. Hakonarson H, Grant SF, Bradfield JP, et al. A genome-wide association study identifies kiaa0350 as a type 1 diabetes gene [J]. Nature, 2007,448(7153):591-594.
39. Liu Y, Helms C, Liao W, et al. A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci [J]. PLoS Genet, 2008,4(3):e1000041.
40. Nair RP, Duffin KC, Helms C, et al. Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways [J]. Nat Genet, 2009,41(2):199-204.
41. Zhang XJ, Huang W, Yang S, et al. Psoriasis genome-wide association study identifies susceptibility variants within Ice gene cluster at 1q21 [J]. Nat Genet, 2009,41 (2):205-210.
42. Dubois PC, Trynka G, Franke L, et al. Multiple common variants for celiac disease influencing immune gene expression [J]. Nat Genet, 2010,42(4):295-302.
43. van Heel DA, Franke L, Hunt KA, et al. A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21 [J]. Nat Genet, 2007,39(7): 827-829.
44. Zhang FR, Huang W, Chen SM, et al. Genomewide association study of leprosy [J]. N Engl J Med, 2009,361 (27):2609-2618.
45. Hildesheim A, Apple RJ, Chen CJ, et al. Association of hla class I and II alleles and extended haplotypes with nasopharyngeal carcinoma in Taiwan [J]. J Natl Cancer Inst, 2002,94(23):1780-1789.
46. Lin HJ, Cherng JM, Hung MS, et al. Functional assays of hla a2-restricted epitope variant of latent membrane protein 1 (lmp-1) of Epstein-Barr virus in nasopharyngeal carcinoma of southern china and taiwan [J]. J Biomed Sci, 2005,12(6):925-936.
47. Sengupta S, den Boon JA, Chen IH, et al. Genome-wide expression profiling reveals EBV-associated inhibition of MHC class I expression in nasopharyngeal carcinoma [J]. Cancer Res, 2006,66(16):7999-8006.
48. Butsch Kovacic M, Martin M, Gao X, et al. Variation of the killer cell immunoglobulin-like receptors and HLA-C genes in nasopharyngeal carcinoma [J]. Cancer Epidemiol Biomarkers Prev, 2005,14(11 Pt 1):2673-2677.
49. Diepstra A, Niens M, Vellenga E, et al. Association with hla class I in Epstein-Barr-virus-positive and with hla class III in Epstein-Barr-virus-negative Hodgkin's lymphoma [J]. Lancet, 2005,365(9478):2216-2224.
50. 4 Hodgkin lymphoma [J]. Blood, 2007,110(9): 3310-3315.
51. Rickinson AB, Moss DJ. Human cytotoxic t lymphocyte responses to Epstein-Barr virus infection [J]. Annu Rev Immunol, 1997,15:405-431.
52. Skibola CF, Bracci PM, Halperin E, et al. Genetic variants at 6p21.33 are associated with susceptibility to follicular lymphoma [J]. Nat Genet, 2009,41 (8):873-875.
53. Gavioli R, Kurilla MG, de Campos-Lima PO, et al. Multiple HLA A11-restricted cytotoxic T-lymphocyte epitopes of different immunogenicities in the Epstein-Barr virus-encoded nuclear antigen 4 [J]. J Virol, 1993,67(3): 1572-1578.
54. Burrows JM, Burrows SR, Poulsen LM, et al. Unusually high frequency of Epstein-Barr virus genetic variants in papua new guinea that can escape cytotoxic T-cell recognition: Implications for virus evolution [J]. J Virol, 1996,70(4):2490-2496.
55. de Campos-Lima PO, Gavioli R, Zhang QJ, et al. HLA-A11 epitope loss isolates of Epstein-Barr virus from a highly A11* population [J]. Science, 1993,260(5104):98-100.