The HLA genomic loci map: Expression, interaction, diversity and disease

Journal of Human Genetics

Volumn 54, Issue 1, 2009, Pages 15-39

  Shiina, Takashi ^a   Hosomichi, Kazuyoshi ^a   Inoko, Hidetoshi ^a   Kulski, Jerzy K ^a,b  

^a TOKAI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

Cancer; Disease association; Gene expression; Gene interaction; Genomic diversity; Human leukocyte antigen; Major histocompatibility complex; Polymorphism

Indexed keywords

AUTOIMMUNE DISEASE; CELL FUNCTION; GENE; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE INTERACTION; GENE LOCUS; GENE MAPPING; GENE NUMBER; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; HAPLOTYPE; HLA SYSTEM; HUMAN; IMMUNE RESPONSE; INFECTION; INFLAMMATION; INTERSPERSED REPEAT; NUCLEOTIDE SEQUENCE; REVIEW; SEQUENCE ANALYSIS; CHROMOSOME MAP; DISEASES; GENETIC PREDISPOSITION; GENETICS;

HLA ANTIGEN;

CHROMOSOME MAPPING; DISEASE; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; HLA ANTIGENS; HUMANS;

EID: 58849104457     PISSN: 14345161     EISSN: None     Source Type: Journal    
DOI: 10.1038/jhg.2008.5     Document Type: Review

References (184)

1. The MHC Sequencing Consortium. Complete structure and gene map of a human major histocompatibility complex (MHC). Nature 401, 921-923 (1999).
2. Smith, W. P., Vu, Q., Li, S. S., Hansen, J. A., Zhao, L. P. & Geraghty, D. E. Toward understanding MHC disease associations: partial resequencing of 46 distinct HLA haplotypes. Genomics 87, 561-571 (2006).
3. Shiina, T., Ota, M., Shimizu, S., Katsuyama, Y., Hashimoto, N., Takasu, M. et al. Rapid evolution of MHC class I genes in primates generates new disease alleles in man via hitchhiking diversity. Genetics 173, 1555-1570 (2006).
4. Muller-Hilke, B. & Mitchison, N. A. The role of HLA promoters in autoimmunity. Curr. Pharm. Des. 12, 3743-3752 (2006).
5. Traherne, J. A. Human MHC architecture and evolution: implications for disease association studies. Int. J. Immunogenet. 35, 179-192 (2008).
6. Solberg, O. D., Mack, S. J., Lancaster, A. K., Single, R. M., Tsai, Y., Sanchez-Mazas, A. et al. Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies. Hum. Immunol. 69, 443-464 (2008).
7. Horton, R., Gibson, R., Coggill, P., Miretti, M., Allcock, R. J., Almeida, J. et al. Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics 60, 1-18 (2008).
8. Fu, S., Zhao, H., Shi, J., Abzhanov, A., Crawford, K., Ohno-Machado, L. et al. Peripheral arterial occlusive disease: global gene expression analyses suggest a major role for immune and inflammatory responses. BMC Genomics 9, 369 (2008).
9. Claas, F. H. J. & Duquesnoy, R. J. The polymorphic alloimmune response in clinical transplantation. Editorial overview. Curr. Opin. Immunol. 20, 566-567 (2008).
10. Choo, S. Y. The HLA system: genetics, immunology, clinical testing, and clinical implications. Yonsei Med. J. 48, 11-23 (2007).
11. Fernando, M. M., Stevens, C. R., Walsh, E. C., De Jager, P. L., Goyette, P., Plenge, R. M. et al. Defining the role of the MHC in autoimmunity: a review and pooled analysis. PLoS Genet. 4, e1000024 (2008).
12. Martin, M. P. & Carrington, M. Immunogenetics of viral infections. Curr. Opin. Immunol. 17, 510-516 (2005).
13. Fellay, J., Shianna, K. V., Ge, D., Colombo, S., Ledergerber, B., Weale, M. et al. A whole-genome association study of major determinants for host control of HIV-1. Science 317, 944-947 (2007).
14. Knapp, L. A. The ABCs of MHC. Evol. Anthropol. 14, 28-37 (2005).
15. Ziegler, A., Kentenich, H. & Uchanska-Ziegler, B. Female choice and the MHC. Trends Immunol. 26, 496-502 (2005).
16. Xiao, B. G. & Link, H. Immune regulation within the central nervous system. J. Neurol. Sci. 157, 1-12 (1998).
17. Huh, G. S., Boulanger, L. M., Du, H., Riquelme, P. A., Brotz, T. M. & Shatz, C. J. Functional requirement for class I MHC in CNS development and plasticity. Science 290, 2155-2159 (2000).
18. Boulanger, L. M. & Shatz, C. J. Immune signaling in neural development, synaptic plasticity and disease. Nat. Rev. Neurosci. 5, 521-531 (2004).
19. Cullheim, S. & Thams, S. The microglial networks of the brain and their role in neuronal network plasticity after lesion. Brain Res. Rev. 55, 89-96 (2007).
20. Ohtsuka, M., Inoko, H., Kulski, J. K. & Yoshimura, S. Major histocompatibility complex (Mhc) class Ib gene duplications, organization and expression patterns in mouse strain C57BL/6. BMC Genomics 9, 178 (2008).
21. Matsuo, R., Asada, A., Fujitani, K. & Inokuchi, K. LIRF, a gene induced during hippocampal long-term potentiation as an immediate-early gene, encodes a novel RING finger protein. Biochem. Biophys. Res. Commun. 289, 479-484 (2001).
22. Patiño-Lopez, G., Hevezi, P., Lee, J., Willhite, D., Verge, G. M., Lechner, S. M. et al. Human class-I restricted T cell associated molecule is highly expressed in the cerebellum and is a marker for activated NKT and CD8+ T lymphocytes. J. Neuroimmunol. 171, 145-155 (2006).
23. Goddard, C. A., Butts, D. A. & Shatz, C. A. Regulation of CNS synapses by neuronal MHC class I. Proc. Natl Acad. Sci. USA 104, 6828-6833 (2007).
24. Tonelli, L. H., Postolache, T. T. & Sternberg, E. M. Inflammatory genes and neural activity: involvement of immune genes in synaptic function and behavior. Front Biosci. 10, 675-680 (2005).
25. Lengen, C., Regard, M., Joller, H., Landis, T. & Lalive, P. Anomalous brain dominance and the immune system: do left-handers have specific immunological patterns? Brain Cogn. (2008) (e-pub ahead of print, 30 August 2008).
26. O'Keefe, G. M., Nguyen, V. T. & Benveniste, E. N. Regulation and function of class II major histocompatibility complex CD40, and B7 expression in macrophages and microglia: implications in neurological diseases. J. Neurovirol. 8, 496-512 (2002).
27. Raha-Chowdhury, R., Andrews, S. R. & Gruen, J. R. CAT 53: a protein phosphatase 1 nuclear targeting subunit encoded in the MHC class I region strongly expressed in regions of the brain involved in memory, learning, and Alzheimer's disease. Brain Res. Mol. Brain Res. 138, 70-83 (2005).
28. Cohly, H. H. & Panja, A. Immunological findings in autism. Int. Rev. Neurobiol. 71, 317-341 (2005).
29. Bailey, S. L., Carpentier, P. A., McMahon, E. J., Begolka, W. S. & Miller, S. D. Innate and adaptive immune responses of the central nervous system. Crit. Rev. Immunol. 26, 149-188 (2006).
30. McElroy, J. P. & Oksenberg, J. R. Multiple sclerosis genetics. Curr. Top Microbiol. Immunol. 318, 45-72 (2008).
31. Shiina, T., Inoko, H. & Kulski, J. K. An update of the HLA genomic region, loci information and disease associations: 2004. Tissue Antigens 64, 631-649 (2004).
32. Horton, R., Wilming, L., Rand, V., Lovering, R. C., Bruford, E. A., Khodiyar, V. K. et al. Gene map of the extended human MHC. Nat. Rev. Genet. 5, 889-899 (2004).
33. Trowsdale, J. HLA genomics in the third millennium. Curr. Opin. Immunol. 17, 498-504 (2005).
34. Stewart, C. A., Horton, R., Allcock, R. J., Ashurst, J. L., Atrazhev, A. M., Coggill, P. et al. Complete MHC haplotype sequencing for common disease gene mapping. Genome Res. 14, 1176-1187 (2004).
35. Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 35 (Database issue), D5-D12 (2007).
36. Maglott, D., Ostell, J., Pruitt, K. D. & Tatusova, T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 33, D54-D58 (2005).
37. Kulski, J. K. & Dawkins, R. L. The P5 multicopy gene family in the MHC is related in sequence to human endogenous retroviruses HERV-L and HERV-16. Immunogenetics 49, 404-412 (1999).
38. Colombo, S., Rauch, A., Rotger, M., Fellay, J., Martinez, R., Fux, C. et al. Swiss HIV Cohort Study. The HCP5 single-nucleotide polymorphism: a simple screening tool for prediction of hypersensitivity reaction to abacavir. J. Infect. Dis. 198, 864-867 (2008).
39. Liu, Y., Helms, C., Liao, W., Zaba, L. C., Duan, S., Gardner, J. et al. A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci. PLoS Genet. 4, e1000041 (2008).
40. Chang, Y. T., Chou, C. T., Shiao, Y. M., Lin, M. W., Yu, C. W., Chen, C. C. et al. Psoriasis vulgaris in Chinese individuals is associated with PSORS1C3 and CDSN genes. Br. J. Dermatol. 155, 663-669 (2006).
41. Semple, J. I., Ribas, G., Hillyard, G., Brown, S. E., Sanderson, C. M. & Campbell, R. D. A novel gene encoding a coiled-coil mitochondrial protein located at the telomeric end of the human MHC class III region. Gene 314, 41-54 (2003).
42. Ostrov, D. A., Barnes, C. L., Smith, L. E., Binns, S., Brusko, T. M., Brown, A. C. et al. Characterization of HKE2: an ancient antigen encoded in the major histocompatibility complex. Tissue Antigens 69, 181-188 (2007).
43. de Vet, E. C., Aguado, B. & Campbell, R. D. G6b, a novel immunoglobulin superfamily member encoded in the human major histocompatibility complex, interacts with SHP-1 and SHP-2. J. Biol. Chem. 276, 42070-42074 (2001).
44. Adams, P. C. & Barton, J. C. Haemochromatosis. Lancet 370, 1855-1860 (2007).
45. Kulski, J. K. & Inoko, H. MHC genes in The Encyclopedia of the Human Genome 778-785 (Nature Publishing Group. Macmillan Publishers Ltd, Houndmills, Basingstoke, Hampshire, UK, 2003).
46. Dawkins, R., Leelayuwat, C., Gaudieri, S., Tay, G., Hui, J., Cattley, S. et al. Genomics of the major histocompatibility complex: haplotypes, duplication, retroviruses and disease. Immunol. Rev. 167, 275-304 (1999).
47. Bahram, S. MIC genes: from genetics to biology. Adv. Immunol. 76, 1-60 (2000).
48. Kulski, J. K., Shiina, T., Anzai, T., Kohara, S. & Inoko, H. Comparative genomic analysis of the MHC: the evolution of class I duplication blocks, diversity and complexity from shark to man. Immunol. Rev. 190, 95-122 (2002).
49. Shiina, T., Tamiya, G., Oka, A., Takishima, N., Yamagata, T., Kikkawa, E. et al. Molecular dynamics of MHC genesis unraveled by sequencing analysis of the 1,796,938 bp HLA class I region. Proc. Natl Acad. Sci. USA 96, 13282-13287 (1999).
50. García, A., Senis, Y. A., Antrobus, R., Hughes, C. E., Dwek, R. A., Watson, S. P. et al. A global proteomics approach identifies novel phosphorylated signaling proteins in GPVI-activated platelets: involvement of G6f, a novel platelet Grb2-binding membrane adapter. Proteomics 6, 5332-5343 (2006).
51. Jady, B. E. & Kiss, T. Characterisation of the U83 and U84 small nucleolar RNAs: two novel 2′-O-ribose methylation guide RNAs that lack complementarities to ribosomal RNAs. Nucleic Acids Res. 28, 1348-1354 (2000).
52. Lestrade, L. & Weber, M. J. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res. 34, D158-D162 (2006).
53. Kiss-Laszlo, Z., Henry, Y., Bachellerie, J. P., Caizergues-Ferrer, M. & Kiss, T. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85, 1077-1088 (1996).
54. Florence, B. & Faller, D. V. You bet-cha: a novel family of transcriptional regulators. Front. Biosci. 6, d1008-d1018 (2001).
55. Kohany, O., Gentles, A. J., Hankus, L. & Jurka, J. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7, 474 (2006).
56. Gourraud, P. A., Mano, S., Barnetche, T., Carrington, M., Inoko, H. & Cambon-Thomsen, A. Integration of microsatellite characteristics in the MHC region: a literature and sequence based analysis. Tissue Antigens 64, 543-555 (2004).
57. Matsuzaka, Y., Tounai, K., Denda, A., Tomizawa, M., Makino, S., Okamoto, K. et al. Identification of novel candidate genes in the diffuse panbronchiolitis critical region of the class I human MHC. Immunogenetics. 54, 301-309 (2002).
58. Oka, A., Tamiya, G., Tomizawa, M., Ota, M., Katsuyama, Y., Makino, S. et al. Association analysis using refined microsatellite markers localizes a susceptibility locus for psoriasis vulgaris within a 111 kb segment telomeric to the HLA-C gene. Hum. Mol. Genet. 8, 2165-2170 (1999).
59. Aly, T. A., Eller, E., Ide, A., Gowan, K., Babu, S. R., Erlich, H. A. et al. Multi-SNP analysis of MHC region: remarkable conservation of HLA-A1-B8-DR3 haplotype. Diabetes 55, 1265-1269 (2006).
60. de Bakker, P. I., McVean, G., Sabeti, P. C., Miretti, M. M., Green, T., Marchini, J. et al. A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat. Genet. 38, 1166-1172 (2006).
61. Smith, W. P., Vu, Q., Li, S. S., Hansen, J. A., Zhao, L. P. & Geraghty, D. E. Toward understanding MHC disease associations: partial resequencing of 46 distinct HLA haplotypes. Genomics 87, 561-571 (2006).
62. Romero, V., Larsen, C. E., Duke-Cohan, J. S., Fox, E. A., Romero, T., Clavijo, O. P. et al. Genetic fixity in the human major histocompatibility complex and block size diversity in the class I region including HLA-E. BMC Genet. 8, 14 (2007).
63. Bjorkman, P. J. & Parham, P. Structure, function, and diversity of class I major histocompatibility complex molecules. Annu. Rev. Biochem. 59, 253-288 (1990).
64. Okamoto, K., Makino, S., Yoshikawa, Y., Takaki, A., Nagatsuka, Y., Ota, M. et al. Identification of I kappa BL as the second major histocompatibility complex-linked susceptibility locus for rheumatoid arthritis. Am. J. Hum. Genet. 72, 303-312 (2003).
65. Valentonyte, R., Hampe, J., Huse, K., Rosenstiel, P., Albrecht, M., Stenzel, A. et al. Sarcoidosis is associated with a truncating splice site mutation in BTNL2. Nat. Genet. 37, 357-364 (2005).
66. Vincek, V., Klein, D., Figueroa, F., Hauptfeld, V., Kasahara, M., O'hUigin, C. et al. The evolutionary origin of the HLA-DR3 haplotype. Immunogenetics 35, 263-271 (1992).
67. Marsh, S. G. WHO Nomenclature Committee for Factors of the HLA System. Nomenclature for factors of the HLA system, update July 2000. Tissue Antigens 56, 476-477 (2000).
68. Yang, Y., Chung, E. K., Wu, Y. L., Savelli, S. L., Nagaraja, H. N., Zhou, B. et al. Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans. Am. J. Hum. Genet. 80, 1037-1054 (2007).
69. Tuzun, E., Sharp, A. J., Bailey, J. A., Kaul, R., Morrison, V. A., Pertz, L. M. et al. Fine-scale structural variation of the human genome. Nat. Genet. 37, 727-732 (2005).
70. Redon, R., Ishikawa, S., Fitch, K. R., Feuk, L., Perry, G. H., Andrews, T. D. et al. Global variation in copy number in the human genome. Nature 444, 444-454 (2006).
71. Conrad, D. F., Andrews, T. D., Carter, N. P., Hurles, M. E. & Pritchard, J. K. A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet. 38, 75-81 (2006).
72. McCarroll, S. A., Hadnott, T. N., Perry, G. H., Sabeti, P. C., Zody, M. C., Barrett, J. C. et al. International HapMap Consortium. Common deletion polymorphisms in the human genome. Nat. Genet. 38, 86-92 (2006).
73. Mills, R. E., Luttig, C. T., Larkins, C. E., Beauchamp, A., Tsui, C., Pittard, W. S. et al. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 16, 1182-1190 (2006).
74. Simon-Sanchez, J., Scholz, S., Fung, H. C., Matarin, M., Hernandez, D., Gibbs, J. R. et al. Genome-wide SNP assay reveals structural genomic variation, extended homozygosity and cell-line induced alterations in normal individuals. Hum. Mol. Genet. 16, 1-14 (2007).
75. Wong, K. K., deLeeuw, R. J., Dosanjh, N. S., Kimm, L. R., Cheng, Z., Horsman, D. E. et al. A comprehensive analysis of common copy-number variations in the human genome. Am. J. Hum. Genet. 80, 91-104 (2007).
76. Korbel, J. O., Urban, A. E., Affourtit, J. P., Godwin, B., Grubert, F., Simons, J. F. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420-426 2007.
77. Levy, S., Sutton, G., Ng, P. C., Feuk, L., Halpern, A. L., Walenz, B. P. et al. The diploid genome sequence of an individual human. PLoS Biol. 5, e254 (2007).
78. Perry, G. H., Ben-Dor, A., Tsalenko, A., Sampas, N., Rodriguez-Revenga, L., Tran, C. W. et al. The fine-scale and complex architecture of human copy-number variation. Am. J. Hum. Genet. 82, 685-695 (2008).
79. Kidd, J. M., Cooper, G. M., Donahue, W. F., Hayden, H. S., Sampas, N., Graves, T. et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56-64 (2008).
80. Komatsu-Wakui, M., Tokunaga, K., Ishikawa, Y., Kashiwase, K., Moriyama, S., Tsuchiya, N. et al. MIC-A polymorphism in Japanese and a MIC-A-MIC-B null haplotype. Immunogenetics 49, 620-628 (1999).
81. Kulski, J. K. & Dunn, D. S. Polymorphic Alu insertions within the major histocompatibility complex class I genomic region: a brief review. Cytogenet. Genome Res. 110, 193-202 (2005).
82. Takasu, M., Hayashi, R., Maruya, E., Ota, M., Imura, K., Kougo, K. et al. Deletion of entire HLA-A gene accompanied by an insertion of a retrotransposon. Tissue Antigens 70, 144-150 (2007).
83. Kulski, J. K., Shigenari, A., Shiina, T., Ota, M., Hosomichi, K., James, I. et al. Human endogenous retrovirus (HERVK9) structural polymorphism with haplotypic HLA-A allelic associations. Genetics 180, 445-457 (2008).
84. Cordell, H. J. Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans. Hum. Mol. Genet. 11, 2463-2468 (2002).
85. Navarro, A. & Barton, N. H. Effects of multilocus balancing selection on neutral variability. Genetics 161, 849-863 (2002).
86. Miretti, M. M., Walsh, E. C., Ke, X., Delgado, M., Griffiths, M., Hunt, S. et al. A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphisms. Am. J. Hum. Genet. 76, 634-646 (2005).
87. Blomhoff, A., Olsson, M., Johansson, S., Akselsen, H. E., Pociot, F., Nerup, J. et al. Linkage disequilibrium and haplotype blocks in the MHC vary in an HLA haplotype specific manner assessed mainly by DRB1*03 and DRB1*04 haplotypes. Genes Immun. 7, 130-140 (2006).
88. Mathivanan, S., Periaswamy, B., Gandhi, T. K., Kandasamy, K., Suresh, S., Mohmood, R. et al. An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics 7 (Suppl 5), S19 (2006).
89. Gomez, J. A., Majumder, P., Nagarajan, U. M. & Boss, J. M. X box-like sequences in the MHC class II region maintain regulatory function. J. Immunol. 175, 1030-1040 (2005).
90. Müller-Hilke, B. & Mitchison, N. A. The role of HLA promoters in autoimmunity. Curr. Pharm. Des. 12, 3743-3752 (2006).
91. Christova, R., Jones, T., Wu, P. J., Bolzer, A., Costa-Pereira, A. P., Watling, D. et al. P-STAT1 mediates higher-order chromatin remodelling of the human MHC in response to IFNgamma. J. Cell Sci. 120, 3262-3270 (2007).
92. Kumar, P. P., Bischof, O., Purbey, P. K., Notani, D., Urlaub, H., Dejean, A. et al. Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus. Nat. Cell Biol. 9, 45-56 (2007).
93. Brown, J. H., Jardetzky, T. S., Gorga, J. C., Stern, L. J., Urban, R. G., Strominger, J. L. et al. Three dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 364, 33-39 (1993).
94. Strominger, J. L. Human histocompatibility proteins. Immunol. Rev. 185, 69-77 (2002).
95. Momburg, F. & Tan, P. Tapasin - the keystone of the loading complex optimizing peptide binding by MHC class I molecules in the endoplasmic reticulum. Mol. Immunol. 39, 217-233 (2002).
96. Sadegh-Nasseri, S., Chen, M., Narayan, K. & Bouvier, M. The convergent roles of tapasin and HLA-DM in antigen presentation. Trends Immunol. 29, 141-147 (2008).
97. Gregersen, J. W., Kranc, K. R., Ke, X., Svendsen, P., Madsen, L. S., Thomsen, A. R. et al. Functional epistasis on a common MHC haplotype associated with multiple sclerosis. Nature 443, 574-577 (2006).
98. Martin, A. M., Kulski, J. K., Witt, C., Pontarotti, P. & Christiansen, F. T. Leukocyte Iglike receptor complex (LRC) in mice and men. Trends Immunol. 23, 81-88 (2002).
99. Thananchai, H., Gillespie, G., Martin, M. P., Bashirova, A., Yawata, N., Yawata, M. et al. Cutting edge: allele-specific and peptide-dependent interactions between KIR3DL1 and HLA-A and HLA-B. J. Immunol. 178, 33-37 (2007).
100. Parham, P. Influence of KIR diversity on human immunity. Adv. Exp. Med. Biol. 560, 47-50 (2005).
101. Khakoo, S. I. & Carrington, M. KIR and disease: a model system or system of models? Immunol. Rev. 214, 186-201 (2006).
102. Swaroop, A., Branham, K. E., Chen, W. & Abecasis, G. Genetic susceptibility to age-related macular degeneration: a paradigm for dissecting complex disease traits. Hum. Mol. Genet. 16 (spec. no. 2), R174-R182 (2007).
103. Lester, S., McLure, C., Williamson, J., Bardy, P., Rischmueller, M. & Dawkins, R. L. Epistasis between the MHC and the RCA alpha block in primary Sjögren syndrome. Ann. Rheum. Dis. 67, 849-854 (2008).
104. Sánchez, F. O., Linga Reddy, M. V., Sakuraba, K., Ståhle, M. & Alarcón-Riquelme, M. E. IFN-regulatory factor 5 gene variants interact with the class I MHC locus in the Swedish psoriasis population. J. Invest. Dermatol. 128, 1704-1709 (2008).
105. Niewold, T. B., Kelly, J. A., Flesch, M. H., Espinoza, L. R., Harley, J. B. & Crow, M. K. Association of the IRF5 risk haplotype with high serum interferon-alpha activity in systemic lupus erythematosus patients. Arthritis Rheum. 58, 2481-2487 (2008).
106. Sugawara, T., Shimizu, H., Hoshi, N., Nakajima, A. & Fujimoto, S. Steroidogenic acute regulatory protein-binding protein cloned by a yeast two-hybrid system. J. Biol. Chem. 278, 42487-42494 (2003).
107. Tiala, I., Suomela, S., Huuhtanen, J., Wakkinen, J., Hölttä- Vuori, M., Kainu, K. et al. The CCHCR1 (HCR) gene is relevant for skin steroidogenesis and downregulated in cultured psoriatic keratinocytes. J. Mol. Med. 85, 589-601 (2007).
108. Kulski, J. K., Kenworthy, W., Bellgard, M., Taplin, R., Okamoto, K., Oka, A. et al. Gene expression profiling of Japanese psoriatic skin reveals an increased activity in molecular stress and immune response signals. J. Mol. Med. 83, 964-975 (2005).
109. Zhou, X., Krueger, J. G., Kao, M. C., Lee, E., Du, F., Menter, A. et al. Novel mechanisms of T-cell and dendritic cell activation revealed by profiling of psoriasis on the 63100-element oligonucleotide array. Physiol. Genomics 13, 69-78 (2003).
110. Mee, J. B., Johnson, C. M., Morar, N., Burslem, F. & Groves, R. W. The psoriatic transcriptome closely resembles that induced by interleukin-1 in cultured keratinocytes: dominance of innate immune responses in psoriasis. Am. J. Pathol. 171, 32-42 (2007).
111. Nomura, I., Gao, B., Boguniewicz, M., Darst, M. A., Travers, J. B. & Leung, D. Y. Distinct patterns of gene expression in the skin lesions of atopic dermatitis and psoriasis: a gene microarray analysis. J. Allergy Clin. Immunol. 112, 1195-1202 (2003).
112. Zhang, Z. H., Wang, Z. M., Crosby, M. E., Wang, H. F., Xiang, L. H., Luan, J. et al. Gene expression profiling of porokeratosis. J. Cutan. Pathol. 35, 1058-1062 (2008).
113. Koczan, D., Guthke, R., Thiesen, H. J., Ibrahim, S. M., Kundt, G., Krentz, H. et al. Gene expression profiling of peripheral blood mononuclear leukocytes from psoriasis patients identifies new immune regulatory molecules. Eur. J. Dermatol. 15, 251-257 (2005).
114. Chaussabel, D., Quinn, C., Shen, J., Patel, P., Glaser, C., Baldwin, N. et al. A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. Immunity 29, 150-164 (2008).
115. Haider, A. S., Lowes, M. A., Suárez-Fariñas, M., Zaba, L. C., Cardinale, I., Khatcherian, A. et al. Identification of cellular pathways of 'type 1,' Th17T cells, and TNF- and inducible nitric oxide synthase-producing dendritic cells in autoimmune inflammation through pharmacogenomic study of cyclosporine A in psoriasis. J. Immunol. 180, 1913-1920 (2008).
116. Nzeusseu Toukap, A., Galant, C., Theate, I., Maudoux, A. L., Lories, R. J., Houssiau, F. A. et al. Identification of distinct gene expression profiles in the synovium of patients with systemic lupus erythematosus. Arthritis Rheum. 56, 1579-1588 (2007).
117. Bovin, L. F., Rieneck, K., Workman, C., Nielsen, H., Sørensen, S. F., Skjødt, H. et al. Blood cell gene expression profiling in rheumatoid arthritis. Discriminative genes and effect of rheumatoid factor. Immunol. Lett. 93, 217-226 (2004).
118. van der Pouw Kraan, T. C., van Baarsen, L. G., Rustenburg, F., Baltus, B., Fero, M. & Verweij, C. L. Gene expression profiling in rheumatology. Methods Mol. Med. 136, 305-327 (2007).
119. Devauchelle, V., Marion, S., Cagnard, N., Mistou, S., Falgarone, G., Breban, M. et al. DNA microarray allows molecular profiling of rheumatoid arthritis and identification of pathophysiological targets. Genes Immun. 5, 597-608 (2004).
120. van der Pouw Kraan, T. C., van Gaalen, F. A., Huizinga, T. W., Pieterman, E., Breedveld, F. C. & Verweij, C. L. Discovery of distinctive gene expression profiles in rheumatoid synovium using cDNA microarray technology: evidence for the existence of multiple pathways of tissue destruction and repair. Genes Immun. 4, 187-196 (2003).
121. Batliwalla, F. M., Li, W., Ritchlin, C. T., Xiao, X., Brenner, M., Laragione, T. et al. Microarray analyses of peripheral blood cells identifies unique gene expression signature in psoriatic arthritis. Mol. Med. 11, 21-29 (2005).
122. Fu, S., Zhao, H., Shi, J., Abzhanov, A., Crawford, K., Ohno-Machado, L. et al. Peripheral arterial occlusive disease: global gene expression analyses suggest a major role for immune and inflammatory responses. BMC Genomics 9, 369 (2008).
123. Nisole, S., Stoye, J. P. & Saïb, A. TRIM family proteins: retroviral restriction and antiviral defence. Nat. Rev. Microbiol. 3, 799-808 (2005).
124. Uchil, P. D., Quinlan, B. D., Chan, W. T., Luna, J. M. & Mothes, W. TRIM E3 ligases interfere with early and late stages of the retroviral life cycle. PLoS Pathog. 4, e16 (2008).
125. Sebat, J., Lakshmi, B., Malhotra, D., Troge, J., Lese-Martin, C., Walsh, T. et al. Strong association of de novo copy number mutations with autism. Science 316, 445-449 (2007).
126. Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y. et al. Detection of large-scale variation in the human genome. Nat. Genet. 36, 949-951 (2004).
127. Fellermann, K., Stange, D. E., Schaeffeler, E., Schmalzl, H., Wehkamp, J., Bevins, C. L. et al. A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon. Am. J. Hum. Genet. 79, 439-448 (2006).
128. Hollox, E. J., Huffmeier, U., Zeeuwen, P. L., Palla, R., Lascorz, J., Rodijk-Olthuis, D. et al. Psoriasis is associated with increased beta-defensin genomic copy number. Nat. Genet. 40, 23-25 (2008).
129. Jiang, L., Yu, Z., Du, W., Tang, Z., Jiang, T., Zhang, C. et al. Development of a fluorescent and colorimetric detection methods-based protein microarray for serodiagnosis of TORCH infections. Biosens. Bioelectron 24, 376-382 (2008).
130. Tomazou, E. M., Rakyan, V. K., Lefebvre, G., Andrews, R., Ellis, P., Jackson, D. K. et al. Generation of a genomic tiling array of the human major histocompatibility complex (MHC) and its application for DNA methylation analysis. BMC Med. Genomics 1, 19 (2008).
131. Serrano, N. C., Millan, P. & Páez, M. C. Non-HLA associations with autoimmune diseases. Autoimmun. Rev. 5, 209-214 (2006).
132. Samanta, M. P., Tongprasit, W. & Stolc, V. In-depth query of large genomes using tiling arrays. Methods Mol. Biol. 377, 163-174 (2007).
133. Borrebaeck, C. A. & Wingren, C. High-throughput proteomics using antibody microarrays: an update. Expert Rev. Mol. Diagn. 7, 673-686 (2007).
134. Tao, S. C., Chen, C. S. & Zhu, H. Applications of protein microarray technology. Comb. Chem. High Throughput Screen. 10, 706-718 (2007).
135. Chen, D. S., Soen, Y., Stuge, T. B., Lee, P. P., Weber, J. S., Brown, P. O. et al. Marked differences in human melanoma antigen-specific T cell responsiveness after vaccination using a functional microarray. PLoS Med. 2, e265 (2005).
136. Fortier, M. H., Caron, E., Hardy, M. P., Voisin, G., Lemieux, S., Perreault, C. et al. The MHC class I peptide repertoire is molded by the transcriptome. J. Exp. Med. 205, 595-610 (2008).
137. Ho, P. P., Higgins, J. P., Kidd, B. A., Tomooka, B., Digennaro, C., Lee, L. Y. et al. Tolerizing DNA vaccines for autoimmune arthritis. Autoimmunity 39, 675-682 (2006).
138. Lueking, A., Huber, O., Wirths, C., Schulte, K., Stieler, K. M., Blume-Peytavi, U. et al. Profiling of alopecia areata autoantigens based on protein microarray technology. Mol. Cell Proteomics 4, 1382-1390 (2005).
139. EI Essawy, B., Otu, H. H., Choy, B., Zheng, X. X., Libermann, T. A. & Strom, T. B. Proteomic analysis of the allograft response. Transplantation 82, 267-274 (2006).
140. Sieberts, S. K. & Schadt, E. E. Moving toward a system genetics view of disease. Mamm. Genome 18, 389-401 (2007).
141. Amiel, J. L. Study of the leukocyte phenotypes in Hodgkin's disease in Histocompatibility Testing 79-81 (eds Curtoni, E.S., Mattiuz, P.L., Tosi, R.M.) (Munksgaard, Copenhagen, 1967).
142. Tiwari, J. L. & Terasaki, P. I. HLA and Disease Association (Springer-Verlag, New York, 1985).
143. Naito, S. The association of HLA with diseases in Japanese. J. Hum. Genet. 31, 323-329 (1986).
144. Geluk, A. & Ottenhoff, T. H. HLA and leprosy in the pre and postgenomic eras. Hum. Immunol. 67, 439-445 (2006).
145. Mehra, N. K. & Kaur, G. 14th International HLA and Immunogenetics Workshop: report on joint study on MHC and infection. Tissue Antigens 69, 226-227 (2007).
146. Goulder, P. J. & Watkins, D. I. Impact of MHC class I diversity on immune control of immunodeficiency virus replication. Nat. Rev. Immunol. 8, 619-630 (2008).
147. Lie, B. A. & Thorsby, E. Several genes in the extended human MHC contribute to predisposition to autoimmune diseases. Curr. Opin. Immunol. 17, 526-531 (2005).
148. Jones, E. Y., Fugger, L., Strominger, J. L. & Siebold, C. MHC class II proteins and disease: a structural perspective. Nat. Rev. Immunol. 6, 271-282 (2006).
149. Schmidt, H., Williamson, D. & Ashley-Koch, A. HLA-DR15 haplotype and multiple sclerosis: a HuGE review. Am. J. Epidemiol. 165, 1097-1109 (2007).
150. Jacobson, E. M., Huber, A. & Tomer, Y. The HLA gene complex in thyroid autoimmunity: from epidemiology to etiology. J. Autoimmun. 30, 58-62 (2008).
151. Hamosh, A., Scott, A. F., Amberger, J., Valle, D. & McKusick, V. A. Online Mendaian Inheritance in Man (OMIM). Hum. Mutat. 15, 57-61 (2000).
152. Hamosh, A., Scott, A. F., Amberger, J. S., Bocchini, C. A. & McKusick, V. A. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33, D514-D517 (2005).
153. Naoum, J. J., Chai, H., Lin, P. H., Lumsden, A. B., Yao, Q. & Chen, C. Lymphotoxin-alpha and cardiovascular disease: clinical association and pathogenic mechanisms. Med. Sci. Monit. 12, RA121-RA124 (2006).
154. London, S. J. Gene-air pollution interactions in asthma. Proc. Am. Thorac. Soc. 4, 217-220 (2007).
155. Sharma, S., Ghosh, B. & Sharma, S. K. Association of TNF polymorphisms with sarcoidosis, its prognosis and tumour necrosis factor (TNF)-alpha levels in Asian Indians. Clin. Exp. Immunol. 151, 251-259 (2008).
156. Vallvé, J. C., Paredes, S., Girona, J., Uliaque, K., Ribalta, J., Hurt-Camejo, E. et al. Tumor necrosis factor-alpha -1031 T/C polymorphism is associated with smaller and more proatherogenic low density lipoprotein particles in patients with rheumatoid arthritis. J. Rheumatol. 35, 1697-1703 (2008).
157. Lee, H. H., Lee, Y. J., Wang, Y. M., Chao, H. T., Niu, D. M., Chao, M. C. et al. Low frequency of the CYP21A2 deletion in ethnic Chinese (Taiwanese) patients with 21 hydroxylase deficiency. Mol. Genet. Metab. 93, 450-457 (2008).
158. Lee, H. H., Tsai, F. J., Lee, Y. J. & Yang, Y. C. Diversity of the CYP21A2 gene:a 6.2-kb TaqI fragment and a 3.2-kb TaqI fragment mistaken as CYP21A1P. Mol. Genet. Metab. 88, 372-377 (2006).
159. Seyrantepe, V., Poupetova, H., Froissart, R., Zabot, M. T., Maire, I. & Pshezhetsky, A. V. Molecular pathology of NEU1 gene in sialidosis. Hum. Mutat. 22, 343-352 (2003).
160. Sjöholm, A. G., Jönsson, G., Braconier, J. H., Sturfelt, G. & Truedsson, L. Complement deficiency and disease: an update. Mol. Immunol. 43, 78-85 (2006).
161. Forabosco, P., Bouzigon, E., Ng, M. Y., Hermanowski, J., Fishe, R. S. A., Criswell, L. A. et al. Meta-analysis of genome-wide linkage studies across autoimmune diseases. Eur. J. Hum. Genet. 2008 (e-pub ahead of print, 10 September 2008).
162. Wellcome Trust Case Control Consortium. Genome-wide association study of 14000 cases of seven common diseases and 3000 shared controls. Nature 447, 661-678 2007.
163. Choi, H. B., Han, H., Youn, J. I., Kim, T. Y. & Kim, T. G. MICA 5.1 allele is a susceptibility marker for psoriasis in the Korean population. Tissue Antigens 56, 548-550 (2000).
164. Asumalahti, K., Veal, C., Laitinen, T., Suomela, S., Allen, M., Elomaa, O. et al. Psoriasis Consortium. Coding haplotype analysis supports HCR as the putative susceptibility gene for psoriasis at the MHC PSORS1 locus. Hum. Mol. Genet. 11, 589-597 (2002).
165. Chang, Y. T., Shiao, Y. M., Chin, P. J., Liu, Y. L., Chou, F. C., Wu, S. et al. Genetic polymorphisms of the HCR gene and a genomic segment in close proximity to HLA-C are associated with patients with psoriasis in Taiwan. Br. J. Dermatol. 150, 1104-1111 (2004).
166. Ameen, M., Allen, M. H., Fisher, S. A., Lewis, C. M., Cuthbert, A., Kondeatis, E. et al. Corneodesmosin (CDSN) gene association with psoriasis vulgaris in Caucasian but not in Japanese populations. Clin. Exp. Dermatol. 30, 414-418 (2005).
167. Helms, C., Saccone, N. L., Cao, L., Daw, J. A., Cao, K., Hsu, T. M. et al. Localization of PSORS1 to a haplotype block harboring HLA-C and distinct from corneodesmosin and HCR. Hum. Genet. 118, 466-476 (2005).
168. Martínez-Borra, J., Brautbar, C., González, S., Enk, C. D., López-Vázquez, A. & López-Larrea, C. The region of 150 kb telometic to HLA-C is associated with psoriasis in the Jewish population. J. Invest. Dermatol. 125, 928-932 (2005).
169. Nair, R. P., Stuart, P. E., Nistor, I., Hiremagalore, R., Chia, N. V., Jenisch, S. et al. Sequence and haplotype analysis supports HLA-C as the psoriasis susceptibility 1 gene. Am. J. Hum. Genet. 78, 827-851 (2006).
170. Takemoto, T., Naruse, T., Namba, K., Kitaichi, N., Ota, M., Shindo, Y. et al. Reevaluation of heterogeneity in HLA-B*510101 associated with Behçet's disease. Tissue Antigens 72, 347-353 (2008).
171. Karasneh, J., Gül, A., Ollier, W. E., Silman, A. J. & Worthington, J. Whole-genome screening for susceptibility genes in multicase families with Behçet's disease. Arthritis Rheum. 52, 1836-1842 (2005).
172. Oksenberg, J. R., Baranzini, S. E., Sawcer, S. & Hauser, S. L. The genetics of multiple sclerosis: SNPs to pathways to pathogenesis. Nat. Rev. Genet. 9, 516-526 (2008).
173. Degli-Esposti, M. A., Leaver, A. L., Christiansen, F. T., Witt, C. S., Abraham, L. J. & Dawkins, R. L. Ancestral haplotypes: conserved population MHC haplotypes. Hum. Immunol. 34, 242-252 (1992).
174. Price, P., Witt, C., Allcock, R., Sayer, D., Garlepp, M., Kok, C. C. et al. The genetic basis for the association of the 8.1 ancestral haplotype (A1, B8, DR3) with multiple immunopathological diseases. Immunol. Rev. 167, 257-274 (1999).
175. Aptsiauri, N., Cabrera, T., Garcia-Lora, A., Lopez-Nevot, M. A., Ruiz-Cabello, F. & Garrido, F. MHC class I antigens and immune surveillance in transformed cells. Int. Rev. Cytol. 256, 139-189 (2007).
176. Sengupta, S., den Boon, J. A., Chen, I. H., Newton, M. A., Dahl, D. B., Chen, M. et al. Genome-wide expression profiling reveals EBV-associated inhibition of MHC class I expression in nasopharyngeal carcinoma. Cancer Res. 66, 7999-8006 (2006).
177. Schlecht, N. F., Burk, R. D., Adrien, L., Dunne, A., Kawachi, N., Sarta, C. et al. Gene expression profiles in HPV-infected head and neck cancer. J. Pathol. 213, 283-293 (2007).
178. Watson, N. F., Ramage, J. M., Madjd, Z., Spendlove, I., Ellis, I. O., Scholefield, J. H. et al. Immunosurveillance is active in colorectal cancer as downregulation but not complete loss of MHC class I expression correlates with a poor prognosis. Int. J. Cancer 118, 6-10 (2006).
179. Wang, H., Yang, D., Xu, W., Wang, Y., Ruan, Z., Zhao, T. et al. Tumor-derived soluble MICs impair CD3(+)CD56(+) NKT-like cell cytotoxicity in cancer patients. Immunol. Lett. 120, 65-71 (2008).
180. Groh, V., Wu, J., Yee, C. & Spies, T. Tumour-derived soluble MIC ligands impair expression of NKG2D and T-cell activation. Nature 419, 734-738 (2002).
181. Lönnroth, C., Andersson, M., Arvidsson, A., Nordgren, S., Brevinge, H., Lagerstedt, K. et al. Preoperative treatment with a non-steroidal anti-inflammatory drug (NSAID) increases tumor tissue infiltration of seemingly activated immune cells in colorectal cancer. Cancer Immun. 8, 5 (2008).
182. Champine, P. J., Michaelson, J., Weimer, B. C., Welch, D. R. & DeWald, D. B. Microarray analysis reveals potential mechanisms of BRMS1-mediated metastasis suppression. Clin. Exp. Metastasis 24, 551-565 (2007).
183. Rimsza, L. M., Roberts, R. A., Campo, E., Grogan, T. M., Bea, S., Salaverria, I. et al. Loss of major histocompatibility class II expression in non-immune-privileged site diffuse large B-cell lymphoma is highly coordinated and not due to chromosomal deletions. Blood 107, 1101-1107 (2006).
184. Dave, S. S., Fu, K., Wright, G. W., Lam, L. T., Kluin, P., Boerma, E. J. et al. Lymphoma/Leukemia Molecular Profiling Project. Molecular diagnosis of Burkitt's lymphoma. N. Engl. J. Med. 354, 2431-2442 (2006).