과제정보
연구 과제 주관 기관 : Ministry for Health and Welfare
참고문헌
- Goodnow CC. Multistep pathogenesis of autoimmune disease. Cell 2007;130:25-35. https://doi.org/10.1016/j.cell.2007.06.033
- Ohno S, Wolf U, Atkin NB. Evolution from fish to mammals by gene duplication. Hereditas 1968;59:169-187.
- Rioux JD, Abbas AK. Paths to understanding the genetic basis of autoimmune disease. Nature 2005;435:584-589. https://doi.org/10.1038/nature03723
- Astorga GP, Williams RC Jr. Altered reactivity in mixed lymphocyte culture of lymphocytes from patients with rheumatoid arthritis. Arthritis Rheum 1969;12:547-554. https://doi.org/10.1002/art.1780120602
- Robinson PC, Brown MA. Genetics of ankylosing spondylitis. Mol Immunol 2014;57:2-11. https://doi.org/10.1016/j.molimm.2013.06.013
- International HapMap Consortium. A haplotype map of the human genome. Nature 2005;437:1299-1320. https://doi.org/10.1038/nature04226
- McCarroll SA, Altshuler DM. Copy-number variation and association studies of human disease. Nat Genet 2007;39(7 Suppl):S37-S42. https://doi.org/10.1038/ng2080
- Yim SH, Kim TM, Hu HJ, et al. Copy number variations in East-Asian population and their evolutionary and functional implications. Hum Mol Genet 2010;19:1001-1008. https://doi.org/10.1093/hmg/ddp564
- Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 2005;6:95-108.
- Wellcome Trust Case Control Consortium, Craddock N, Hurles ME, et al. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 2010;464:713-720. https://doi.org/10.1038/nature08979
- Stahl EA, Raychaudhuri S, Remmers EF, et al. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat Genet 2010;42:508-514. https://doi.org/10.1038/ng.582
- Graham RR, Cotsapas C, Davies L, et al. Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Nat Genet 2008;40:1059-1061. https://doi.org/10.1038/ng.200
- Jung SH, Yim SH, Hu HJ, et al. Genome-wide copy number variation analysis identifies deletion variants associated with ankylosing spondylitis. Arthritis Rheumatol 2014;66:2103-2112. https://doi.org/10.1002/art.38650
- Kim JH, Jung SH, Bae JS, et al. Deletion variants of RABGAP1L, 10q21.3, and C4 are associated with the risk of systemic lupus erythematosus in Korean women. Arthritis Rheum 2013;65:1055-1063. https://doi.org/10.1002/art.37854
- Okada Y, Wu D, Trynka G, et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature 2014;506:376-381. https://doi.org/10.1038/nature12873
- McCarroll SA, Hadnott TN, Perry GH, et al. Common deletion polymorphisms in the human genome. Nat Genet 2006;38:86-92. https://doi.org/10.1038/ng1696
- Iafrate AJ, Feuk L, Rivera MN, et al. Detection of largescale variation in the human genome. Nat Genet 2004;36:949-951. https://doi.org/10.1038/ng1416
- Sebat J, Lakshmi B, Troge J, et al. Large-scale copy number polymorphism in the human genome. Science 2004;305:525-528. https://doi.org/10.1126/science.1098918
- Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet 2006;7:85-97.
- Human Genome Structural Variation Working Group, Eichler EE, Nickerson DA, et al. Completing the map of human genetic variation. Nature 2007;447:161-165. https://doi.org/10.1038/447161a
- The Centre for Applied Genomics. Database of genomic variants [Internet]. Toronto (ON): The Centre for Applied Genomics, 2014 [cited 2015 Feb 2]. Available from: http://dgv.tcag.ca/dgv/app/statistics?ref=.
- Kidd JM, Cooper GM, Donahue WF, et al. Mapping and sequencing of structural variation from eight human genomes. Nature 2008;453:56-64. https://doi.org/10.1038/nature06862
- Chen L, Zhou W, Zhang L, Zhang F. Genome architecture and its roles in human copy number variation. Genomics Inform 2014;12:136-144. https://doi.org/10.5808/GI.2014.12.4.136
- van Ommen GJ. Frequency of new copy number variation in humans. Nat Genet 2005;37:333-334. https://doi.org/10.1038/ng0405-333
- Aten E, White SJ, Kalf ME, et al. Methods to detect CNVs in the human genome. Cytogenet Genome Res 2008;123:313-321. https://doi.org/10.1159/000184723
- Kim TM, Yim SH, Chung YJ. Copy number variations in the human genome: potential source for individual diversity and disease association studies. Genomics Inform 2008;6:1-7. https://doi.org/10.5808/GI.2008.6.1.001
- Lin CF, Naj AC, Wang LS. Analyzing copy number variation using SNP array data: protocols for calling CNV and association tests. Curr Protoc Hum Genet 2013;79:Unit 1.27.
- Wang J, Wang W, Li R, et al. The diploid genome sequence of an Asian individual. Nature 2008;456:60-65. https://doi.org/10.1038/nature07484
- Kim JI, Ju YS, Park H, et al. A highly annotated whole-genome sequence of a Korean individual. Nature 2009; 460:1011-1015. https://doi.org/10.1038/nature08211
- Abel HJ, Duncavage EJ. Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches. Cancer Genet 2013;206:432-440. https://doi.org/10.1016/j.cancergen.2013.11.002
- Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 2002;30:e57. https://doi.org/10.1093/nar/gnf056
- Shin GW, Jung SH, Yim SH, Chung B, Yeol Jung G, Chung YJ. Stuffer-free multiplex ligation-dependent probe amplification based on conformation-sensitive capillary electrophoresis: a novel technology for robust multiplex determination of copy number variation. Electrophoresis 2012;33:3052-3061. https://doi.org/10.1002/elps.201200334
- Zerrahn J, Held W, Raulet DH. The MHC reactivity of the T cell repertoire prior to positive and negative selection. Cell 1997;88:627-636. https://doi.org/10.1016/S0092-8674(00)81905-4
- Cho JH, Gregersen PK. Genomics and the multifactorial nature of human autoimmune disease. N Engl J Med 2011;365:1612-1623. https://doi.org/10.1056/NEJMra1100030
- Chung EK, Yang Y, Rupert KL, et al. Determining the one, two, three, or four long and short loci of human complement C4 in a major histocompatibility complex haplotype encoding C4A or C4B proteins. Am J Hum Genet 2002;71:810-822. https://doi.org/10.1086/342778
- Yang Y, Chung EK, Wu YL, 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 2007;80:1037-1054. https://doi.org/10.1086/518257
- Lv Y, He S, Zhang Z, et al. Confirmation of C4 gene copy number variation and the association with systemic lupus erythematosus in Chinese Han population. Rheumatol Int 2012;32:3047-3053. https://doi.org/10.1007/s00296-011-2023-7
- Boteva L, Morris DL, Cortes-Hernandez J, Martin J, Vyse TJ, Fernando MM. Genetically determined partial complement C4 deficiency states are not independent risk factors for SLE in UK and Spanish populations. Am J Hum Genet 2012;90:445-456. https://doi.org/10.1016/j.ajhg.2012.01.012
- Rigby WF, Wu YL, Zan M, et al. Increased frequency of complement C4B deficiency in rheumatoid arthritis. Arthritis Rheum 2012;64:1338-1344. https://doi.org/10.1002/art.33472
- Nimmerjahn F, Ravetch JV. Fc-receptors as regulators of immunity. Adv Immunol 2007;96:179-204. https://doi.org/10.1016/S0065-2776(07)96005-8
- Kocher M, Siegel ME, Edberg JC, Kimberly RP. Cross-linking of Fc gamma receptor IIa and Fc gamma receptor IIIb induces different proadhesive phenotypes on human neutrophils. J Immunol 1997;159:3940-3948.
- Aitman TJ, Dong R, Vyse TJ, et al. Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 2006;439:851-855. https://doi.org/10.1038/nature04489
- Fanciulli M, Norsworthy PJ, Petretto E, et al. FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. Nat Genet 2007;39:721-723. https://doi.org/10.1038/ng2046
- Mamtani M, Anaya JM, He W, Ahuja SK. Association of copy number variation in the FCGR3B gene with risk of autoimmune diseases. Genes Immun 2010;11:155-160. https://doi.org/10.1038/gene.2009.71
- Morris DL, Roberts AL, Witherden AS, et al. Evidence for both copy number and allelic (NA1/NA2) risk at the FCGR3B locus in systemic lupus erythematosus. Eur J Hum Genet 2010;18:1027-1031. https://doi.org/10.1038/ejhg.2010.56
- McKinney C, Fanciulli M, Merriman ME, et al. Association of variation in Fcgamma receptor 3B gene copy number with rheumatoid arthritis in Caucasian samples. Ann Rheum Dis 2010;69:1711-1716. https://doi.org/10.1136/ard.2009.123588
- Robinson JI, Carr IM, Cooper DL, et al. Confirmation of association of FCGR3B but not FCGR3A copy number with susceptibility to autoantibody positive rheumatoid arthritis. Hum Mutat 2012;33:741-749. https://doi.org/10.1002/humu.22031
- McKinney C, Merriman TR. Meta-analysis confirms a role for deletion in FCGR3B in autoimmune phenotypes. Hum Mol Genet 2012;21:2370-2376. https://doi.org/10.1093/hmg/dds039
- McKinney C, Merriman ME, Chapman PT, et al. Evidence for an inf luence of chemokine ligand 3-like 1 (CCL3L1) gene copy number on susceptibility to rheumatoid arthritis. Ann Rheum Dis 2008;67:409-413.
- Gonzalez E, Kulkarni H, Bolivar H, et al. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 2005;307:1434-1440. https://doi.org/10.1126/science.1101160
- Mamtani M, Rovin B, Brey R, et al. CCL3L1 gene-containing segmental duplications and polymorphisms in CCR5 affect risk of systemic lupus erythaematosus. Ann Rheum Dis 2008;67:1076-1083. https://doi.org/10.1136/ard.2007.078048
- Burns JC, Shimizu C, Gonzalez E, et al. Genetic variations in the receptor-ligand pair CCR5 and CCL3L1 are important determinants of susceptibility to Kawasaki disease. J Infect Dis 2005;192:344-349. https://doi.org/10.1086/430953
- Ganz T. Defensins: antimicrobial peptides of innate immunity. Nat Rev Immunol 2003;3:710-720. https://doi.org/10.1038/nri1180
- Yang D, Chertov O, Bykovskaia SN, et al. Beta-defensins: linking innate and adaptive immunity through dendritic and T cell CCR6. Science 1999;286:525-528. https://doi.org/10.1126/science.286.5439.525
- Niyonsaba F, Ogawa H, Nagaoka I. Human beta-defensin-2 functions as a chemotactic agent for tumour necrosis factor-alpha-treated human neutrophils. Immunology 2004;111:273-281. https://doi.org/10.1111/j.0019-2805.2004.01816.x
- Hollox EJ, Huffmeier U, Zeeuwen PL, et al. Psoriasis is associated with increased beta-defensin genomic copy number. Nat Genet 2008;40:23-25. https://doi.org/10.1038/ng.2007.48
- Wehkamp J, Harder J, Weichenthal M, et al. Inducible and constitutive beta-defensins are differentially expressed in Crohn's disease and ulcerative colitis. Inflamm Bowel Dis 2003;9:215-223. https://doi.org/10.1097/00054725-200307000-00001
- Fellermann K, Stange DE, Schaeffeler E, 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 2006;79:439-448. https://doi.org/10.1086/505915
- Bentley RW, Pearson J, Gearry RB, et al. Association of higher DEFB4 genomic copy number with Crohn's disease. Am J Gastroenterol 2010;105:354-359. https://doi.org/10.1038/ajg.2009.582
- Aldhous MC, Abu Bakar S, Prescott NJ, et al. Measurement methods and accuracy in copy number variation: failure to replicate associations of beta-defensin copy number with Crohn's disease. Hum Mol Genet 2010;19:4930-4938. https://doi.org/10.1093/hmg/ddq411
- Zhou XJ, Cheng FJ, Lv JC, et al. Higher DEFB4 genomic copy number in SLE and ANCA-associated small vasculitis. Rheumatology (Oxford) 2012;51:992-995. https://doi.org/10.1093/rheumatology/ker419
- Singh SB, Davis AS, Taylor GA, Deretic V. Human IRGM induces autophagy to eliminate intracellular mycobacteria. Science 2006;313:1438-1441. https://doi.org/10.1126/science.1129577
- Parkes M, Barrett JC, Prescott NJ, et al. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat Genet 2007;39:830-832. https://doi.org/10.1038/ng2061
- McCarroll SA, Huett A, Kuballa P, et al. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat Genet 2008;40:1107-1112. https://doi.org/10.1038/ng.215
- Brest P, Lapaquette P, Souidi M, et al. A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease. Nat Genet 2011;43:242-245. https://doi.org/10.1038/ng.762
- Prescott NJ, Dominy KM, Kubo M, et al. Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease. Hum Mol Genet 2010;19:1828-1839. https://doi.org/10.1093/hmg/ddq041
- Viau M, Zouali M. B-lymphocytes, innate immunity, and autoimmunity. Clin Immunol 2005;114:17-26. https://doi.org/10.1016/j.clim.2004.08.019
- Zouali M. Transcriptional and metabolic pre-B cell receptor-mediated checkpoints: implications for autoimmune diseases. Mol Immunol 2014;62:315-320. https://doi.org/10.1016/j.molimm.2014.01.009
- Yim SH, Chung YJ, Jin EH, et al. The potential role of VPREB1 gene copy number variation in susceptibility to rheumatoid arthritis. Mol Immunol 2011;48:1338-1343. https://doi.org/10.1016/j.molimm.2010.11.009
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