Rare variation at the TNFAIP3 locus and susceptibility to rheumatoid arthritis

Human Genetics

Volumn 128, Issue 6, 2010, Pages 627-633

  Bowes, John ^f   Orozco, Gisela ^f   Wilson, Dr Anthony G ^a   Morgan, Ann W ^b   Emery, Paul ^b   Steer, Sophia ^c   Hocking, Lynne J ^d   Reid, David M ^d   Harrison, Pille ^e   Wordsworth, Paul ^e  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b UNIVERSITY OF LEEDS   (United Kingdom)

^c KING'S COLLEGE HOSPITAL NHS FOUNDATION TRUST   (United Kingdom)

^d UNIVERSITY OF ABERDEEN   (United Kingdom)

^e UNIVERSITY OF OXFORD   (United Kingdom)

^f NONE

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN TNFAIP3; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ADULT; ARTICLE; CONTROLLED STUDY; FEMALE; FOLLOW UP; GENE LOCUS; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MALE; PRIORITY JOURNAL; QUALITY CONTROL; RHEUMATOID ARTHRITIS; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 78649319964     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-010-0889-1     Document Type: Article

References (32)

1. N Ahituv N Kavaslar W Schackwitz A Ustaszewska J Martin S Hebert H Doelle B Ersoy G Kryukov S Schmidt N Yosef E Ruppin R Sharan C Vaisse S Sunyaev R Dent J Cohen R McPherson LA Pennacchio 2007 Medical sequencing at the extremes of human body mass Am J Hum Genet 80 779 791 1:CAS:528:DC%2BD2sXktVOis7o%3D 10.1086/513471 17357083 (Pubitemid 46564414)
2. KR Ahmadi ME Weale ZY Xue N Soranzo DP Yarnall JD Briley Y Maruyama M Kobayashi NW Wood NK Spurr DK Burns AD Roses AM Saunders DB Goldstein 2005 A single-nucleotide polymorphism tagging set for human drug metabolism and transport Nat Genet 37 84 89 1:CAS:528:DC%2BD2cXhtFChsLzI 10.1038/ng0905-916 15608640 (Pubitemid 43086141)
3. L Backdahl JP Guo M Jagodic K Becanovic B Ding T Olsson JC Lorentzen 2008 Definition of arthritis candidate risk genes by combining rat linkage-mapping results with human case control association data Ann Rheum Dis 67 1742 1749 10.1136/ard.2007.076976 18250113
4. A Barton S Eyre A Myerscough B Brintnell D Ward WE Ollier JC Lorentzen L Klareskog A Silman S John J Worthington 2001 High resolution linkage and association mapping identifies a novel rheumatoid arthritis susceptibility locus homologous to one linked to two rat models of inflammatory arthritis Hum Mol Genet 10 1901 1906 1:CAS:528:DC%2BD3MXntlSgsb8%3D 10.1093/hmg/10.18.1901 11555626
5. W Bodmer C Bonilla 2008 Common and rare variants in multifactorial susceptibility to common diseases Nat Genet 40 695 701 1:CAS:528: DC%2BD1cXmsVejtrs%3D 10.1038/ng.f.136 18509313 (Pubitemid 351748875)
6. JC Cohen RS Kiss A Pertsemlidis YL Marcel R McPherson HH Hobbs 2004 Multiple rare alleles contribute to low plasma levels of HDL cholesterol Science 305 869 872 1:CAS:528:DC%2BD2cXmt1Krsbk%3D 10.1126/science.1099870 15297675 (Pubitemid 39038422)
7. M Fanciulli PJ Norsworthy E Petretto R Dong L Harper L Kamesh JM Heward SC Gough SA De AI Blakemore P Froguel CJ Owen SH Pearce L Teixeira L Guillevin DS Graham CD Pusey HT Cook TJ Vyse TJ Aitman 2007 FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity Nat Genet 39 721 723 1:CAS:528:DC%2BD2sXlvVSgtL8%3D 10.1038/ng2046 17529978 (Pubitemid 46848593)
8. NS Fearnhead JL Wilding B Winney S Tonks S Bartlett DC Bicknell IP Tomlinson NJ Mortensen WF Bodmer 2004 Multiple rare variants in different genes account for multifactorial inherited susceptibility to colorectal adenomas Proc Natl Acad Sci USA 101 15992 15997 1:CAS:528:DC%2BD2cXhtVGis77K 10.1073/pnas.0407187101 15520370 (Pubitemid 39507915)
9. K Fellermann DE Stange E Schaeffeler H Schmalzl J Wehkamp CL Bevins W Reinisch A Teml M Schwab P Lichter B Radlwimmer EF Stange 2006 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 1:CAS:528:DC%2BD28Xpt1Sntrs%3D 10.1086/505915 16909382 (Pubitemid 44384253)
10. E Gonzalez H Kulkarni H Bolivar A Mangano R Sanchez G Catano RJ Nibbs BI Freedman MP Quinones MJ Bamshad KK Murthy BH Rovin W Bradley RA Clark SA Anderson RJ O'connell BK Agan SS Ahuja R Bologna L Sen MJ Dolan SK Ahuja 2005 The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility Science 307 1434 1440 1:CAS:528:DC%2BD2MXhslKrtLs%3D 10.1126/science.1101160 15637236 (Pubitemid 40321934)
11. IP Gorlov OY Gorlova SR Sunyaev MR Spitz CI Amos 2008 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms Am J Hum Genet 82 100 112 1:CAS:528:DC%2BD1cXhsFOks7k%3D 10.1016/j.ajhg.2007.09.006 18179889 (Pubitemid 351726083)
12. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106:9362-9367
13. EJ Hollox U Huffmeier PL Zeeuwen R Palla J Lascorz D Rodijk-Olthuis PC van de Kerkhof H Traupe JG De HM den A Reis JA Armour J Schalkwijk 2008 Psoriasis is associated with increased beta-defensin genomic copy number Nat Genet 40 23 25 1:CAS:528:DC%2BD1cXhtVyrtg%3D%3D 10.1038/ng.2007.48 18059266
14. AJ Iafrate L Feuk MN Rivera ML Listewnik PK Donahoe Y Qi SW Scherer C Lee 2004 Detection of large-scale variation in the human genome Nat Genet 36 949 951 1:CAS:528:DC%2BD2cXntFSku7w%3D 10.1038/ng1416 15286789 (Pubitemid 39167488)
15. D Jawaheer MF Seldin CI Amos WV Chen R Shigeta J Monteiro M Kern LA Criswell S Albani JL Nelson DO Clegg R Pope HW Schroeder Jr SL Bridges Jr DS Pisetsky R Ward DL Kastner RL Wilder T Pincus LF Callahan D Flemming MH Wener PK Gregersen 2001 A genomewide screen in multiplex rheumatoid arthritis families suggests genetic overlap with other autoimmune diseases Am J Hum Genet 68 927 936 1:CAS:528:DC%2BD3MXkvFars7s%3D 10.1086/319518 11254450 (Pubitemid 32289739)
16. W Ji JN Foo BJ O'Roak H Zhao MG Larson DB Simon C Newton-Cheh MW State D Levy RP Lifton 2008 Rare independent mutations in renal salt handling genes contribute to blood pressure variation Nat Genet 40 592 599 1:CAS:528: DC%2BD1cXltFylurg%3D 10.1038/ng.118 18391953 (Pubitemid 351601207)
17. B Li SM Leal 2008 Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data Am J Hum Genet 83 311 321 1:CAS:528:DC%2BD1cXhtFOisbfE 10.1016/j.ajhg.2008.06.024 18691683
18. B Maher 2008 Personal genomes: the case of the missing heritability Nature 456 18 21 1:CAS:528:DC%2BD1cXhtlCjtrnM 10.1038/456018a 18987709
19. MI McCarthy JN Hirschhorn 2008 Genome-wide association studies: potential next steps on a genetic journey Hum Mol Genet 17 R156 R165 1:CAS:528: DC%2BD1cXhtlyjsrfJ 10.1093/hmg/ddn289 18852205
20. C McKinney ME Merriman PT Chapman PJ Gow AA Harrison J Highton PB Jones L McLean JL O'Donnell V Pokorny M Spellerberg LK Stamp J Willis S Steer TR Merriman 2008 Evidence for an influence of chemokine ligand 3-like 1 (CCL3L1) gene copy number on susceptibility to rheumatoid arthritis Ann Rheum Dis 67 409 413 1:CAS:528:DC%2BD1cXjs1ejsLk%3D 10.1136/ard.2007.075028 17604289 (Pubitemid 351281279)
21. AP Morris E Zeggini 2010 An evaluation of statistical approaches to rare variant analysis in genetic association studies Genet Epidemiol 34 188 193 10.1002/gepi.20450 19810025
22. S Nejentsev N Walker D Riches M Egholm JA Todd 2009 Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes Science 324 387 389 1:CAS:528:DC%2BD1MXksVOltr8%3D 10.1126/science.1167728 19264985
23. G Orozco A Hinks S Eyre X Ke LJ Gibbons J Bowes E Flynn P Martin AG Wilson DE Bax AW Morgan P Emery S Steer L Hocking DM Reid P Wordsworth P Harrison W Thomson A Barton J Worthington 2009 Combined effects of three independent SNPs greatly increase the risk estimate for RA at 6q23 Hum Mol Genet 18 2693 2699 1:CAS:528:DC%2BD1MXnvVOnt70%3D 10.1093/hmg/ddp193 19417005
24. RM Plenge C Cotsapas L Davies AL Price PI de Bakker J Maller I Pe'er NP Burtt B Blumenstiel M DeFelice M Parkin R Barry W Winslow C Healy RR Graham BM Neale E Izmailova R Roubenoff AN Parker R Glass EW Karlson N Maher DA Hafler DM Lee MF Seldin EF Remmers AT Lee L Padyukov L Alfredsson J Coblyn ME Weinblatt SB Gabriel S Purcell L Klareskog PK Gregersen NA Shadick MJ Daly D Altshuler 2007 Two independent alleles at 6q23 associated with risk of rheumatoid arthritis Nat Genet 39 1477 1482 1:CAS:528:DC%2BD2sXhtlKmtL3L 10.1038/ng.2007.27 17982456 (Pubitemid 350191346)
25. JK Pritchard 2001 Are rare variants responsible for susceptibility to complex diseases? Am J Hum Genet 69 124 137 1:CAS:528:DC%2BD3MXls1emt7g%3D 10.1086/321272 11404818 (Pubitemid 32614025)
26. JK Pritchard NJ Cox 2002 The allelic architecture of human disease genes: common disease-common variant or not? Hum Mol Genet 11 2417 2423 1:CAS:528:DC%2BD38XnvVenu7k%3D 10.1093/hmg/11.20.2417 12351577
27. S Raychaudhuri EF Remmers AT Lee R Hackett C Guiducci NP Burtt L Gianniny BD Korman L Padyukov FA Kurreeman M Chang JJ Catanese B Ding S Wong AH Van der Helm-van Mil BM Neale J Coblyn J Cui PP Tak GJ Wolbink JB Crusius IE van der Horst-Bruinsma LA Criswell CI Amos MF Seldin DL Kastner KG Ardlie L Alfredsson KH Costenbader D Altshuler TW Huizinga NA Shadick ME Weinblatt N de Vries J Worthington M Seielstad RE Toes EW Karlson AB Begovich L Klareskog PK Gregersen MJ Daly RM Plenge 2008 Common variants at CD40 and other loci confer risk of rheumatoid arthritis Nat Genet 40 1216 1223 1:CAS:528:DC%2BD1cXhtFKht7vJ 10.1038/ng.233 18794853
28. R Redon S Ishikawa KR Fitch L Feuk GH Perry TD Andrews H Fiegler MH Shapero AR Carson W Chen EK Cho S Dallaire JL Freeman JR Gonzalez M Gratacos J Huang D Kalaitzopoulos D Komura JR MacDonald CR Marshall R Mei L Montgomery K Nishimura K Okamura F Shen MJ Somerville J Tchinda A Valsesia C Woodwark F Yang J Zhang T Zerjal J Zhang L Armengol DF Conrad X Estivill C Tyler-Smith NP Carter H Aburatani C Lee KW Jones SW Scherer ME Hurles 2006 Global variation in copy number in the human genome Nature 444 444 454 1:CAS:528:DC%2BD28Xht1aku7zI 10.1038/nature05329 17122850 (Pubitemid 44809057)
29. J Sebat B Lakshmi J Troge J Alexander J Young P Lundin S Maner H Massa M Walker M Chi N Navin R Lucito J Healy J Hicks K Ye A Reiner TC Gilliam B Trask N Patterson A Zetterberg M Wigler 2004 Large-scale copy number polymorphism in the human genome Science 305 525 528 1:CAS:528:DC%2BD2cXlvVOkur4%3D 10.1126/science.1098918 15273396 (Pubitemid 38971344)
30. The Wellcome Trust Case Control Consortium 2007 Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 447 661 678 10.1038/nature05911 (Pubitemid 46889737)
31. W Thomson A Barton X Ke S Eyre A Hinks J Bowes R Donn D Symmons S Hider IN Bruce AG Wilson I Marinou A Morgan P Emery A Carter S Steer L Hocking DM Reid P Wordsworth P Harrison D Strachan J Worthington 2007 Rheumatoid arthritis association at 6q23 Nat Genet 39 1431 1433 1:CAS:528:DC%2BD2sXhtlKmtL3J 10.1038/ng.2007.32 17982455 (Pubitemid 350191348)
32. E Zeggini W Rayner AP Morris AT Hattersley M Walker GA Hitman P Deloukas LR Cardon MI McCarthy 2005 An evaluation of HapMap sample size and tagging SNP performance in large-scale empirical and simulated data sets Nat Genet 37 1320 1322 1:CAS:528:DC%2BD2MXht1Ggsr7I 10.1038/ng1670 16258542 (Pubitemid 41722186)