Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis

Nature Genetics

Volumn 44, Issue 10, 2012, Pages 1137-1141

  Liu, Jimmy Z ^a   Almarri, Mohamed A ^a   Gaffney, Daniel J ^a   Mells, George F ^b,c   Jostins, Luke ^a   Cordell, Heather J ^d   Ducker, Samantha J ^e   Day, Darren B ^b   Heneghan, Michael A ^f   Neuberger, James M ^g   Donaldson, Peter T ^e   Bathgate, Andrew J ^h   Burroughs, Andrew ⁱ   Davies, Mervyn H ^j   Jones, David E ^e   Alexander, Graeme J ^c   Barrett, Jeffrey C ^a   Sandford, Richard N ^b   Anderson, Carl A ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c CAMBRIDGE UNIVERSITY HOSPITALS NHS FOUNDATION TRUST   (United Kingdom)

^d NEWCASTLE UNIVERSITY   (United Kingdom)

^e NEWCASTLE UNIVERSITY   (United Kingdom)

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

^g QUEEN ELIZABETH HOSPITAL   (United Kingdom)

^h ROYAL INFIRMARY OF EDINBURGH   (United Kingdom)

ⁱ ROYAL FREE AND UNIVERSITY COLLEGE MEDICAL SCHOOL   (United Kingdom)

^j ST JAMES S UNIVERSITY HOSPITAL   (United Kingdom)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CYTOKINE; STAT PROTEIN; STRESS ACTIVATED PROTEIN KINASE;

ARTICLE; AUTOIMMUNITY; CHROMATIN; CHROMOSOME 6; CONTROLLED STUDY; GENE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENETIC ASSOCIATION; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; HLA SYSTEM; HUMAN; HUMAN CELL; IMMUNOPATHOGENESIS; LYMPHOBLASTOID CELL; MAJOR CLINICAL STUDY; PRIMARY BILIARY CIRRHOSIS; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; TYK2 GENE; UNITED KINGDOM;

CASE-CONTROL STUDIES; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 19; GENE FREQUENCY; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HLA ANTIGENS; HUMANS; LINKAGE DISEQUILIBRIUM; LIVER CIRRHOSIS, BILIARY; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEINS; REGRESSION ANALYSIS; SEQUENCE ANALYSIS, DNA; TYK2 KINASE;

EID: 84866924593     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.2395     Document Type: Article

References (40)

1. Kaplan, M.M. & Gershwin, M.E. Primary biliary cirrhosis. N. Engl. J. Med. 353, 1261-1273 (2005).
2. James, O.F. et al. Primary biliary cirrhosis once rare, now common in the United Kingdom? Hepatology 30, 390-394 (1999).
3. Jones, D.E., Watt, F.E., Metcalf, J.V., Bassendine, M.F. & James, O.F. Familial primary biliary cirrhosis reassessed: a geographically-based population study. J. Hepatol. 30, 402-407 (1999).
4. Hirschfield, G.M. et al. Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants. N. Engl. J. Med. 360, 2544-2555 (2009).
5. Liu, X. et al. Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis. Nat. Genet. 42, 658-660 (2010).
6. Mells, G.F. et al. Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis. Nat. Genet. 43, 329-332 (2011).
7. Zhernakova, A., van Diemen, C.C. & Wijmenga, C. Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat. Rev. Genet. 10, 43-55 (2009).
8. Cortes, A. & Brown, M. Promise and pitfalls of the Immunochip. Arthritis Res. Ther. 13, 101 (2011).
9. Trynka, G. et al. Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat. Genet. 43, 1193-1201 (2011).
10. Cordell, H.J. & Clayton, D.G. A unified stepwise regression procedure for evaluating the relative effects of polymorphisms within a gene using case/control or family data: application to HLA in type 1 diabetes. Am. J. Hum. Genet. 70, 124-141 (2002).
11. Ban, M. et al. Replication analysis identifies TYK2 as a multiple sclerosis susceptibility factor. Eur. J. Hum. Genet. 17, 1309-1313 (2009).
12. Wallace, C. et al. The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes. Nat. Genet. 42, 68-71 (2010).
13. Strange, A. et al. A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. Nat. Genet. 42, 985-990 (2010).
14. Franke, A. et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat. Genet. 42, 1118-1125 (2010).
15. Hunt, K.A. et al. Newly identified genetic risk variants for celiac disease related to the immune response. Nat. Genet. 40, 395-402 (2008).
16. Stahl, E.A. et al. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat. Genet. 42, 508-514 (2010).
17. Barrett, J.C. et al. Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat. Genet. 41, 703-707 (2009).
18. Wang, D. et al. CD4+CD25+ but not CD4+Foxp3+ T cells as a regulatory subset in primary biliary cirrhosis. Cell. Mol. Immunol. 7, 485-490 (2010).
19. Rong, G. et al. Imbalance between T helper type 17 and T regulatory cells in patients with primary biliary cirrhosis: the serum cytokine profile and peripheral cell population. Clin. Exp. Immunol. 156, 217-225 (2009).
20. Couturier, N. et al. Tyrosine kinase 2 variant influences T lymphocyte polarization and multiple sclerosis susceptibility. Brain 134, 693-703 (2011).
21. Zhernakova, A. et al. Evolutionary and functional analysis of celiac risk loci reveals SH2B3 as a protective factor against bacterial infection. Am. J. Hum. Genet. 86, 970-977 (2010).
22. Donaldson, P.T. et al. HLA class II alleles, genotypes, haplotypes, and amino acids in primary biliary cirrhosis: a large-scale study. Hepatology 44, 667-674 (2006).
23. Mullarkey, M.E. et al. Human leukocyte antigen class II alleles in Caucasian women with primary biliary cirrhosis. Tissue Antigens 65, 199-205 (2005).
24. Wassmuth, R. et al. HLA class II markers and clinical heterogeneity in Swedish patients with primary biliary cirrhosis. Tissue Antigens 59, 381-387 (2002).
25. Invernizzi, P. et al. Human leukocyte antigen polymorphisms in Italian primary biliary cirrhosis: a multicenter study of 664 patients and 1992 healthy controls. Hepatology 48, 1906-1912 (2008).
26. Leslie, S., Donnelly, P. & McVean, G. A statistical method for predicting classical HLA alleles from SNP data. Am. J. Hum. Genet. 82, 48-56 (2008).
27. Dilthey, A.T., Moutsianas, L., Leslie, S. & McVean, G. HLA*IMP-an integrated framework for imputing classical HLA alleles from SNP genotypes. Bioinformatics 27, 968-972 (2011).
28. Gaffney, D.J. et al. Dissecting the regulatory architecture of gene expression QTLs. Genome Biol. 13, R7 (2012).
29. Song, L. et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 21, 1757-1767 (2011).
30. ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 9 e1001046 (2011).
31. Shah, T.S. et al. optiCall: a robust genotype-calling algorithm for rare, low frequency and common variants. Bioinformatics 28, 1598-1603 (2012).
32. Teo, Y.Y. et al. A genotype calling algorithm for the Illumina BeadArray platform. Bioinformatics 23, 2741-2746 (2007).
33. Giannoulatou, E., Yau, C., Colella, S., Ragoussis, J. & Holmes, C.C. GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population. Bioinformatics 24, 2209-2214 (2008).
34. Price, A.L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904-909 (2006).
35. Devlin, B. & Roeder, K. Genomic control for association studies. Biometrics 55, 997-1004 (1999).
36. Howie, B.N., Donnelly, P. & Marchini, J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 5, e1000529 (2009).
37. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007).
38. Morris, J.A., Randall, J.C., Maller, J.B. & Barrett, J.C. Evoker: a visualization tool for genotype intensity data. Bioinformatics 26, 1786-1787 (2010).
39. So, H.C., Gui, A.H., Cherny, S.S. & Sham, P.C. Evaluating the heritability explained by known susceptibility variants: a survey of ten complex diseases. Genet. Epidemiol. 35, 310-317 (2011).
40. Falconer, D. & Mackay, T. Introduction to Quantitative Genetics 464 (Longman, London, 1996).