Meta-analysis of genome-wide linkage studies across autoimmune diseases

European Journal of Human Genetics

Volumn 17, Issue 2, 2009, Pages 236-243

  Forabosco, Paola ^a,b   Bouzigon, Emmanuelle ^c   Ng, Mandy Y ^a   Hermanowski, Jane ^a   Fisher, Sheila A ^a   Criswell, Lindsey A ^d   Lewis, Cathryn M ^a,e  

^a KING'S COLLEGE LONDON   (United Kingdom)

^b CNR   (Italy)

^c INSERM   (France)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOTOXIC T LYMPHOCYTE ANTIGEN 4; PROTEIN TYROSINE PHOSPHATASE;

ANKYLOSING SPONDYLITIS; ARTICLE; AUTOIMMUNE DISEASE; CELIAC DISEASE; CHROMOSOME 16; CHROMOSOME ANALYSIS; ENTERITIS; GENETIC ASSOCIATION; GENETIC PREDISPOSITION; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENOME ANALYSIS; HLA SYSTEM; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; JUVENILE RHEUMATOID ARTHRITIS; LINKAGE ANALYSIS; MULTIPLE SCLEROSIS; PHENOTYPE; PLEIOTROPY; PRIORITY JOURNAL; PSORIASIS; RHEUMATOID ARTHRITIS; RISK ASSESSMENT; SYSTEMIC LUPUS ERYTHEMATOSUS; THYROID DISEASE; VITILIGO;

AUTOIMMUNE DISEASES; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MAJOR HISTOCOMPATIBILITY COMPLEX;

EID: 58349089435     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2008.163     Document Type: Article

References (77)

1. Vyse TJ, Todd JA: Genetic analysis of autoimmune disease. Cell 1996; 85: 311-318.
2. Heward J, Gough SC: Genetic susceptibility to the development of autoimmune disease. Clin Sci (Lond) 1997; 93: 479-491.
3. Torfs CP, King MC, Huey B, Malmgren J, Grumet FC: Genetic interrelationship between insulin-dependent diabetes mellitus, the autoimmune thyroid diseases, and rheumatoid arthritis. Am J Hum Genet 1986; 38: 170-187.
4. Becker KG, Simon RM, Bailey-Wilson JE et al: Clustering of non-major histocompatibility complex susceptibility candidate loci in human autoimmune diseases. Proc Natl Acad Sci USA 1998; 95: 9979-9984.
5. Brand O, Gough S, Teward J: HLA, CTLA-4 and PTPN22: the shared genetic master-key to autoimmunity? Expert Rev Mol Med 2005; 7: 1-15.
6. Duerr RH, Taylor KD, Brant SR et al: A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 2006; 314: 1461-1463.
7. 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. Nat Genet 2007; 39: 827-829.
8. WTCCC: Genome-wide association study of 14 000 cases of seven common diseases and 3000 shared controls. Nature 2007; 447: 661-678.
9. Todd JA, Walker NM, Cooper JD et al: Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Nat Genet 2007; 39: 857-864.
10. Hakonarson H, Grant SF, Bradfield JP et al: A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene. Nature 2007; 448: 591-594.
11. 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. Nat Genet 2008; 40: 204-210.
12. Wise LH, Lanchbury JS, Lewis CM: Meta-analysis of genome searches. Ann Hum Genet 1999; 63: 263-272.
13. van Heel DA, Fisher SA, Kirby A, Daly MJ, Rioux JD, Lewis CM: Inflammatory bowel disease susceptibility loci defined by genome scan meta-analysis of 1952 affected relative pairs. Hum Mol Genet 2004; 13: 763-770.
14. Forabosco P, Gorman JD, Cleveland C et al: Meta-analysis of genome-wide linkage studies of systemic lupus erythematosus. Genes Immun 2006; 7: 609-614.
15. Hermanowski J, Bouzigon E, Forabosco P, Ng MY, Fisher SA, Lewis CM: Meta-analysis of genome-wide linkage studies for multiple sclerosis, using an extended GSMA method. Eur J Hum Genet 2007; 15: 703-710.
16. Choi SJ, Rho YH, Ji JD, Song GG, Lee YH: Genome scan meta-analysis of rheumatoid arthritis. Rheumatology (Oxford) 2006; 45: 166-170.
17. Sagoo GS, Tazi-Ahnini R, Barker JW et al: Meta-analysis of genome-wide studies of psoriasis susceptibility reveals linkage to chromosomes 6p21 and 4q28-q31 in Caucasian and Chinese Hans population. J Invest Dermatol 2004; 122: 1401-1405.
18. Babron MC, Nilsson S, Adamovic S et al: Meta and pooled analysis of European coeliac disease data. Eur J Hum Genet 2003; 11: 828-834.
19. Forabosco P, Ng MY, Bouzigon E, Fisher SA, Levinson DF, Lewis CM: Data acquisition for meta-analysis of genome-wide linkage studies using the genome search meta-analysis method. Hum Hered 2007; 64: 74-81.
20. Concannon PE Erlich HA, Julier C et al: Type 1 diabetes: evidence for susceptibility loci from four genome-wide linkage scans in 1,435 multiplex families. Diabetes 2005; 54: 2995-3001.
21. Barmada MM, Brant SR, Nicolae DL et al: A genome scan in 260 inflammatory bowel disease-affected relative pairs. Inflamm Bowel Dis 2004; 10: 513-520.
22. Cho JH, Nicolae DL, Gold LH et al: Identification of novel susceptibility loci for inflammatory bowel disease on chromosomes 1p, 3q, and 4q: Evidence for epistasis between 1p and IBD1. Proc Natl Acad Sci USA 1998; 95: 7502-7507.
23. Hampe J, Schreiber S, Shaw SH et al: A genomewide analysis provides evidence for novel linkages in inflammatory bowel disease in a large European cohort. Am J Hum Genet 1999; 64: 808-816.
24. Ma Y, Ohmen JD, Li Z et al: A genome-wide search identifies potential new susceptibility loci for Crohn's disease. Inflamm Bowel Dis 1999; 5: 271-278.
25. Paavola-Sakki P, Ollikainen V, Helio T et al: Genome-wide search in Finnish families with inflammatory bowel disease provides evidence for novel susceptibility loci. Eur J Hum Genet 2003; 11: 112-120.
26. Rioux JD, Silverberg MS, Daly MJ et al: Genomewide search in Canadian families with inflammatory bowel disease reveals two novel susceptibility loci. Am J Hum Genet 2000; 66: 1863-1870.
27. van Heel DA, Dechairo BM, Dawson G et al: The IBD6 Crohn's disease locus demonstrates complex interactions with CARD15 and IBD5 disease-associated variants. Hum Mol Genet 2003; 12: 2569-2575.
28. Vermeire S, Rutgeerts P, Van Steen K et al: Genome wide scan in a Flemish inflammatory bowel disease population: Support for the IBD4 locus, population heterogeneity, and epistasis. Gut 2004; 53 980-986.
29. Williams CN, Kocher K, Lander ES, Daly MJ, Rioux JD: Using a genome-wide scan and meta-analysis to identify a novel IBD locus and confirm previously identified IBD loci. Inflamm Bowel Dis 2002; 8: 375-381.
30. Broadley S, Sawcer S, D'Alfonso S et al: A genome screen for multiple sclerosis in Italian families. Genes Immun 2001; 2: 205-210.
31. Coraddu F, Sawcer S, D'Alfonso S et al: A genome screen for multiple sclerosis in Sardinian multiplex families. Eur J Hum Genet 2001; 9: 621-626.
32. Dyment DA, Sadovnick AD, Willer CJ et al: An extended genome scan in 442 canadian multiple sclerosis-affected sibships: A report from the canadian collaborative study group. Hum Mol Genet 2004; 13: 1005-1015.
33. Eraksoy M, Kurtuncu M, Akman-Demir G et al: A whole genome screen for linkage in Turkish multiple sclerosis. J Neuroimmunol 2003; 143: 17-24.
34. Kenealy SJ, Babron MC, Bradford Y et al: A second-generation genomic screen for multiple sclerosis. Am J Hum Genet 2004; 75 1070-1078.
35. Kuokkanen S, Gschwend M, Rioux JD et al: Genomewide scan of multiple sclerosis in Finnish multiplex families. Am J Hum Genet 1997; 61: 1379-1387.
36. Sawcer S, Ban M, Maranian M et al: A high-density screen for linkage in multiple sclerosis. Am J Hum Genet 2005; 77: 454-467.
37. Sakai K, Shirasawa S, Ishikawa N et al: Identification of susceptibility loci for autoimmune thyroid disease to 5q31-q33 and Hashimoto's thyroiditis to 8q23-q24 by multipoint affected sib-pair linkage analysis in Japanese. Hum Mol Genet 2001; 10: 1379-1386.
38. Taylor JC, Gough SC, Hunt PJ et al: A genome-wide screen in 1119 relative pairs with autoimmune thyroid disease. J Clin Endocrinol Metab 2006; 91: 646-653.
39. Tomer Y, Barbesino G, Greenberg DA, Concepcion E, Davies TF: A new Graves disease-susceptibility locus maps to chromosome 20q11. 2. International Consortium for the Genetics of Autoimmune Thyroid Disease. Am J Hum Genet 1998; 63: 1749-1756.
40. Asumalahti K, Laitinen T, Lahermo P et al: Psoriasis susceptibility locus on 18p revealed by genome scan in Finnish families not associated with PSORS1. J Invest Dermatol 2003; 121: 735-740.
41. Karason A, Gudjonsson JE, Jonsson HH et al: Genetics of psoriasis in Iceland: Evidence for linkage of subphenotypes to distinct Loci. J Invest Dermatol 2005; 124: 1177-1185.
42. Lee YA, Ruschendorf F, Windemuth C et al: Genomewide scan in german families reveals evidence for a novel psoriasis-susceptibility locus on chromosome 19p13. Am J Hum Genet 2000; 67: 1020-1024.
43. Miceli-Richard C, Zouali H, Said-Nahal R et al: Significant linkage to spondyloarthropathy on 9q31-34. Hum Mol Genet 2004; 13: 1641-1648.
44. Nair RP, Henseler T, Jenisch S et al: Evidence for two psoriasis susceptibility loci (HLA and 17q) and two novel candidate regions (16q and 20p) by genome-wide scan. Hum Mol Genet 1997; 6: 1349-1356.
45. Samuelsson L, Enlund F, Torinsson A et al: A genome-wide search for genes predisposing to familial psoriasis by using a stratification approach. Hum Genet 1999; 105: 523-529.
46. Veal CD, Clough RL, Barber RC et al: Identification of a novel psoriasis susceptibility locus at 1p and evidence of epistasis between PSORS1 and candidate loci. J Med Genet 2001; 38: 7-13.
47. Amos CI, Chen WV, Lee A et al: High-density SNP analysis of 642 Caucasian families with rheumatoid arthritis identifies two new linkage regions on 11p12 and 2q33. Genes Immun 2006; 7: 277-286.
48. John S, Shephard N, Liu G et al: Whole-genome scan, in a complex disease, using 11 245 single-nucleotide polymorphisms: Comparison with microsatellites. Am J Hum Genet 2004; 75: 54-64.
49. Osorio YFJ, Bukulmez H, Petit-Teixeira E et al: Dense genome-wide linkage analysis of rheumatoid arthritis, including covariates. Arthritis Rheum 2004; 50: 2757-2765.
50. Shiozawa S, Hayashi S, Tsukamoto Y et al: Identification of the gene loci that predispose to rheumatoid arthritis. Int Immunol 1998; 10: 1891-1895.
51. Garner CP, Ding YC, Steele L et al: Genome-wide linkage analysis of 160 north american families with celiac disease. Genes Immun 2007; 8: 108-114.
52. Naluai AT, Nilsson S, Gudjonsdottir AH et al: Genome-wide linkage analysis of Scandinavian affected sib-pairs supports presence of susceptibility loci for celiac disease on chromosomes 5 and 11. Eur J Hum Genet 2001; 9: 938-944.
53. Popat S, Bevan S, Braegger CP et al: Genome screening of coeliac disease. J Med Genet 2002; 39: 328-331.
54. Rioux JD, Karinen H, Kocher K et al: Genomewide search and association studies in a Finnish celiac disease population: Identification of a novel locus and replication of the HLA and CTLA4 loci. Am J Med Genet A 2004; 130: 345-350.
55. Laval SH, Timms A, Edwards S et al: Whole-genome screening in ankylosing spondylitis: Evidence of non-MHC genetic-susceptibility loci. Am J Hum Genet 2001; 68: 918-926.
56. Zhang G, Luo J, Bruckel J et al: Genetic studies in familial ankylosing spondylitis susceptibility. Arthritis Rheum 2004; 50 2246-2254.
57. Gaffney PM, Ortmann WA, Selby SA et al: Genome screening in human systemic lupus erythematosus: Results from a second Minnesota cohort and combined analyses of 187 sib-pair families. Am J Hum Genet 2000; 66: 547-556.
58. Koskenmies S, Lahermo P, Julkunen H, Ollikainen V, Kere J, Widen E: Linkage mapping of systemic lupus erythematosus (SLE) in Finnish families multiply affected by SLE. J Med Genet 2004; 41: e2-e5.
59. Nath SK, Quintero-Del-Rio AI, Kilpatrick J, Feo L, Ballesteros M, Harley JB: Linkage at 12q24 with systemic lupus erythematosus (SLE) is established and confirmed in hispanic and european american families. Am J Hum Genet 2004; 74: 73-82.
60. Thompson SD, Moroldo MB, Guyer L et al: A genome-wide scan for juvenile rheumatoid arthritis in affected sibpair families provides evidence of linkage. Arthritis Rheum 2004; 50: 2920-2930.
61. Chen JJ, Huang W, Gui JP et al: A novel linkage to generalized vitiligo on 4q13-q21 identified in a genomewide linkage analysis of chinese families. Am J Hum Genet 2005; 76: 1057-1065.
62. Sardi F, Levinson DF, Lewis CM: GSMA: software implementation of the genome search meta-analysis method. Bioinformatics 2005; 21: 4430-4431.
63. Broman KW, Murray JC, Sheffield VC, White RL, Weber JL: Comprehensive human genetic maps: Individual and sex-specific variation in recombination. Am J Hum Genet 1998; 63: 861-869.
64. Barcellos LF, Kamdar BB, Ramsay PP et al: Clustering of autoimmune diseases in families with a high-risk for multiple sclerosis: A descriptive study. Lancet Neurol 2006; 5: 924-931.
65. Risch N: Linkage strategies for genetically complex traits. III. The effect of marker polymorphism on analysis of affected relative pairs. Am J Hum Genet 1990; 46: 242-253.
66. Lander E, Kruglyak L: Genetic diGsection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet 1995; 11: 241-247.
67. Levinson DF, Levinson MD, Segurado R, Lewis CM: Genome scan meta-analysis of schizophrenia and bipolar disorder, part I: Methods and power analysis. Am J Hum Genet 2003; 73: 17-33.
68. Kong X, Murphy K, Raj T, He C, White PS, Matise TC: A combined linkage-physical map of the human genome. Am J Hum Genet 2004; 75: 1143-1148.
69. Fernando MM, Stevens CR, Walsh EC et al: Defining the role of the MHC in autoimmunity: A review and pooled analysis. PLoS Genet 2008; 4: E1000024.
70. Lee YH, Rho YH, Choi SJ et al: The PTPN22 C1858T functional polymorphism and autoimmune diseases - a meta-analysis. Rheumatology (Oxford) 2007; 46: 49-56.
71. Laberge GS, Bennett DC, Fain PR, Spritz RA: PTPN22 is genetically associated with risk of generalized vitiligo, but CTLA4 is not. J Invest Dermatol 2008; 128: 1757-1762.
72. Kavvoura FK, Akamizu T, Awata T et al: Cytotoxic T-lymphocyte associated antigen 4 gene polymorphisms and autoimmune thyroid disease: a meta-analysis. J Clin Endocrinol Metab 2007; 92: 3162-3170.
73. van Belzen MJ, Mulder CJ, Zhernakova A, Pearson PL, Houwen RH, Wijmenga C: CTLA4 +49 A/G and CT60 polymorphisms in Dutch coeliac disease patients. Eur J Hum Genet 2004; 12: 782-785.
74. Torres B, Aguilar F, Franco E et al: Association of the CT60 marker of the CTLA4 gene with systemic lupus erythematosus. Arthritis Rheum 2004; 50: 2211-2215.
75. Saunders CL, Chiodini BD, Sham P et al: Meta-analysis of genome-wide linkage studies in BMI and obesity. Obesity (Silver Spring) 2007; 15: 2263-2275.
76. Gorlov IP, Gorlova OY, Sunyaev SR, Spitz MR, Amos CI: Shifting paradigm of association studies: Value of rare single-nucleotide polymorphisms. Am J Hum Genet 2008; 82: 100-112.
77. Walsh T, McClellan JM, McCarthy SE et al: Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science 2008; 320: 539-543.