Genomic profiling of interpopulation diversity guides prioritization of candidate-genes for autoimmunity

Genes and Immunity

Volumn 5, Issue 6, 2004, Pages 493-504

  Grossman, I ^a,b   Avidan, N ^b   Singer, C ^b   Paperna, T ^a   Lancet, D ^b   Beckmann, J S ^c   Miller, A ^a  

^a CARMEL MEDICAL CENTER   (Israel)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^c LAUSANNE UNIVERSITY HOSPITAL   (Switzerland)

Author keywords

Association study; Autoimmunity; Candidate genes; Genetic susceptibility; Haplotype; Multiple sclerosis; SNP

Indexed keywords

APOLIPOPROTEIN E; AUTOANTIGEN; B7 ANTIGEN; CD86 ANTIGEN; CHEMOKINE; CHEMOKINE RECEPTOR; CYTOTOXIC T LYMPHOCYTE ANTIGEN 4; INTERLEUKIN 1 RECEPTOR; INTERLEUKIN 12 RECEPTOR; INTERLEUKIN 2 RECEPTOR; PROTEINASE; TRANSFORMING GROWTH FACTOR BETA1; TRANSFORMING GROWTH FACTOR BETA2; TRANSFORMING GROWTH FACTOR BETA3; VASCULAR CELL ADHESION MOLECULE 1;

ARAB; AUTOIMMUNE DISEASE; CONTROLLED STUDY; ENVIRONMENTAL FACTOR; ETHNIC DIFFERENCE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE THERAPY; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HOMOZYGOSITY; HUMAN; HUMAN CELL; IMMUNOLOGY; ISRAEL; JEW; POPULATION DIFFERENTIATION; POPULATION RESEARCH; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

ADULT; ARABS; AUTOIMMUNITY; CONSERVED SEQUENCE; ETHNIC GROUPS; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOTYPE; HAPLOTYPES; HOMOZYGOTE; HUMANS; JEWS; LINKAGE DISEQUILIBRIUM; PILOT PROJECTS; POLYMORPHISM, SINGLE NUCLEOTIDE; VARIATION (GENETICS);

EID: 4644344988     PISSN: 14664879     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.gene.6364117     Document Type: Review

References (88)

1. 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.
2. Encinas JA, Kuchroo VK. Mapping and identification of autoimmunity genes. Curr Opin Immunol 2000; 12: 691-697.
3. Reboul J, Mertens C, Levillayer F et al. Cytokines in genetic susceptibility to multiple sclerosis: a candidate gene approach. French Multiple Sclerosis Genetics Group. J Neuroimmunol 2000; 102: 107-112.
4. Henderson RD, Bain CJ, Pender MP. The occurrence of autoimmune diseases in patients with multiple sclerosis and their families. J Clin Neurosci 2000; 7: 434-437.
5. Fialkow PJ, Zavala C, Nielsen R. Thyroid autoimmunity: increased frequency in relatives of insulin-dependent diabetes patients. Ann Intern Med 1975; 83: 170-176.
6. Salvetti M, Ristori G, Bomprezzi R, Pozzilli P, Leslie RD. Twins: mirrors of the immune system. Immunol Today 2000; 21: 342-347.
7. Aune TM, Maas K, Moore JH, Olsen NJ. Gene expression profiles in human autoimmune disease. Curr Pharm Des 2003; 9: 1905-1917.
8. Kristiansen OP, Larsen ZM, Pociot F. CTLA-4 in autoimmune diseases - a general susceptibility gene to autoimmunity? Genes Immun 2000; 1: 170-184.
9. Merriman TR, Cordell HJ, Eaves IA et al. Suggestive evidence for association of human chromosome 18q12-q21 and its orthologue on rat and mouse chromosome 18 with several autoimmune diseases. Diabetes 2001; 50: 184-194.
10. Svejgaard A, Platz P, Ryder LP. HLA and disease 1982 - a survey. Immunol Rev 1983; 70: 193-218.
11. Vyse TJ, Todd JA. Genetic analysis of autoimmune disease. Cell 1996; 85: 311-318.
12. Nishimura Y, Oiso M, Fujisao S et al. Peptide-based molecular analyses of HLA class II-associated susceptibility to autoimmune diseases. Int Rev Immunol 1998; 17: 229-262.
13. Daly AK. Candidate gene case-control studies. Pharmacogenomics 2003; 4: 127-139.
14. Bomprezzi R, Kovanen PE, Martin R. New approaches to investigating heterogeneity in complex traits. J Med Genet 2003; 40: 553-559.
15. Devlin B, Roeder K. Genomic control for association studies. Biometrics 1999; 55: 997-1004.
16. Lio D, Pes GM, Carru C et al. Association between the HLA-DR alleles and longevity: a study in Sardinian population. Exp Gerontol 2003; 38: 313-317.
17. Sgambato A, Campisi B, Zupa A et al. Glutathione S-transferase (GST) polymorphisms as risk factors for cancer in a highly homogeneous population from southern Italy. Anticancer Res 2002; 22: 3647-3652.
18. Garte S. Locus-specific genetic diversity between human populations: an analysis of the literature. Am J Human Biol 2003; 15: 814-823.
19. Nebel A, Filon D, Weiss DA et al. High-resolution Y chromosome haplotypes of Israeli and Palestinian Arabs reveal geographic substructure and substantial overlap with haplotypes of Jews. Hum Genet 2000; 107: 630-641.
20. Behar DM, Thomas MG, Skoreoki K et al. Multiple origins of Ashkenazi levites: Y chromosome evidence for both near eastern and European ancestries. Am J Hum Genet 2003; 73: 768-779.
21. Lucotte G, Mercier G. Y-chromosome DNA haplotypes in Jews: comparisons with Lebanese and Palestinians. Genet Test 2003; 7: 67-71.
22. Zlotogora J. Molecular basis of autosomal recessive diseases among the Palestinian Arabs. Am J Med Genet 2002; 109: 176-182.
23. Darwish H, Trejo IE, Shapira I et al. Fighting colorectal cancer: molecular epidemiology differences among Ashkenazi and Sephardic Jews and Palestinians. Ann Oncol 2002; 13: 1497-1501.
24. Kwon OJ, Brautbar C, Weintrob N et al. Immunogenetics of HLA class II in Israeli Ashkenazi Jewish, Israeli non-Ashkenazi Jewish, and in Israeli Arab IDDM patients. Hum Immunol 2001; 62: 85-91.
25. Shohat T, Green MS, Davidson Y et al. Differences in the prevalence of asthma and current wheeze between Jews and Arabs: results from a national survey of schoolchildren in Israel. Ann Allergy Asthma Immunol 2002; 89: 386-392.
26. Kark JD, Gordon ES, Haklai Z. Coronary heart disease mortality among Arab and Jewish residents of Jerusalem. Lancet 2000; 356: 1410-1411.
27. Amar A, Kwon OJ, Motro U et al. Molecular analysis of HLA class II polymorphisms among different ethnic groups in Israel. Hum Immunol 1999; 60: 723-730.
28. Rosenberg NA, Woolf E, Pritchard JK et al. Distinctive genetic signatures in the Libyan Jews. Proc Natl Acad Sci USA 2001; 98: 858-863.
29. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc 1995; Series B: 289-300.
30. Chistiakov DA, Turakulov RI. CTLA-4 and its role in autoimmune thyroid disease. J Mol Endocrinol 2003; 31: 21-36.
31. Kantarci OH, Hebrink DD, Achenbach SJ et al. CTLA4 is associated with susceptibility to multiple sclerosis. J Neuroimmunol 2003; 134: 133-141.
32. Donn RP, Farhan A, Stevans A et al. Neuroendocrine gene polymorphisms and susceptibility to juvenile idiopathic arthritis. Rheumatology (Oxford) 2002; 41: 930-936.
33. Mack R, Chowdary D, Samaan P, Podolak I, Dermody J. Prevalence of CTLA-4 polymorphism A49G in Ashkenazi Jews. Genet Test 2001; 5: 269-271.
34. Stephens M, Smith NJ, Donnelly P. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001; 68: 978-989.
35. Wright S. Systems of mating, I-V. Genetics 1921; 6: 111-178.
36. Tishkoff SA, Verrelli BC. Patterns of human genetic diversity: implications for human evolutionary history and disease. Annu Rev Genom Hum Genet 2003; 4: 293-340.
37. Wall JD, Pritchard JK. Haplotype blocks and linkage disequilibrium in the human genome. Nat Rev Genet 2003; 4:587-597.
38. Thomas MG, Weale ME, Jones AL et al. Founding mothers of Jewish communities: geographically separated Jewish groups were independently founded by very few female ancestors. Am J Hum Genet 2002; 70: 1411-1420.
39. Zlotogora J. High frequencies of human genetic diseases: founder effect with genetic drift or selection? Am J Med Genet 1994; 49: 10-13.
40. Kruglyak L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 1999; 22: 139-144.
41. Abecasis GR, Cookson WO. GOLD - graphical overview of linkage disequilibrium. Bioinformatics 2000; 16: 182-183.
42. Pritchard JK, Donnelly P. Case-control studies of association in structured or admixed populations. Theor Popul Biol 2001; 60: 227-237.
43. Teare MD, Dunning AM, Durocher F, Rennart G, Easton DF. Sampling distribution of summary linkage disequilibrium measures. Ann Hum Genet 2002; 66: 223-233.
44. Devlin B, Risch N. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 1995; 29: 311-322.
45. Nebel A, Filon D, Brinkmann B et al. The Y chromosome pool of Jews as part of the genetic landscape of the Middle East. Am J Hum Genet 2001; 69: 1095-1112.
46. Karni A, Kahana E, Zilber N et al. The frequency of multiple sclerosis in jewish and arab populations in greater jerusalem. Neuroepidemiology 2003; 22: 82-86.
47. Gribben JG, Freeman GJ, Boussiotis VA et al. CTLA4 mediates antigen-specific apoptosis of human T cells. Proc Natl Acad Sci USA 1995; 92: 811-815.
48. Ueda H, Howson JM, Esposito L et al. Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease. Nature 2003; 423: 506-511.
49. Lee YJ, Lo FS, Shu SG et al. The promoter region of the CTLA4 gene is associated with type 1 diabetes mellitus. J Pediatr Endocrinol Metab 2001; 14: 383-388.
50. Walsh EC, Guschwan-McMahon S, Daly MJ, Hafler DA, Rioux JD. Genetic analysis of multiple sclerosis. J Autoimmun 2003; 21: 111-116.
51. Devlin B, Roeder K, Bacanu SA. Unbiased methods for population-based association studies. Genet Epidemiol 2001; 21: 273-284.
52. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. Association mapping in structured populations. Am J Hum Genet 2000; 67: 170-181.
53. Valdes AM, McWeeney SK, Meyer D, Nelson MP, Thomson G. Locus and population specific evolution in HLA class II genes. Ann Hum Genet 1999; 63: 27-43.
54. Bugawan TL, Klitz W, Blair A, Erlich HA. High-resolution HLA class I typing in the CEPH families: analysis of linkage disequilibrium among HLA loci. Tissue Antigens 2000; 56: 392-404.
55. Kwon OJ, Karni A, Israel S et al. HLA class II susceptibility to multiple sclerosis among Ashkenazi and non-Ashkenazi Jews. Arch Neurol 1999; 56: 555-560.
56. Saegusa K, Ishimaru N, Yanagi K et al. Cathepsin S inhibitor prevents autoantigen presentation and autoimmunity. J Clin Invest 2002; 110: 361-369.
57. Friedlander RM, Yuan J. ICE, neuronal apoptosis and neurodegeneration. Cell Death Differ 1998; 5: 823-831.
58. Li P, Allen H, Banerjee S, Seshadri T. Characterization of mice deficient in interleukin-1 beta converting enzyme. J Cell Biochem 1997; 64: 27-32.
59. Galboiz Y, Shapiro S, Lahat N, Rawashdeh H, Miller A. Matrix metalloproteinases and their tissue inhibitors as markers of disease subtype and response to interferon-beta therapy in relapsing and secondary-progressive multiple sclerosis patients. Ann Neurol 2001; 50: 443-451.
60. Fisher GH, Rosenberg FJ, Straus SE et al. Dominant interfering Fas gene mutations impair apoptosis in a human autoimmune lymphoproliferative syndrome. Cell 1995; 81: 935-946.
61. Kuhtreiber WM, Hayashi T, Dale EA, Faustman DL. Central role of defective apoptosis in autoimmunity. J Mol Endocrinol 2003; 31: 373-399.
62. Descamps FJ, Van den Steen PE, Nelissen I, Van Damme J, Opdenakker G. Remnant epitopes generate autoimmunity: from rheumatoid arthritis and multiple sclerosis to diabetes. Adv Exp Med Biol 2003; 535: 69-77.
63. Ahmed Z, Deward AI, Pryce G et al. A role for caspase-1 and -3 in the pathology of experimental allergic encephalomyelitis: inflammation versus degeneration. Am J Pathol 2002; 161: 1577-1586.
64. Murphy CA, Langrish CL, Chen Y et al. Divergent pro- and antiinflammatory roles for IL-23 and IL-12 in joint autoimmune inflammation. J Exp Med 2003; 198: 1951-1957.
65. Berard JL, Velez RL, Freeman RB, Tsunoda SM. A review of interleukin-2 receptor antagonists in solid organ transplantation. Pharmacotherapy 1999; 19: 1127-1137.
66. Kovarik JM, Burtin P. Immunosuppressants in advanced clinical development for organ transplantation and selected autoimmune diseases. Exp Opin Emerg Drugs 2003; 8: 47-62.
67. Hirschhorn JN, Lohmueller K, Byrne E, Hirschhorn K. A comprehensive review of genetic association studies. Genet Med 2002; 4: 45-61.
68. Gershoni-Baruch R, Shinawi M, Leah K, Badarnah K, Brik R. Familial Mediterranean fever: prevalence, penetrance and genetic drift. Eur J Hum Genet 2001; 9: 634-637.
69. Zondervan KT, Cardon LR. The complex interplay among factors that influence allelic association. Nat Rev Genet 2004; 5: 89-100.
70. Slager SL, Huang J, Vieland VJ. Effect of allelic heterogeneity on the power of the transmission disequilibrium test. Genet Epidemiol 2000; 18: 143-156.
71. Kirstein-Grossman I, Beckmann JS, Lancet D, Miller A. Pharmacogenetic development of personalized medicine: multiple sclerosis treatment as a model. Drug News Perspect 2002; 15: 558-567.
72. Steinman L, Martin R, Bernard C, Conlon P, Oksenberg JR. Multiple sclerosis: deeper understanding of its pathogenesis reveals new targets for therapy. Annu Rev Neurosci 2002; 25: 491-505.
73. Chapman J, Vinokurov S, Achiron A et al. APOE genotype is a major predictor of long-term progression of disability in MS. Neurology 2001; 56: 312-316.
74. Shapiro S, Galboiz Y, Lahat N, Kinarty A, Miller A. The 'immunological-synapse' at its APC side in relapsing and secondary-progressive multiple sclerosis: modulation by interferon-b. J Neuroimmunol 2003; 144: 116-124.
75. Kaneko H, Saito K, Hashimoto H et al. Preferential elimination of CD28+ T cells in systemic lupus erythematosus (SLE) and the relation with activation-induced apoptosis. Clin Exp Immunol 1996; 106: 218-229.
76. Wang B, Andre I, Gonzalez A et al. Interferon-gamma impacts at multiple points during the progression of autoimmune diabetes. Proc Natl Acad Sci USA 1997; 94: 13844-13849.
77. Dolhain RJ, ter Haar NT, Hoefakker S et al. Increased expression of interferon (IFN)-gamma together with IFN-gamma receptor in the rheumatoid synovial membrane compared with synovium of patients with osteoarthritis. Br J Rheumatol 1996; 35: 24-32.
78. Weale ME, Depondt C, Macdonald SJ et al. Selection and evaluation of tagging SNPs in the neuronal-sodium-channel gene SCN1A: implications for linkage-disequilibrium gene mapping. Am J Hum Genet 2003; 73: 551-565.
79. Ke X, Cardon LR. Efficient selective screening of haplotype tag SNPs. Bioinformatics 2003; 19: 287-288.
80. Abecasis GR, Noguchi E, Heinzmann A et al. Extent and distribution of linkage disequilibrium in three genomic regions. Am J Hum Genet 2001; 68: 191-197.
81. Carlson CS, Eberle MA, Rieder MJ et al. Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat Genet 2003; 33: 518-521.
82. Reich DE, Gabriel SB, Altshuler D. Quality and completeness of SNP databases. Nat Genet 2003; 33: 457-458.
83. Rodi CP, Darnhofer-Patel B, Stanssens P, Zabeau M, van den Boom D. A strategy for the rapid discovery of disease markers using the MassARRAY system. Biotechniques 2002; Suppl: 62-66: 68-69.
84. Reiner A, Yekutieli D, Benjamini Y. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 2003; 19: 368-375.
85. Hartl LH, Clark AG. Principles of population genetics, 2nd ed. Sinauer Associates, Inc.: Sunderland, Mass, 1989.
86. Weir BS. Genetic Data Analysis. Sinauer Associates: Sunderland, MA, 1996.
87. Crawford DC, Carlson CS, Rieder MJ et al. Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am J Hum Genet 2004; 74: 610-622.
88. Rousset F, Raymond M. Testing heterozygote excess and deficiency. Genetics 1995; 140: 1413-1419.