What is next after the genes for autoimmunity?

BMC Medicine

Volumn 11, Issue 1, 2013, Pages

  Castiblanco, John ^a,b,c   Arcos Burgos, Mauricio ^d   Anaya, Juan Manuel ^a  

^a UNIVERSIDAD DEL ROSARIO   (Colombia)

^b UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

^c Mays Cancer Center at UT Health San Antonio   (United States)

^d Biology and Environment   (Australia)

Author keywords

Autoimmunity; Common; Genetics; Genomics; Personalized; Polyautoimmunity; Predictive medicine; Translational medicine

Indexed keywords

ARTICLE; AUTOIMMUNE DISEASE; AUTOIMMUNITY; BEHCET DISEASE; BIOINFORMATICS; CELIAC DISEASE; CHROMATIN IMMUNOPRECIPITATION; CROHN DISEASE; ENTERITIS; FOLLOW UP; GENE MAPPING; GENETIC ASSOCIATION; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE ENVIRONMENT INTERACTION; HUMAN; HUMAN GENOME; IMMUNOGENETICS; INSULIN DEPENDENT DIABETES MELLITUS; JUVENILE RHEUMATOID ARTHRITIS; MAJOR HISTOCOMPATIBILITY COMPLEX; META ANALYSIS; MUCOCUTANEOUS LYMPH NODE SYNDROME; MULTIPLE SCLEROSIS; NATIONAL HEALTH ORGANIZATION; PERSONALIZED MEDICINE; PHARMACOGENOMICS; PHENOTYPE; PRIMARY BILIARY CIRRHOSIS; PRIMARY SCLEROSING CHOLANGITIS; PSORIASIS; RISK FACTOR; SYSTEMIC LUPUS ERYTHEMATOSUS; SYSTEMIC SCLEROSIS; THYROID DISEASE; VITILIGO;

AUTOIMMUNE DISEASES; AUTOIMMUNITY; GENOME, HUMAN; GENOMICS; HUMANS; TRANSLATIONAL MEDICAL RESEARCH;

EID: 84888049974     PISSN: None     EISSN: 17417015     Source Type: Journal    
DOI: 10.1186/1741-7015-11-197     Document Type: Article

References (61)

1. Green ED, Guyer MS. Charting a course for genomic medicine from base pairs to bedside. Nature 2011, 470:204-213.
2. Hennekam RC, Biesecker LG. Next-generation sequencing demands next-generation phenotyping. Hum Mutat 2012, 33:884-886.
3. Chan IS, Ginsburg GS. Personalized medicine: progress and promise. Ann Rev Genomics Hum Genet 2011, 12:217-244.
4. Anaya JM. Common mechanisms of autoimmune diseases (the autoimmune tautology). Autoimmun Rev 2012, 11:781-784.
5. Arcos-Burgos M, Velez JI, Solomon BD, Muenke M. A common genetic network underlies substance use disorders and disruptive or externalizing disorders. Hum Genet 2012, 131:917-929.
6. Solovieff N, Cotsapas C, Lee PH, Purcell SM, Smoller JW. Pleiotropy in complex traits: challenges and strategies. Nature Rev Genet 2013, 14:483-495.
7. Cardenas-Roldan J, Rojas-Villarraga A, Anaya JM. How do autoimmune diseases cluster in families? A systematic review and meta-analysis. BMC Med 2013, 11:73.
8. Tobon GJ, Pers JO, Canas CA, Rojas-Villarraga A, Youinou P, Anaya JM. Are autoimmune diseases predictable?. Autoimmun Rev 2012, 11:259-266.
9. Anaya JM, Gomez L, Castiblanco J. Is there a common genetic basis for autoimmune diseases?. Clin Dev Immunol 2006, 13:185-195.
10. Somers EC, Thomas SL, Smeeth L, Hall AJ. Autoimmune diseases co-occurring within individuals and within families: a systematic review. Epidemiology 2006, 17:202-217.
11. Anaya JM, Corena R, Castiblanco J, Rojas-Villarraga A, Shoenfeld Y. The kaleidoscope of autoimmunity: multiple autoimmune syndromes and familial autoimmunity. Expert Rev Clin Immunol 2007, 3:623-635.
12. Rojas-Villarraga A, Amaya-Amaya J, Rodriguez-Rodriguez A, Mantilla RD, Anaya JM. Introducing polyautoimmunity: secondary autoimmune diseases no longer exist. Autoimmune Dis 2012, 2012:254319.
13. Richard-Miceli C, Criswell LA. Emerging patterns of genetic overlap across autoimmune disorders. Genome Med 2012, 4:6.
14. Becker KG, Simon RM, Bailey-Wilson JE, Freidlin B, Biddison WE, McFarland HF, Trent JM. Clustering of non-major histocompatibility complex susceptibility candidate loci in human autoimmune diseases. Proc Natl Acad Sci U S A 1998, 95:9979-9984.
15. Goris A, Liston A. The immunogenetic architecture of autoimmune disease. Cold Spring Harb Perspect Biol 2012, 4:a007260.
16. Bogdanos DP, Smyk DS, Rigopoulou EI, Mytilinaiou MG, Heneghan MA, Selmi C, Gershwin ME. Twin studies in autoimmune disease: genetics, gender and environment. J Autoimmun 2012, 38:J156-J169.
17. Czyz W, Morahan JM, Ebers GC, Ramagopalan SV. Genetic, environmental and stochastic factors in monozygotic twin discordance with a focus on epigenetic differences. BMC Med 2012, 10:93.
18. Selmi C, Lu Q, Humble MC. Heritability versus the role of the environment in autoimmunity. J Autoimmun 2012, 39:249-252.
19. Bias WB, Reveille JD, Beaty TH, Meyers DA, Arnett FC. Evidence that autoimmunity in man is a Mendelian dominant trait. Am J Hum Genet 1986, 39:584-602.
20. Arcos-Burgos M, Parodi E, Salgar M, Bedoya E, Builes J, Jaramillo D, Ceballos G, Uribe A, Rivera N, Rivera D, Fonseca I, Camargo M, Palacio G. Vitiligo: complex segregation and linkage disequilibrium analyses with respect to microsatellite loci spanning the HLA. Hum Genet 2002, 110:334-342.
21. Lin JP, Cash JM, Doyle SZ, Peden S, Kanik K, Amos CI, Bale SJ, Wilder RL. Familial clustering of rheumatoid arthritis with other autoimmune diseases. Hum Genet 1998, 103:475-482.
22. Miller FW, Alfredsson L, Costenbader KH, Kamen DL, Nelson LM, Norris JM, De Roos AJ. Epidemiology of environmental exposures and human autoimmune diseases: findings from a National Institute of Environmental Health Sciences Expert Panel Workshop. J Autoimmun 2012, 39:259-271.
23. Barragan-Martinez C, Speck-Hernandez CA, Montoya-Ortiz G, Mantilla RD, Anaya JM, Rojas-Villarraga A. Organic solvents as risk factor for autoimmune diseases: a systematic review and meta-analysis. PLoS One 2012, 7:e51506.
24. Feinberg J. Wordle http://www.wordle.net.
25. Hindorff LA, MacArthur J, Morales J, Junkins HA, Hall PN, Klemm AK, Manolio TA, (European Bioinformatics Institute) A Catalog of Published Genome-Wide Association Studies http://www.genome.gov/gwastudies, (European Bioinformatics Institute).
26. The Database of Genotypes and Phenotypes http://www.ncbi.nlm.nih.gov/gap.
27. Hsu HC, Mountz JD. Origin of late-onset autoimmune disease. Immunol Allergy Clin North Am 2003, 23:65-82. vi.
28. Sloka S. Observations on recent studies showing increased co-occurrence of autoimmune diseases. J Autoimmun 2002, 18:251-257.
29. Quintero OL, Amador-Patarroyo MJ, Montoya-Ortiz G, Rojas-Villarraga A, Anaya JM. Autoimmune disease and gender: plausible mechanisms for the female predominance of autoimmunity. J Autoimmun 2012, 38:J109-J119.
30. Hirschhorn JN, Gajdos ZK. Genome-wide association studies: results from the first few years and potential implications for clinical medicine. Ann Rev Med 2011, 62:11-24.
31. Lessard CJ, Ice JA, Adrianto I, Wiley GB, Kelly JA, Gaffney PM, Montgomery CG, Moser KL. The genomics of autoimmune disease in the era of genome-wide association studies and beyond. Autoimmun Rev 2012, 11:267-275.
32. Pearson TA, Manolio TA. How to interpret a genome-wide association study. JAMA 2008, 299:1335-1344.
33. Barsh GS, Copenhaver GP, Gibson G, Williams SM. Guidelines for genome-wide association studies. PLoS Genet 2012, 8:e1002812.
34. Austin MA, Hair MS, Fullerton SM. Research guidelines in the era of large-scale collaborations: an analysis of Genome-wide Association Study Consortia. Am J Epidemiol 2012, 175:962-969.
35. Cotsapas C, Hafler DA. Immune-mediated disease genetics: the shared basis of pathogenesis. Trends Immunol 2013, 34:22-26.
36. Cotsapas C, Voight BF, Rossin E, Lage K, Neale BM, Wallace C, Abecasis GR, Barrett JC, Behrens T, Cho J, De Jager PL, Elder JT, Graham RR, Gregersen P, Klareskog L, Siminovitch KA, van Heel DA, Wijmenga C, Worthington J, Todd JA, Hafler DA, Rich SS, Daly MJ, FOCiS Network of Consortia Pervasive sharing of genetic effects in autoimmune disease. PLoS Genet 2011, 7:e1002254. FOCiS Network of Consortia.
37. Lee S, Kwon MS, Park T. Network graph analysis of gene-gene interactions in genome-wide association study data. Genomics Inform 2012, 10:256-262.
38. Shendure J, Lieberman Aiden E. The expanding scope of DNA sequencing. Nature Biotechnol 2012, 30:1084-1094.
39. Li J, Burmeister M. Genetical genomics: combining genetics with gene expression analysis. Hum Mol Genet 2005, 14 Spec No. 2:R163-R169.
40. Costa V, Aprile M, Esposito R, Ciccodicola A. RNA-Seq and human complex diseases: recent accomplishments and future perspectives. Eur J Hum Genet 2013, 21:134-142.
41. Veyrieras JB, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M, Pritchard JK. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet 2008, 4:e1000214.
42. Fairfax BP, Makino S, Radhakrishnan J, Plant K, Leslie S, Dilthey A, Ellis P, Langford C, Vannberg FO, Knight JC. Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. Nature Genet 2012, 44:502-510.
43. Cruz-Tapias P, Perez-Fernandez OM, Rojas-Villarraga A, Rodriguez-Rodriguez A, Arango MT, Anaya JM. Shared HLA class II in six autoimmune diseases in Latin America: a meta-analysis. Autoimmune Dis 2012, 2012:569728.
44. Lehner B. Genotype to phenotype: lessons from model organisms for human genetics. Nature Rev Genet 2013, 14:168-178.
45. Mori M, Yamada R, Kobayashi K, Kawaida R, Yamamoto K. Ethnic differences in allele frequency of autoimmune-disease-associated SNPs. J Hum Genet 2005, 50:264-266.
46. Molineros JE, Maiti AK, Sun C, Looger LL, Han S, Kim-Howard X, Glenn S, Adler A, Kelly JA, Niewold TB, Gilkeson GS, Brown EE, Alarcón GS, Edberg JC, Petri M, Ramsey-Goldman R, Reveille JD, Vilá LM, Freedman BI, Tsao BP, Criswell LA, Jacob CO, Moore JH, Vyse TJ, Langefeld CL, Guthridge JM, Gaffney PM, Moser KL, Scofield RH, Alarcón-Riquelme ME, et al. Admixture mapping in lupus identifies multiple functional variants within IFIH1 associated with apoptosis, inflammation, and autoantibody production. PLoS Genet 2013, 9:e1003222.
47. Boechat AL, Ogusku MM, Sadahiro A, Dos Santos MC. Association between the PTPN22 1858C/T gene polymorphism and tuberculosis resistance. Infect Genet Evol 2013, 16:310-313.
48. Seldin MF, Pasaniuc B, Price AL. New approaches to disease mapping in admixed populations. Nature Rev Genet 2011, 12:523-528.
49. Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nature Rev Genet 2012, 13:260-270.
50. Markle JG, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U, von Bergen M, McCoy KD, Macpherson AJ, Danska JS. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science 2013, 339:1084-1088.
51. Cho JH, Gregersen PK. Genomics and the multifactorial nature of human autoimmune disease. N Engl J Med 2011, 365:1612-1623.
52. Castiblanco J, Anaya JM. The nature and nurture of common autoimmunity. Ann N Y Acad Sci 2007, 1109:1-8.
53. Nsengimana J, Bishop DT. Design considerations for genetic linkage and association studies. Methods Mol Biol 2012, 850:237-262.
54. Hunt KA, Mistry V, Bockett NA, Ahmad T, Ban M, Barker JN, Barrett JC, Blackburn H, Brand O, Burren O, Capon F, Compston A, Gough SC, Jostins L, Kong Y, Lee JC, Lek M, MacArthur DG, Mansfield JC, Mathew CG, Mein CA, Mirza M, Nutland S, Onengut-Gumuscu S, Papouli E, Parkes M, Rich SS, Sawcer S, Satsangi J, Simmonds MJ, et al. Negligible impact of rare autoimmune-locus coding-region variants on missing heritability. Nature 2013, 498:232-235.
55. Voight BF, Cotsapas C. Human genetics offers an emerging picture of common pathways and mechanisms in autoimmunity. Curr Opin Immunol 2012, 24:552-557.
56. Maecker HT, Lindstrom TM, Robinson WH, Utz PJ, Hale M, Boyd SD, Shen-Orr SS, Fathman CG. New tools for classification and monitoring of autoimmune diseases. Nature Rev Rheumatol 2012, 8:317-328.
57. Knaup P, Ammenwerth E, Brandner R, Brigl B, Fischer G, Garde S, Lang E, Pilgram R, Ruderich F, Singer R, Wolff AC, Haux R, Kulikowski C. Towards clinical bioinformatics: advancing genomic medicine with informatics methods and tools. Methods Inf Med 2004, 43:302-307.
58. Kann MG. Advances in translational bioinformatics: computational approaches for the hunting of disease genes. Brief Bioinform 2010, 11:96-110.
59. Feero WG, Guttmacher AE, Collins FS. Genomic medicine-an updated primer. N Engl J Med 2010, 362:2001-2011.
60. Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, O'Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, Boyle AP, Kasowski M, Grubert F, Seki S, Garcia M, Whirl-Carrillo M, Gallardo M, Blasco MA, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 2012, 148:1293-1307.
61. Bernal JE. Human diversity in Colombia. Science 1995, 267:774.