Evaluation of European coeliac disease risk variants in a north Indian population

European Journal of Human Genetics

Volumn 23, Issue 4, 2015, Pages 530-535

  Senapati, Sabyasachi ^a   Gutierrez Achury, Javier ^b   Sood, Ajit ^c   Midha, Vandana ^c   Szperl, Agata ^b   Romanos, Jihane ^b   Zhernakova, Alexandra ^b   Franke, Lude ^b   Alonso, Santos ^d   Thelma, B K ^a   Wijmenga, Cisca ^b   Trynka, Gosia ^b,e  

^a UNIVERSITY OF DELHI   (India)

^b UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

^c DAYANAND MEDICAL COLLEGE AND HOSPITAL   (India)

^d UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

^e HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HLA ANTIGEN; INTERLEUKIN 12P35; 6 PHOSPHOFRUCTO 2 KINASE; CARRIER PROTEIN; FAS LIGAND; FASLG PROTEIN, HUMAN; ICOSLG PROTEIN, HUMAN; IL12A PROTEIN, HUMAN; INDUCIBLE T CELL COSTIMULATOR LIGAND; ISOENZYME; PFKFB3 PROTEIN, HUMAN; PRKCQ PROTEIN, HUMAN; PROTEIN KINASE C; SCHIP1 PROTEIN, HUMAN; TNFSF18 PROTEIN, HUMAN; TRANSCRIPTION FACTOR; TUMOR NECROSIS FACTOR; ZMIZ1 PROTEIN, HUMAN;

ALLELE; ARTICLE; CELIAC DISEASE; CONSANGUINITY; CONTROLLED STUDY; GENE LOCUS; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HOMOZYGOSITY; HUMAN; INDIA; INDIAN; MAJOR CLINICAL STUDY; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; CAUCASIAN; CHROMOSOMAL MAPPING; GENETIC PREDISPOSITION; GENETICS; GENOTYPING TECHNIQUE; REPRODUCIBILITY; RISK FACTOR;

ALLELES; CARRIER PROTEINS; CELIAC DISEASE; CHROMOSOME MAPPING; EUROPEAN CONTINENTAL ANCESTRY GROUP; FAS LIGAND PROTEIN; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOTYPING TECHNIQUES; HUMANS; INDIA; INDUCIBLE T-CELL CO-STIMULATOR LIGAND; INTERLEUKIN-12 SUBUNIT P35; ISOENZYMES; PHOSPHOFRUCTOKINASE-2; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN KINASE C; REPRODUCIBILITY OF RESULTS; RISK FACTORS; TRANSCRIPTION FACTORS; TUMOR NECROSIS FACTORS;

EID: 84924661068     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2014.137     Document Type: Article

References (63)

1. Welter D, Macarthur J, Morales J et al: The NHGRI GWAS catalog, a curated resource of SNP-trait associations. Nucleic Acids Res 2014; 42: D1001-D1006.
2. Ng MC, Saxena R, Li J et al: Transferability and fine mapping of type 2 diabetes loci in African Americans: the Candidate Gene Association Resource Plus Study. Diabetes 2013; 62: 965-976.
3. Liu CT, Ng MC, Rybin D et al: Transferability and fine-mapping of glucose and insulin quantitative trait loci across populations: CARe, the Candidate Gene Association Resource. Diabetologia 2012; 55: 2970-2984.
4. Teslovich TM, Musunuru K, Smith AV et al: Biological, clinical and population relevance of 95 loci for blood lipids. Nature 2010; 466: 707-713.
5. Bustamante CD, Burchard EG, De la Vega FM: Genomics for the world. Nature 2011; 475: 163-165.
6. Makharia GK, Verma AK, Amarchand R et al: Prevalence of celiac disease in the northern part of India: a community based study. J Gastroenterol Hepatol 2011; 26: 894-900.
7. Gutierrez-Achury J, Coutinho de Almeida R, Wijmenga C: Shared genetics in coeliac disease and other immune-mediated diseases. J Intern Med 2011; 269: 591-603.
8. 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.
9. Hunt KA, Zhernakova A, Turner G et al: Newly identified genetic risk variants for celiac disease related to the immune response. Nat Genet 2008; 40: 395-402.
10. Dubois PC, Trynka G, Franke L et al: Multiple common variants for celiac disease influencing immune gene expression. Nat Genet 2010; 42: 295-302.
11. Trynka G, Hunt KA, Bockett NA et al: Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat Genet 2011; 43: 1193-1201.
12. Reich D, Thangaraj K, Patterson N, Price AL, Singh L: Reconstructing Indian population history. Nature 2009; 461: 489-494.
13. Husby S, Koletzko S, Korponay-Szabo IR et al: European Society for Pediatric Gastroenterology, Hepatology, and Nutrition guidelines for the diagnosis of coeliac disease. J Pediatr Gastroenterol Nutr 2012; 54: 136-160.
14. Hinrichs AS, Karolchik D, Baertsch R et al: The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 2006; 34: D590-D598.
15. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D: Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006; 38: 904-909.
16. Patterson N, Price AL, Reich D: Population structure and eigenanalysis. PLoS Genet 2006; 2: e190.
17. Narang A, Jha P, Rawat V et al: Recent admixture in an Indian population of African ancestry. Am J Hum Genet 2011; 89: 111-120.
18. Metspalu M, Romero IG, Yunusbayev B et al: Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia. Am J Hum Genet 2011; 89: 731-744.
19. Moorjani P, Thangaraj K, Patterson N et al: Genetic evidence for recent population mixture in India. Am J Hum Genet 2013; 93: 422-438.
20. Lencz T, Lambert C, DeRosse P et al: Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci USA 2007; 104: 19942-19947.
21. McQuillan R, Leutenegger AL, Abdel-Rahman R et al: Runs of homozygosity in European populations. Am J Hum Genet 2008; 83: 359-372.
22. Keller MC, Simonson MA, Ripke S et al: Runs of homozygosity implicate autozygosity as a schizophrenia risk factor. PLoS Genet 2012; 8: e1002656.
23. Purcell S, Neale B, Todd-Brown K et al: PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559-575.
24. Waters KM, Stram DO, Hassanein MT et al: Consistent association of type 2 diabetes risk variants found in europeans in diverse racial and ethnic groups. PLoS Genet 2010; 6: pii: e1001078.
25. Kurreeman F, Liao K, Chibnik L et al: Genetic basis of autoantibody positive and negative rheumatoid arthritis risk in a multi-ethnic cohort derived from electronic health records. Am J Hum Genet 2011; 88: 57-69.
26. Need AC, Goldstein DB: Next generation disparities in human genomics: concerns and remedies. Trends Genet 2009; 25: 489-494.
27. Negi S, Juyal G, Senapati S et al: A genome-wide association study reveals ARL15, a novel non-HLA susceptibility gene for rheumatoid arthritis in north Indians. Arthritis Rheum 2013; 65: 3026-3035.
28. Tabassum R, Chauhan G, Dwivedi OP et al: Genome-wide association study for type 2 diabetes in Indians identifies a new susceptibility locus at 2q21. Diabetes 2013; 62: 977-986.
29. Okada Y, Wu D, Trynka G et al: Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature 2014; 506: 376-381.
30. Brar P, Lee AR, Lewis SK, Bhagat G, Green PH: Celiac disease in African-Americans. Digest Dis Sci 2006; 51: 1012-1015.
31. Almeida RC, Gandolfi L, De Nazare Klautau-Guimaraes M et al: Does celiac disease occur in Afro-derived Brazilian populations? Am J Hum Biol 2012; 24: 710-712.
32. Remes-Troche JM, Ramirez-Iglesias MT, Rubio-Tapia A, Alonso-Ramos A, Velazquez A, Uscanga LF: Celiac disease could be a frequent disease in Mexico: prevalence of tissue transglutaminase antibody in healthy blood donors. J Clin Gastroenterol 2006; 40: 697-700.
33. Perez-Bravo F, Araya M, Mondragon A et al: Genetic differences in HLA-DQA1∗ and DQB1∗ allelic distributions between celiac and control children in Santiago, Chile. Hum Immunol 1999; 60: 262-267.
34. Akbari MR, Mohammadkhani A, Fakheri H et al: Screening of the adult population in Iran for coeliac disease: comparison of the tissue-transglutaminase antibody and anti-endomysial antibody tests. Eur J Gastroenterol Hepatol 2006; 18: 1181-1186.
35. Srivastava A, Yachha SK, Mathias A, Parveen F, Poddar U, Agrawal S: Prevalence, human leukocyte antigen typing and strategy for screening among Asian first-degree relatives of children with celiac disease. J Gastroenterol Hepatol 2010; 25: 319-324.
36. El-Akawi ZJ, Al-Hattab DM, Migdady MA: Frequency of HLA-DQA1∗0501 and DQB1∗0201 alleles in patients with coeliac disease, their first-degree relatives and controls in Jordan. Ann Tropl Paediatr 2010; 30: 305-309.
37. Bondar C, Plaza-Izurieta L, Fernandez-Jimenez N et al: THEMIS and PTPRK in celiac intestinal mucosa: coexpression in disease and after in vitro gliadin challenge. Eur J Hum Genet 2013; 22: 358-362.
38. Sandholm N, Salem RM, McKnight AJ et al: New susceptibility loci associated with kidney disease in type 1 diabetes. PLoS Genet 2012; 8: e1002921.
39. Stahl EA, Raychaudhuri S, Remmers EF et al: Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat Genet 2010; 42: 508-514.
40. 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.
41. Bratanic N, Smigoc Schweiger D, Mendez A, Bratina N, Battelino T, Vidan-Jeras B: An influence of HLA-A, B, DR, DQ, and MICA on the occurrence of celiac disease in patients with type 1 diabetes. Tissue Antigens 2010; 76: 208-215.
42. Tinto N, Ciacci C, Calcagno G et al: Increased prevalence of celiac disease without gastrointestinal symptoms in adults MICA 5.1 homozygous subjects from the Campania area. Digest Liver Dis 2008; 40: 248-252.
43. Martin-Pagola A, Ortiz L, Perez de Nanclares G, Vitoria JC, Castano L, Bilbao JR: Analysis of the expression of MICA in small intestinal mucosa of patients with celiac disease. J Clin Immunol 2003; 23: 498-503.
44. Fernandez L, Fernandez-Arquero M, Gual L et al: Triplet repeat polymorphism in the transmembrane region of the MICA gene in celiac disease. Tissue Antigens 2002; 59: 219-222.
45. Kumar V, Kato N, Urabe Y et al: Genome-wide association study identifies a susceptibility locus for HCV-induced hepatocellular carcinoma. Nat Genet 2011; 43: 455-458.
46. Hou S, Yang Z, Du L et al: Identification of a susceptibility locus in STAT4 for Behcet's disease in Han Chinese in a genome-wide association study. Arthritis Rheum 2012; 64: 4104-4113.
47. Eleftherohorinou H, Hoggart CJ, Wright VJ, Levin M, Coin LJ: Pathway-driven gene stability selection of two rheumatoid arthritis GWAS identifies and validates new susceptibility genes in receptor mediated signalling pathways. Hum Mol Genet 2011; 20: 3494-3506.
48. Chen SJ, Chao YL, Chen CY et al: Prevalence of autoimmune diseases in in-patients with schizophrenia: nationwide population-based study. Br J Psychiatry 2012; 200: 374-380.
49. Ludvigsson JF, Osby U, Ekbom A, Montgomery SM: Coeliac disease and risk of schizophrenia and other psychosis: a general population cohort study. Scand J Gastroenterol 2007; 42: 179-185.
50. Anderson CA, Boucher G, Lees CW et al: Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet 2011; 43: 246-252.
51. Athanasiu L, Mattingsdal M, Kahler AK et al: Gene variants associated with schizophrenia in a Norwegian genome-wide study are replicated in a large European cohort. J Psychiatr Res 2010; 44: 748-753.
52. Barrett JC, Clayton DG, Concannon P et al: Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet 2009; 41: 703-707.
53. Chen DT, Jiang X, Akula N et al: Genome-wide association study meta-analysis of European and Asian-ancestry samples identifies three novel loci associated with bipolar disorder. Mol Psychiatry 2013; 18: 195-205.
54. Cooper JD, Smyth DJ, Smiles AM et al: Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. Nat Genet 2008; 40: 1399-1401.
55. Ferreira MA, O'Donovan MC, Meng YA et al: Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder. Nat Genet 2008; 40: 1056-1058.
56. Franke A, McGovern DP, Barrett JC et al: Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet 2010; 42: 1118-1125.
57. Hsu YH, Zillikens MC, Wilson SG et al: An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility loci for osteoporosis-related traits. PLoS Genet 2010; 6: e1000977.
58. Liu Y, Blackwood DH, Caesar S et al: Meta-analysis of genome-wide association data of bipolar disorder and major depressive disorder. Mol Psychiatry 2011; 16: 2-4.
59. Rajaraman P, Melin BS, Wang Z et al: Genome-wide association study of glioma and meta-analysis. Hum Genet 2012; 131: 1877-1888.
60. Raychaudhuri S, Remmers EF, Lee AT et al: Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nat Genet 2008; 40: 1216-1223.
61. Sanson M, Hosking FJ, Shete S et al: Chromosome 7p11.2 (EGFR) variation influences glioma risk. Hum Mol Genet 2011; 20: 2897-2904.
62. Shete S, Hosking FJ, Robertson LB et al: Genome-wide association study identifies five susceptibility loci for glioma. Nat Genet 2009; 41: 899-904.
63. Sklar P, Ripke S, Scott LJ et al: Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. Nat Genet 2011; 43: 977-983.