Exome sequencing identifies DLG1 as a novel gene for potential susceptibility to Crohn's disease in a Chinese family study

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Xu, Shufang ^a   Zhou, Feng ^a,b   Tao, Jinsheng ^c   Song, Lu ^a   Siew Chien, N G ^d   Wang, Xiaobing ^a   Chen, Liping ^a,b   Yi, Fengming ^a   Ran, Zhihua ^e   Zhou, Rui ^b   Xia, Bing ^a,b  

^a WUHAN UNIVERSITY   (China)

^b Hubei Cancer Clinical Study Center   (China)

^c BGI SHENZHEN   (China)

^d CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

^e SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; CYTOSINE; DISCS LARGE HOMOLOG 1; GUANINE; MEMBRANE PROTEIN; T LYMPHOCYTE RECEPTOR; TYROSINE; UNCLASSIFIED DRUG; DLG1 PROTEIN, HUMAN; SIGNAL TRANSDUCING ADAPTOR PROTEIN;

ADOLESCENT; ADULT; ARTICLE; BIOINFORMATICS; CELL POLARITY; CELL PROLIFERATION; CONTROLLED STUDY; CROHN DISEASE; DLG1 GENE; EXOME; EXON; FAMILY STUDY; FEMALE; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCUS; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; HAN CHINESE; HIGH RISK PATIENT; HOMOZYGOSITY; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; MALE; MONOZYGOTIC TWINS; PATHOGENESIS; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; T LYMPHOCYTE; ULCERATIVE COLITIS; CASE CONTROL STUDY; CHINA; GENETIC PREDISPOSITION; GENETICS; INDEL MUTATION; MIDDLE AGED; NUCLEOTIDE SEQUENCE; YOUNG ADULT;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; ADOLESCENT; ADULT; BASE SEQUENCE; CASE-CONTROL STUDIES; CHINA; CROHN DISEASE; DNA MUTATIONAL ANALYSIS; EXOME; FEMALE; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; HUMANS; INDEL MUTATION; MALE; MEMBRANE PROTEINS; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; YOUNG ADULT;

EID: 84903317884     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0099807     Document Type: Article

References (45)

1. Van Assche G, Dignass A, Panes J, Beaugerie L, Karagiannis J, et al. (2010) The second European evidence-based Consensus on the diagnosis and management of Crohn's disease: Definitions and diagnosis. J Crohns Colitis 4: 7-27.
2. Mowat C, Cole A, Windsor A, Ahmad T, Arnott I, et al. (2011) Guidelines for the management of inflammatory bowel disease in adults. Gut 60: 571-607.
3. Freeman HJ (2002) Familial Crohn's disease in single or multiple first-degree relatives. J Clin Gastroenterol 35: 9-13.
4. Brant SR (2011) Update on the heritability of inflammatory bowel disease: the importance of twin studies. Inflamm Bowel Dis 17: 1-5.
5. Majewski J, Schwartzentruber J, Lalonde E, Montpetit A, Jabado N (2011) What can exome sequencing do for you? J Med Genet 48: 580-589.
6. Teer JK, Mullikin JC (2010) Exome sequencing: the sweet spot before whole genomes. Hum Mol Genet 19: R145-151.
7. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, et al. (2009) Finding the missing heritability of complex diseases. Nature 461: 747-753.
8. Nazarian A, Sichtig H, Riva A (2012) Knowledge-Based Method for Association Studies on Complex Diseases. PLoS One 7: e44162.
9. Gilissen C, Hoischen A, Brunner HG, Veltman JA (2012) Disease gene identification strategies for exome sequencing. Eur J Hum Genet 20: 490-497.
10. Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, et al. (2011) Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med 13: 255-262.
11. Mao H, Yang W, Lee PP, Ho MH, Yang J, et al. (2012) Exome sequencing identifies novel compound heterozygous mutations of IL-10 receptor 1 in neonatal-onset Crohn's disease. Genes Immun 13: 437-442.
12. Christodoulou K, Wiskin AE, Gibson J, Tapper W, Willis C, et al. (2013) Next generation exome sequencing of paediatric inflammatory bowel disease patients identifies rare and novel variants in candidate genes. Gut 62: 977-984.
13. Li R, Yu C, Li Y, Lam TW, Yiu SM, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
14. Li R, Li Y, Fang X, Yang H, Wang J, et al. (2009) SNP detection for massively parallel whole-genome resequencing. Genome Re Li R, Li Y, Fang X, Yang H, Wang J, search 19: 1124-1132.
15. Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.
16. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The genome analysis toolkit: a MapReduc framework for analyzing next-generation DNA sequencing data. Genome Research 20: 1297-1303.
17. Wang J, Wang W, Li R, Li Y, Tian G, et al. (2008) The diploid genome sequence of an Asian individual. Nature 456: 60-65.
18. Cho JH, Brant SR (2011) Recent insights into the genetics of inflammatory bowel disease. Gastroenterology 140: 1704-1712.
19. O'Neill AK, Gallegos LL, Justilien V, Garcia EL, Leitges M, et al. (2011) Protein kinase Cα promotes cell migration through a PDZ-dependent interaction with its novel substrate discs large homolog 1 (DLG1). J Biol Chem 286: 43559-43568.
20. Humphries LA, Shaffer MH, Sacirbegovic F, Tomassian T, McMahon KA, et al. (2012) Characterization of in vivo Dlg1 deletion on T cell development and function. PLoS One 7: e45276.
21. Xavier R, Rabizadeh S, Ishiguro K, Andre N, Ortiz JB, et al. (2004) Discs large (Dlg1) complexes in lymphocyte activation. J Cell Biol 166: 173-178. (Pubitemid 38988770)
22. Gmyrek GB, Graham DB, Sandoval GJ, Blaufuss GS, Akilesh HM, et al. (2013) Polarity gene discs large homolog 1 regulates the generation of memory T cells. Eur J Immunol 43: 1185-1194.
23. Chatterjee S, Seifried L, Feigin ME, Gibbons DL, Scuoppo C, et al. (2012) Dysregulation of cell polarity proteins synergize with oncogenes or the microenvironment to induce invasive behavior in epithelial cells. PLoS One 7: e34343.
24. Surena AL, de Faria GP, Studler JM, Peiretti F, Pidoux M, et al. (2009) DLG1/ SAP97 modulates transforming growth factor alpha bioavailability. Biochim Biophys Acta 1793: 264-272.
25. Strober W, Fuss IJ (2011) Proinflammatory cytokines in the pathogenesis of inflammatory bowel diseases. Gastroenterology 140: 1756-1767.
26. MacDonald TT, Monteleone I, Fantini MC, Monteleone G. (2011) Regulation of homeostasis and inflammation in the intestine. Gastroenterology 140: 1768-1775.
27. Plevy SE, Targan SR (2011) Future therapeutic approaches for inflammatory bowel diseases. Gastroenterology 140: 1838-1846.
28. Danese S (2012) New therapies for inflammatory bowel disease: from the bench to the bedside. Gut 61: 918-932.
29. McClellan J, King MC (2010) Genetic heterogeneity in human disease. Cell 141: 210-217.
30. Altshuler D, Daly MJ, Lander ES (2008) Genetic mapping in human disease. Science 322: 881-888.
31. Zhao J, Ng SC, Lei Y, Yi F, Li J, et al. (2013) First Prospective, Population-Based Inflammatory Bowel Disease Incidence Study in Mainland of China: The Emergence of "Western" Disease. Inflamm Bowel Dis 19: 1839-1845.
32. Ng SC, Tang W, Ching JY, Wong M, Chow CM, et al. (2013) Incidence and Phenotype of Inflammatory Bowel Disease Based on Results From the Asia-Pacific Crohn's and Colitis Epidemiology Study. Gastroenterology 145: 158-165.
33. Yi F, Chen M, Huang M, Li J, Zhao J, et al. (2012) The trend in newly diagnosed Crohn's disease and extraintestinal manifestations of Crohn's disease in central China: a retrospective study of a single center. Eur J Gastroenterol Hepatol 24: 1424-1429.
34. Franke A, McGovern DP, Barrett JC, Wang K, Radford-Smith GL, et al. (2010) Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet 42: 1118-1125.
35. Clarke AJ, Cooper DN (2010) GWAS: heritability missing in action? Eur J Hum Genet 18: 859-861.
36. Gibson G. (2012) Rare and common variants: twenty arguments. Nat Rev Genet 13: 135-145.
37. Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, et al. (2012) Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337: 64-69.
38. Ng PC, Henikoff S (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 31: 3812-3814. (Pubitemid 37442253)
39. Schwarz JM, Rödelsperger C, Schuelke M, Seelow D (2010) MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods 7: 575-576.
40. Liu X, Jian X, Boerwinkle E (2011) dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat 32: 894-899.
41. Brunham LR, Hayden MR (2013) Hunting human disease genes: lessons from the past, challenges for the future. Hum Genet 132: 603-617.
42. Glocker EO, Frede N, Perro M, Sebire N, Elawad M, et al. (2010) Infant colitis-it's in the genes. Lancet 376: 1272.
43. Glocker EO, Kotlarz D, Boztug K, Gertz EM, Schäffer AA, et al. (2009) Inflammatory bowel disease and mutations affecting the interleukin-10 receptor. N Engl J Med 361: 2033-2045.
44. Kevin J, Mitchell (2012) What is complex about complex disorders? Genome Biol 13: 237.
45. Gibson G. (2009) Decanalization and the origin of complex disease. Nat Rev Genet 10: 134-140.