A genome-wide association study identifies new susceptibility loci for esophageal adenocarcinoma and Barrett's esophagus

Nature Genetics

Volumn 45, Issue 12, 2013, Pages 1487-1493

  Levine, David M ^a   Ek, Weronica E ^b   Zhang, Rui ^a   Liu, Xinxue ^c   Onstad, Lynn ^d   Sather, Cassandra ^d   Lao Sirieix, Pierre ^c   Gammon, Marilie D ^e   Corley, Douglas A ^f,g   Shaheen, Nicholas J ^h   Bird, Nigel C ⁱ   Hardie, Laura J ^j   Murray, Liam J ^k   Reid, Brian J ^d   Chow, Wong Ho ^l   Risch, Harvey A ^m   Nyrén, Olof ⁿ   Ye, Weimin ⁿ   Liu, Geoffrey ^o   Romero, Yvonne ^p   Bernstein, Leslie ^q   Wu, Anna H ^r   Casson, Alan G ^s   Chanock, Stephen J ^t   Harrington, Patricia ^c   Caldas, Isabel ^c   Debiram Beecham, Irene ^c   Caldas, Carlos ^c   Hayward, Nicholas K ^b   Pharoah, Paul D ^c   Fitzgerald, Rebecca C ^c   MacGregor, Stuart ^b   Whiteman, David C ^b   Vaughan, Thomas L ^d   more..

^a UNIVERSITY OF WASHINGTON   (United States)

^b QIMR BERGHOFER MEDICAL RESEARCH INSTITUTE   (Australia)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d Fred Hutchinson Cancer Research Center   (United States)

^e IL   (United States)

^f DIVISION OF RESEARCH   (United States)

^g San Francisco Medical Center   (United States)

^h UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

ⁱ UNIVERSITY OF SHEFFIELD   (United Kingdom)

^j UNIVERSITY OF LEEDS   (United Kingdom)

^k QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^l UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^m YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁿ KAROLINSKA INSTITUTE   (Sweden)

^o PRINCESS MARGARET HOSPITAL   (Canada)

^p MAYO CLINIC   (United States)

^q CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

^r UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^s UNIVERSITY OF SASKATCHEWAN   (Canada)

^t NATIONAL CANCER INSTITUTE   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR FOXP1; UNCLASSIFIED DRUG;

ARTICLE; BARRETT ESOPHAGUS; BARX1 GENE; CANCER SUSCEPTIBILITY; CHROMOSOME 16; CRTC1 GENE; ESOPHAGEAL ADENOCARCINOMA; FOXF1 GENE; GENE ACTIVATION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; HUMAN; META ANALYSIS (TOPIC); PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR GENE; TUMOR SUPPRESSOR GENE;

ADENOCARCINOMA; BARRETT ESOPHAGUS; CASE-CONTROL STUDIES; ESOPHAGEAL NEOPLASMS; FEMALE; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84888320412     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.2796     Document Type: Article

References (39)

1. Jochem, V. J., Fuerst, P. A. & Fromkes, J. J. Familial Barrett's esophagus associated with adenocarcinoma. Gastroenterology 102, 1400-1402 (1992).
2. Crabb, D. W. et al. Familial gastroesophageal reflux and development of Barrett's esophagus. Ann. Intern. Med. 103, 52-54 (1985). (Pubitemid 15068499)
3. Poynton, A. R., Walsh, T. N., O'Sullivan, G. & Hennessy, T. P. Carcinoma arising in familial Barrett's esophagus. Am. J. Gastroenterol. 91, 1855-1856 (1996). (Pubitemid 26307199)
4. Romero, Y. et al. Familial aggregation of gastroesophageal reflux in patients with Barrett's esophagus and esophageal adenocarcinoma. Gastroenterology 113, 1449-1456 (1997). (Pubitemid 27461230)
5. Melzer, E., Shtoyerman, R., Appelman, Z. & Kashtan, H. Familial Barrett's adenocarcinoma. Am. J. Gastroenterol. 101, 677 (2006).
6. Groves, C., Jankowski, J., Barker, F. & Holdstock, G. A family history of Barrett's oesophagus: another risk factor Scand. J. Gastroenterol. 40, 1127-1128 (2005). (Pubitemid 41291365)
7. Trudgill, N. J., Kapur, K. C. & Riley, S. A. Familial clustering of reflux symptoms. Am. J. Gastroenterol. 94, 1172-1178 (1999). (Pubitemid 29214623)
8. Chak, A. et al. Identification of Barrett's esophagus in relatives by endoscopic screening. Am. J. Gastroenterol. 99, 2107-2114 (2004). (Pubitemid 39524698)
9. Fitzgerald, R. C. Complex diseases in gastroenterology and hepatology: GERD, Barrett's, and esophageal adenocarcinoma. Clin. Gastroenterol. Hepatol. 3, 529-537 (2005). (Pubitemid 40824745)
10. Amos, C. I. et al. Genome-wide association study identifies novel loci predisposing to cutaneous melanoma. Hum. Mol. Genet. 20, 5012-5023 (2011).
11. Gogarten, S. M. et al. GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies. Bioinformatics 28, 3329-3331 (2012).
12. Strange, A. et al. A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. Nat. Genet. 42, 985-990 (2010).
13. Willer, C. J., Li, Y. & Abecasis, G. R. METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics 26, 2190-2191 (2010).
14. Su, Z. et al. Common variants at the MHC locus and at chromosome 16q24. 1 predispose to Barrett's esophagus. Nat. Genet. 44, 1131-1136 (2012).
15. Ek, W. E. et al. Germline genetic contributions to risk for esophageal adenocarcinoma, Barrett's esophagus and gastroesophageal reflux. J. Natl. Cancer Inst. (in the press).
16. Gu, Y. et al. Altered LKB1/CREB-regulated transcription co-activator (CRTC) signaling axis promotes esophageal cancer cell migration and invasion. Oncogene 31, 469-479 (2012).
17. Montgomery, S. B. et al. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464, 773-777 (2010).
18. Cheung, L. W. T. et al. High frequency of PIK3R1 and PIK3R2 mutations in endometrial cancer elucidates a novel mechanism for regulation of PTEN protein stability. Cancer Discov. 1, 170-185 (2011).
19. Cortés, I. et al. p85phosphoinositide 3-kinase subunit regulates tumor progression. Proc. Natl. Acad. Sci. USA 109, 11318-11323 (2012).
20. Venturi, S. & Venturi, M. Iodine in evolution of salivary glands and in oral health. Nutr. Health 20, 119-134 (2009).
21. Jankowski, J., Hopwood, D. & Wormsley, K. G. Expression of epidermal growth factor, transforming growth factor and their receptor in gastro-oesophageal diseases. Dig. Dis. 11, 1-11 (1993).
22. Menke, V. et al. Functional single-nucleotide polymorphism of epidermal growth factor is associated with the development of Barrett's esophagus and esophageal adenocarcinoma. J. Hum. Genet. 57, 26-32 (2012).
23. Lanuti, M. et al. A functional epidermal growth factor (EGF) polymorphism, EGF serum levels, and esophageal adenocarcinoma risk and outcome. Clin. Cancer Res. 14, 3216-3222 (2008).
24. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
25. Elks, C. E. et al. Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. Nat. Genet. 42, 1077-1085 (2010).
26. Altarejos, J. Y. et al. The Creb1 coactivator Crtc1 is required for energy balance and fertility. Nat. Med. 14, 1112-1117 (2008).
27. Koon, H. B., Ippolito, G. C., Banham, A. H. & Tucker, P. W. FOXP1: a potential therapeutic target in cancer. Expert Opin. Ther. Targets 11, 955-965 (2007). (Pubitemid 47061317)
28. Shu, W. et al. Foxp2 and Foxp1 cooperatively regulate lung and esophagus development. Development 134, 1991-2000 (2007). (Pubitemid 46939243)
29. Boyle, A. P. et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 22, 1790-1797 (2012).
30. Woo, J., Miletich, I., Kim, B.-M., Sharpe, P. T. & Shivdasani, R. A. Barx1-mediated inhibition of Wnt signaling in the mouse thoracic foregut controls tracheo-esophageal septation and epithelial differentiation. PLoS ONE 6, e22493 (2011).
31. Dura, P. et al. Barrett associated MHC and FOXF1 variants also increase esophageal carcinoma risk. Int. J. Cancer 133, 1751-1755 (2013).
32. Laurie, C. C. et al. Quality control and quality assurance in genotypic data for genome-wide association studies. Genet. Epidemiol. 34, 591-602 (2010).
33. Peiffer, D. A. et al. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res. 16, 1136-1148 (2006). (Pubitemid 44320401)
34. Price, A. L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904-909 (2006). (Pubitemid 44141658)
35. Novembre, J. et al. Genes mirror geography within Europe. Nature 456, 98-101 (2008).
36. R Development Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, 2006).
37. Zheng, X. et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28, 3326-3328 (2012).
38. Li, Y., Willer, C. J., Ding, J., Scheet, P. & Abecasis, G. R. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet. Epidemiol. 34, 816-834 (2010).
39. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007). (Pubitemid 47330214)