A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33

Nature Genetics

Volumn 42, Issue 3, 2010, Pages 224-228

  Petersen, Gloria M ^a   Amundadottir, Laufey ^b   Fuchs, Charles S ^c,d   Kraft, Peter ^e   Stolzenberg Solomon, Rachael Z ^b   Jacobs, Kevin B ^b,f,g   Arslan, Alan A ^h,i   Bueno De Mesquita, H Bas ^j,k   Gallinger, Steven ^l   Gross, Myron ^m   Helzlsouer, Kathy ⁿ   Holly, Elizabeth A ^o   Jacobs, Eric J ^p   Klein, Alison P ^q,r   Lacroix, Andrea ^s   Li, Donghui ^t   Mandelson, Margaret T ^s   Olson, Sara H ^t   Risch, Harvey A ^w   Zheng, Wei ^x   Albanes, Demetrius ^b   Bamlet, William R ^a   Berg, Christine D ^b   Boutron Ruault, Marie Christine ^y   Buring, Julie E ^d,z   Bracci, Paige M ^o   Canzian, Federico ^aa   Clipp, Sandra ^r   Cotterchio, Michelle ^ab   De Andrade, Mariza ^a   Duell, Eric J ^ac   Gaziano, J Michael ^d,ad   Giovannucci, Edward L ^d,e   Goggins, Michael ^q   Hallmans, Göran ^ae   Hankinson, Susan E ^d,e   Hassan, Manal ^t   Howard, Barbara ^af   Hunter, David J ^d,e   Hutchinson, Amy ^b,f   Jenab, Mazda ^ac   Kaaks, Rudolf ^aa   Kooperberg, Charles ^s   Krogh, Vittorio ^ag   Kurtz, Robert C ^v   Lynch, Shannon M ^b   McWilliams, Robert R ^a   Mendelsohn, Julie B ^b   Michaud, Dominique S ^e,v   Parikh, Hemang ^b   Patel, Alpa V ^p   Peeters, Petra H M ^k,v   Rajkovic, Aleksandar ^ai   Riboli, Elio ^ah   Rodriguez, Laudina ^aj   Seminara, Daniela ^b   Shu, Xiao Ou ^x   Thomas, Gilles ^b,y   Tjønneland, Anne ^ak   Tobias, Geoffrey S ^b   Trichopoulos, Dimitrios ^e,al   Van Den Eeden, Stephen K ^am   Virtamo, Jarmo ^an   Wactawski Wende, Jean ^ao   Wang, Zhaoming ^b,f   Wolpin, Brian M ^c,d   Yu, Herbert ^w   Yu, Kai ^b   Zeleniuch Jacquotte, Anne ^h,i   Fraumeni, Joseph F ^b   Hoover, Robert N ^b   Hartge, Patricia ^b   Chanock, Stephen J ^b,u,v   more..

^a Mayo Clinic   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

^d BRIGHAM AND WOMEN S HOSPITAL   (United States)

^e HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^f SAIC FREDERICK INC   (United States)

^g Bioinformed Consulting Services   (United States)

^h NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁱ NEW YORK UNIVERSITY   (United States)

^j NATIONAL INSTITUTE FOR PUBLIC HEALTH AND THE ENVIRONMENT   (Netherlands)

^k UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^l MOUNT SINAI HOSPITAL   (Canada)

^m UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

ⁿ MERCY MEDICAL CENTER   (United States)

^o UNIVERSITY OF CALIFORNIA   (United States)

^p AMERICAN CANCER SOCIETY   (United States)

^q JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^r JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^s Fred Hutchinson Cancer Research Center   (United States)

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

^u CENTER FOR HEALTH STUDIES   (United States)

^v MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^w YALE UNIVERSITY   (United States)

^x VANDERBILT INGRAM CANCER CENTER   (United States)

^y INSERM   (France)

^z HARVARD MEDICAL SCHOOL   (United States)

^aa GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^ab UNIVERSITY OF TORONTO   (Canada)

^ac CATALAN INSTITUTE OF ONCOLOGY   (Spain)

^ad VETERANS AFFAIRS MEDICAL CENTER   (United States)

^ae UMEÅ UNIVERSITY   (Sweden)

^af GEORGETOWN UNIVERSITY   (United States)

^ag NATIONAL CANCER INSTITUTE   (Italy)

^ah IMPERIAL COLLEGE LONDON   (United Kingdom)

^ai UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^aj Health and Health Care Services Council   (Spain)

^ak INSTITUTE OF CANCER EPIDEMIOLOGY   (Denmark)

^al BIOMEDICAL RESEARCH FOUNDATION   (Greece)

^am DIVISION OF RESEARCH   (United States)

^an NATIONAL PUBLIC HEALTH INSTITUTE   (Finland)

^ao UNIVERSITY AT BUFFALO   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BRCA1 PROTEIN; BRCA2 PROTEIN;

ARTICLE; CANCER SUSCEPTIBILITY; CELL CYCLE; CHROMOSOME 13Q; CHROMOSOME 1Q; CHROMOSOME 5Q; FOLLOW UP; GENE EXPRESSION; GENE MUTATION; GENETIC LINKAGE; GENOTYPE; HAPLOTYPE; HUMAN; KNOCKOUT MOUSE; NONHUMAN; PANCREAS CANCER; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM;

CARCINOMA; CASE-CONTROL STUDIES; CHROMOSOMES, HUMAN, PAIR 1; CHROMOSOMES, HUMAN, PAIR 13; CHROMOSOMES, HUMAN, PAIR 5; COHORT STUDIES; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; PANCREATIC NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77649188501     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.522     Document Type: Article

References (63)

1. Ferlay, J., Bray, F., Pisani, P. & Parkin, D.M. GLOBOCAN 2002: Cancer Incidence, Mortality and Prevalence Worldwide. IARC CancerBase vol.5 (IARCPress, Lyon, 2004).
2. Anderson, K.E.Mack, T.M. & Silverman, D. Cancer of the pancreas. in Cancer Epidemiology and Prevention (ed. Schottenfeld, D. & Fraumeni, J.J.) 721-762 (Oxford University Press, New York, (2006)).
3. Shi, C., Hruban, R.H. & Klein, A.P. Familial pancreatic cancer. Arch. Pathol. Lab. Med. 133, 365-374 (2009).
4. Jones, S. et al. Exomic sequencing identifes PALB2 as a pancreatic cancer susceptibility gene. Science 324, 217 (2009).
5. Tischkowitz, M.D. et al. Analysis of the gene coding for the BRCA2-interacting protein PALB2 in familial and sporadic pancreatic cancer. Gastroenterology 137, 1183-1186 (2009).
6. Amundadottir, L. et al. Genome-wide association study identifes variants in the ABO locus associated with susceptibility to pancreatic cancer. Nat. Genet. 41, 986-990 (2009).
7. Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661-678 (2007).
8. Li, Y., Sung, W.K. & Liu, J.J. Association mapping via regularized regression analysis of single-nucleotide-polymorphism haplotypes in variable-sized sliding windows. Am. J. Hum. Genet. 80, 705-715 (2007).
9. Yu, Z. & Schaid, D.J. Sequential haplotype scan methods for association analysis. Genet. Epidemiol. 31, 553-564 (2007).
10. Dong, J.T. & Chen, C. Essential role of KLF5 transcription factor in cell proliferation and differentiation and its implications for human diseases. Cell. Mol. Life Sci. 66, 2691-2706 (2009).
11. Nakamura, Y. et al. Kruppel-like factor 12 plays a signifcant role in poorly differentiated gastric cancer progression. Int. J. Cancer 125, 1859-1867 (2009).
12. Chen, C. et al. Defning a common region of deletion at 13q21 in human cancers. Genes Chromosom. Cancer 31, 333-344 (2001).
13. Baudis, M. & Cleary, M.L. Progenetix.net: an online repository for molecular cytogenetic aberration data. Bioinformatics 17, 1228-1229 (2001).
14. Kainu, T. et al. Somatic deletions in hereditary breast cancers implicate 13q21 as a putative novel breast cancer susceptibility locus. Proc. Natl. Acad. Sci. USA 97, 9603-9608 (2000).
15. Paré, J.F. et al. The fetoprotein transcription factor (FTF) gene is essential to embryogenesis and cholesterol homeostasis and is regulated by a DR4 element. J. Biol. Chem. 279, 21206-21216 (2004).
16. Lee, Y.K. & Moore, D.D. Liver receptor homolog-1, an emerging metabolic modulator. Front. Biosci. 13, 5950-5958 (2008).
17. Botrugno, O.A. et al. Synergy between LRH-1 and beta-catenin induces G1 cyclin-mediated cell proliferation. Mol. Cell 15, 499-509 (2004).
18. Yamamoto, K., Okamoto, A., Isonishi, S., Ochiai, K. & Ohtake, Y. A novel gene, CRR9, which was up-regulated in CDDP-resistant ovarian tumor cell line, was associated with apoptosis. Biochem. Biophys. Res. Commun. 280, 1148-1154 (2001). (Pubitemid 32924460)
19. Bodnar, A.G. et al. Extension of life-span by introduction of telomerase into normal human cells. Science 279, 349-352 (1998).
20. Hahn, W.C. et al. Creation of human tumor cells with defned genetic elements. Nature 400, 464-468 (1999).
21. Kim, N.W. et al. Specifc association of human telomerase activity with immortal cells and cancer. Science 266, 2011-2015 (1994).
22. Wang, Y. et al. Common 5p15.33 and 6p21.33 variants infuence lung cancer risk. Nat. Genet. 40, 1407-1409 (2008).
23. McKay, J.D. et al. Lung cancer susceptibility locus at 5p15.33. Nat. Genet. 40, 1404-1406 (2008).
24. Rafnar, T. et al. Sequence variants at the TERT-CLPTM1L locus associate with many cancer types. Nat. Genet. 41, 221-227 (2009).
25. Stacey, S.N. et al. New common variants affecting susceptibility to basal cell carcinoma. Nat. Genet. 41, 909-914 (2009).
26. Shete, S. et al. Genome-wide association study identifes fve susceptibility loci for glioma. Nat. Genet. 41, 899-904 (2009).
27. Landi, M.T. et al. A genome-wide association study of lung cancer identifes a region of chromosome 5p15 associated with risk for adenocarcinoma. Am. J. Hum. Genet. 85, 679-691 (2009).
28. Zienolddiny, S. et al. The TERT-CLPTM1L lung cancer susceptibility variant associates with higher DNA adduct formation in the lung. Carcinogenesis 30, 1368-1371 (2009).
29. Calado, R.T. et al. Constitutional hypomorphic telomerase mutations in patients with acute myeloid leukemia. Proc. Natl. Acad. Sci. USA 106, 1187-1192 (2009).
30. Savage, S.A. & Alter, B.P. Dyskeratosis congenita. Hematol. Oncol. Clin. North Am. 23, 215-231 (2009).
31. Yamaguchi, H. et al. Mutations in TERT, the gene for telomerase reverse transcriptase, in aplastic anemia. N. Engl. J. Med. 352, 1413-1424 (2005).
32. Calle, E.E. et al. The American Cancer Society Cancer Prevention Study II Nutrition Cohort: rationale, study design, and baseline characteristics. Cancer 94, 2490-2501 (2002)
33. The ATBC Cancer Prevention Study Group. The alpha-tocopherol, beta-carotene lung cancer prevention study: design, methods, participant characteristics, and compliance. Ann. Epidemiol. 4, 1-10 (1994).
34. Riboli, E. et al. European Prospective Investigation into Cancer and Nutrition (EPIC): study populations and data collection. Public Health Nutr. 5, 1113-1124 (2002). (Pubitemid 36313608)
35. Gallicchio, L. et al. Single nucleotide polymorphisms in infammation-related genes and mortality in a community-based cohort in Washington County, Maryland. Am. J. Epidemiol. 167, 807-813 (2008).
36. Wolpin, B.M. et al. Circulating insulin-like growth factor binding protein-1 and the risk of pancreatic cancer. Cancer Res. 67, 7923-7928 (2007).
37. Zeleniuch-Jacquotte, A. et al. Postmenopausal levels of sex hormones and risk of breast carcinoma in situ: results of a prospective study. Int. J. Cancer 114, 323-327 (2005).
38. Hayes, R.B. et al. Methods for etiologic and early marker investigations in the PLCO trial. Mutat. Res. 592, 147-154 (2005).
39. Anderson, G.L. et al. Implementation of the Women's Health Initiative study design. Ann. Epidemiol. 13, S5-S17 (2003).
40. Rexrode, K.M., Lee, I.M., Cook, N.R., Hennekens, C.H. & Buring, J.E. Baseline characteristics of participants in the Women's Health Study. J. Womens Health Gend. Based Med. 9, 19-27 (2000).
41. Eppel, A., Cotterchio, M. & Gallinger, S. Allergies are associated with reduced pancreas cancer risk: a population-based case-control study in Ontario, Canada. Int. J. Cancer 121, 2241-2245 (2007).
42. Duell, E.J. et al. Detecting pathway-based gene-gene and gene-environment interactions in pancreatic cancer. Cancer Epidemiol. Biomarkers Prev. 17, 1470-1479 (2008).
43. Hassan, M.M. et al. Risk factors for pancreatic cancer: case-control study. Am. J. Gastroenterol. 102, 2696-2707 (2007).
44. Olson, S.H. et al. Allergies, variants in IL-4 and IL-4R alpha genes, and risk of pancreatic cancer. Cancer Detect. Prev. 31, 345-351 (2007).
45. Risch, H.A. Etiology of pancreatic cancer, with a hypothesis concerning the role of N-nitroso compounds and excess gastric acidity. J. Natl. Cancer Inst. 95, 948-960 (2003).
46. McWilliams, R.R. et al. Polymorphisms in DNA repair genes, smoking, and pancreatic adenocarcinoma risk. Cancer Res. 68, 4928-4935 (2008).
47. Wigginton, J.E., Cutler, D.J. & Abecasis, G.R. A note on exact tests of Hardy-Weinberg equilibrium. Am. J. Hum. Genet. 76, 887-893 (2005).
48. de Bakker, P.I. et al. Practical aspects of imputation-driven meta-analysis of genome-wide association studies. Hum. Mol. Genet. 17, R122-R128 (2008).
49. Pritchard, J.K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945-959 (2000).
50. Frazer, K.A. et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861 (2007).
51. Thomas, G. et al. Multiple loci identifed in a genome-wide association study of prostate cancer. Nat. Genet. 40, 310-315 (2008).
52. Hunter, D.J. et al. A genome-wide association study identifes alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat. Genet. 39, 870-874 (2007).
53. Yu, K. et al. Population substructure and control selection in genome-wide association studies. PLoS One 3, e2551 (2008).
54. Price, A.L. et al. Principal components analysis corrects for stratifcation in genome-wide association studies. Nat. Genet. 38, 904-909 (2006).
55. Patterson, N., Price, A.L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).
56. Sun, L., Wilder, K. & McPeek, M.S. Enhanced pedigree error detection. Hum. Hered. 54, 99-110 (2002).
57. Clayton, D. Testing for association on the X chromosome. Biostatistics 9, 593-600 (2008).
58. Lettre, G., Lange, C. & Hirschhorn, J.N. Genetic model testing and statistical power in population-based association studies of quantitative traits. Genet. Epidemiol. 31, 358-362 (2007).
59. Higgins, J.P. & Thompson, S.G. Quantifying heterogeneity in a meta-analysis. Stat. Med. 21, 1539-1558 (2002).
60. Fearnhead, P. SequenceLDhot: detecting recombination hotspots. Bioinformatics 22, 3061-3066 (2006).
61. Fearnhead, P., Harding, R.M, Schneider, J.A, Myers, S. & Donnelly, P. Application of coalescent methods to reveal fne-scale rate variation and recombination hotspots. Genetics 167, 2067-2081 (2004).
62. Crawford, D.C. et al. Evidence for substantial fne-scale variation in recombination rates across the human genome. Nat. Genet. 36, 700-706 (2004).
63. Li, N.P. & Stephens, M. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165, 2213-2233 (2003).