Genome-Wide Diet-Gene Interaction Analyses for Risk of Colorectal Cancer

PLoS Genetics

Volumn 10, Issue 4, 2014, Pages

  Figueiredo, Jane C ^a   Hsu, Li ^b   Hutter, Carolyn M ^c   Lin, Yi ^b   Campbell, Peter T ^d   Baron, John A ^e   Berndt, Sonja I ^c   Jiao, Shuo ^b   Casey, Graham ^a   Fortini, Barbara ^a   Chan, Andrew T ^f,g   Cotterchio, Michelle ^h   Lemire, Mathieu ⁱ   Gallinger, Steven ^j   Harrison, Tabitha A ^b   Le Marchand, Loic ^k   Newcomb, Polly A ^b   Slattery, Martha L ^l   Caan, Bette J ^m   Carlson, Christopher S ^b   Zanke, Brent W ⁿ   Rosse, Stephanie A ^b   Brenner, Hermann ^o   Giovannucci, Edward L ^g   Wu, Kana ^p   Chang Claude, Jenny ^o   Chanock, Stephen J ^c   Curtis, Keith R ^b   Duggan, David ^q   Gong, Jian ^b   Haile, Robert W ^r   Hayes, Richard B ^s   Hoffmeister, Michael ^o   Hopper, John L ^t   Jenkins, Mark A ^t   Kolonel, Laurence N ^k   Qu, Conghui ^b   Rudolph, Anja ^o   Schoen, Robert E ^u   Schumacher, Fredrick R ^a   Seminara, Daniela ^c   Stelling, Deanna L ^b   Thibodeau, Stephen N ^v   Thornquist, Mark ^b   Warnick, Greg S ^b   Henderson, Brian E ^a   Ulrich, Cornelia M ^b,o   Gauderman, W James ^a   Potter, John D ^b,w   White, Emily ^b   Peters, Ulrike ^b   more..

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

^c NATIONAL CANCER INSTITUTE   (United States)

^d AMERICAN CANCER SOCIETY   (United States)

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

^f MASSACHUSETTS GENERAL HOSPITAL   (United States)

^g BRIGHAM AND WOMEN S HOSPITAL   (United States)

^h CANCER CARE ONTARIO   (Canada)

ⁱ ONTARIO INSTITUTE FOR CANCER RESEARCH   (Canada)

^j TORONTO GENERAL HOSPITAL   (Canada)

^k UNIVERSITY OF HAWAII CANCER CENTER   (United States)

^l UNIVERSITY OF UTAH HEALTH SCIENCES CENTER   (United States)

^m DIVISION OF RESEARCH   (United States)

ⁿ UNIVERSITY OF OTTAWA   (Canada)

^o GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^p HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^q TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

^r STANFORD CANCER INSTITUTE   (United States)

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

^t UNIVERSITY OF MELBOURNE   (Australia)

^u UNIVERSITY OF PITTSBURGH MEDICAL CENTER   (United States)

^v MAYO CLINIC   (United States)

^w MASSEY UNIVERSITY   (New Zealand)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER RISK; CASE CONTROL STUDY; CHROMOSOME; CHROMOSOME 10P14; COLORECTAL CANCER; CONTROLLED STUDY; DIETARY FIBER; DIETARY INTAKE; FRUIT; GENE FREQUENCY; GENE INTERACTION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; RED MEAT; SINGLE NUCLEOTIDE POLYMORPHISM; VEGETABLE; ADMINISTRATION AND DOSAGE; ADULT; AGED; COLORECTAL NEOPLASMS; DIET; FEMALE; GENETICS; MALE; MEAT; MIDDLE AGED; PROCEDURES; RISK; RISK FACTOR; YOUNG ADULT;

ADULT; AGED; CASE-CONTROL STUDIES; COLORECTAL NEOPLASMS; DIET; DIETARY FIBER; FEMALE; FRUIT; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MALE; MEAT; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK; RISK FACTORS; VEGETABLES; YOUNG ADULT;

EID: 84901304828     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004228     Document Type: Article

References (64)

1. Siegel R, Naishadham D, Jemal A, (2012) Cancer statistics, 2012. CA Cancer J Clin 62: 10-29.
2. Alexander DD, Cushing CA, (2011) Red meat and colorectal cancer: a critical summary of prospective epidemiologic studies. Obes Rev 12: e472-493.
3. Alexander DD, Miller AJ, Cushing CA, Lowe KA, (2010) Processed meat and colorectal cancer: a quantitative review of prospective epidemiologic studies. Eur J Cancer Prev 19: 328-341.
4. van Duijnhoven FJ, Bueno-De-Mesquita HB, Ferrari P, Jenab M, Boshuizen HC, et al. (2009) Fruit, vegetables, and colorectal cancer risk: the European Prospective Investigation into Cancer and Nutrition. The American journal of clinical nutrition 89: 1441-1452.
5. Wu QJ, Yang Y, Vogtmann E, Wang J, Han LH, et al. (2013) Cruciferous vegetables intake and the risk of colorectal cancer: a meta-analysis of observational studies. Annals of oncology: official journal of the European Society for Medical Oncology/ESMO 24: 1079-1087.
6. Nomura AM, Hankin JH, Henderson BE, Wilkens LR, Murphy SP, et al. (2007) Dietary fiber and colorectal cancer risk: the multiethnic cohort study. Cancer causes & control: CCC 18: 753-764.
7. Park Y, Hunter DJ, Spiegelman D, Bergkvist L, Berrino F, et al. (2005) Dietary fiber intake and risk of colorectal cancer: a pooled analysis of prospective cohort studies. JAMA: the journal of the American Medical Association 294: 2849-2857.
8. Dahm CC, Keogh RH, Spencer EA, Greenwood DC, Key TJ, et al. (2010) Dietary fiber and colorectal cancer risk: a nested case-control study using food diaries. Journal of the National Cancer Institute 102: 614-626.
9. Lin J, Zhang SM, Cook NR, Rexrode KM, Liu S, et al. (2005) Dietary intakes of fruit, vegetables, and fiber, and risk of colorectal cancer in a prospective cohort of women (United States). Cancer causes & control: CCC 16: 225-233.
10. Ollberding NJ, Wilkens LR, Henderson BE, Kolonel LN, Le Marchand L, (2012) Meat consumption, heterocyclic amines and colorectal cancer risk: the Multiethnic Cohort Study. International journal of cancer Journal international du cancer 131: E1125-1133.
11. Liu AY, Scherer D, Poole E, Potter JD, Curtin K, et al. (2013) Gene-diet-interactions in folate-mediated one-carbon metabolism modify colon cancer risk. Molecular nutrition & food research 57: 721-734.
12. Cotterchio M, Boucher BA, Manno M, Gallinger S, Okey AB, et al. (2008) Red meat intake, doneness, polymorphisms in genes that encode carcinogen-metabolizing enzymes, and colorectal cancer risk. Cancer epidemiology, biomarkers & prevention: a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 17: 3098-3107.
13. Figueiredo JC, Lewinger JP, Song C, Campbell PT, Conti DV, et al. (2011) Genotype-environment interactions in microsatellite stable/microsatellite instability-low colorectal cancer: results from a genome-wide association study. Cancer epidemiology, biomarkers & prevention: a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 20: 758-766.
14. Hutter CM, Chang-Claude J, Slattery ML, Pflugeisen BM, Lin Y, et al. (2012) Characterization of gene-environment interactions for colorectal cancer susceptibility loci. Cancer research 72: 2036-2044.
15. Hsu L, Jiao S, Dai JY, Hutter C, Peters U, et al. (2012) Powerful cocktail methods for detecting genome-wide gene-environment interaction. Genetic epidemiology 36: 183-194.
16. Gauderman WJ, Zhang P, Morrison JL, Lewinger JP, (2013) Finding novel genes by testing G×E interactions in a genome-wide association study. Genetic epidemiology 37: 603-613.
17. Dai JY, Kooperberg C, Leblanc M, Prentice RL, (2012) Two-stage testing procedures with independent filtering for genome-wide gene-environment interaction. Biometrika 99: 929-944.
18. Tenesa A, Farrington SM, Prendergast JG, Porteous ME, Walker M, et al. (2008) Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. Nat Genet 40: 631-637.
19. Tomlinson IP, Webb E, Carvajal-Carmona L, Broderick P, Howarth K, et al. (2008) A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3. Nat Genet 40: 623-630.
20. Broderick P, Carvajal-Carmona L, Pittman AM, Webb E, Howarth K, et al. (2007) A genome-wide association study shows that common alleles of SMAD7 influence colorectal cancer risk. Nat Genet 39: 1315-1317.
21. Tomlinson I, Webb E, Carvajal-Carmona L, Broderick P, Kemp Z, et al. (2007) A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21. Nat Genet 39: 984-988.
22. Zanke BW, Greenwood CM, Rangrej J, Kustra R, Tenesa A, et al. (2007) Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. Nat Genet 39: 989-994.
23. Houlston RS, Webb E, Broderick P, Pittman AM, Di Bernardo MC, et al. (2008) Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. Nat Genet 40: 1426-1435.
24. Jia WH, Zhang B, Matsuo K, Shin A, Xiang YB, et al. (2012) Genome-wide association analyses in east Asians identify new susceptibility loci for colorectal cancer. Nature genetics 45: 191-196.
25. Hosoya T, Maillard I, Engel JD, (2010) From the cradle to the grave: activities of GATA-3 throughout T-cell development and differentiation. Immunol Rev 238: 110-125.
26. Christophi GP, Rong R, Holtzapple PG, Massa PT, Landas SK, (2012) Immune markers and differential signaling networks in ulcerative colitis and Crohn's disease. Inflammatory bowel diseases 18: 2342-2356.
27. Gupta RB, Harpaz N, Itzkowitz S, Hossain S, Matula S, et al. (2007) Histologic inflammation is a risk factor for progression to colorectal neoplasia in ulcerative colitis: a cohort study. Gastroenterology 133: 1099-1105 quiz 1340-1091.
28. Chou J, Provot S, Werb Z, (2010) GATA3 in development and cancer differentiation: cells GATA have it!. Journal of cellular physiology 222: 42-49.
29. Nguyen AH, Tremblay M, Haigh K, Koumakpayi IH, Paquet M, et al. (2013) Gata3 antagonizes cancer progression in Pten-deficient prostates. Human molecular genetics 22: 2400-2410.
30. Zheng R, Blobel GA, (2010) GATA Transcription Factors and Cancer. Genes Cancer 1: 1178-1188.
31. Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, et al. (2013) ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic acids research 41: D56-63.
32. Hedlund M, Padler-Karavani V, Varki NM, Varki A, (2008) Evidence for a human-specific mechanism for diet and antibody-mediated inflammation in carcinoma progression. Proceedings of the National Academy of Sciences of the United States of America 105: 18936-18941.
33. Bennett SN, Caporaso N, Fitzpatrick AL, Agrawal A, Barnes K, et al. (2011) Phenotype harmonization and cross-study collaboration in GWAS consortia: the GENEVA experience. Genetic epidemiology 35: 159-173.
34. Fortier I, Doiron D, Burton P, Raina P, (2011) Invited commentary: consolidating data harmonization-how to obtain quality and applicability? American journal of epidemiology 174: 261-264 author reply 265-266.
35. Skol AD, Scott LJ, Abecasis GR, Boehnke M, (2006) Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nature genetics 38: 209-213.
36. Pearce CL, Rossing MA, Lee AW, Ness RB, Webb PM, et al. (2013) Combined and interactive effects of environmental and GWAS-identified risk factors in ovarian cancer. Cancer epidemiology, biomarkers & prevention: a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 22: 880-890.
37. Peters U, Jiao S, Schumacher FR, Hutter CM, Aragaki AK, et al. (2013) Identification of Genetic Susceptibility Loci for Colorectal Tumors in a Genome-Wide Meta-analysis. Gastroenterology 144: 799-e724, 799-807, e724.
38. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909.
39. Newcomb PA, Baron J, Cotterchio M, Gallinger S, Grove J, et al. (2007) Colon Cancer Family Registry: an international resource for studies of the genetic epidemiology of colon cancer. Cancer Epidemiol Biomarkers Prev 16: 2331-2343.
40. Slattery ML, Potter J, Caan B, Edwards S, Coates A, et al. (1997) Energy balance and colon cancer-beyond physical activity. Cancer research 57: 75-80.
41. Christen WG, Gaziano JM, Hennekens CH, (2000) Design of Physicians' Health Study II-a randomized trial of beta-carotene, vitamins E and C, and multivitamins, in prevention of cancer, cardiovascular disease, and eye disease, and review of results of completed trials. Annals of epidemiology 10: 125-134.
42. Prorok PC, Andriole GL, Bresalier RS, Buys SS, Chia D, et al. (2000) Design of the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial. Controlled clinical trials 21: 273S-309S.
43. Design of the Women's Health Initiative clinical trial and observational study. The Women's Health Initiative Study Group. Controlled clinical trials 19: 61-109.
44. Hoffmeister M, Raum E, Krtschil A, Chang-Claude J, Brenner H, (2009) No evidence for variation in colorectal cancer risk associated with different types of postmenopausal hormone therapy. Clinical pharmacology and therapeutics 86: 416-424.
45. Brenner H, Chang-Claude J, Seiler CM, Rickert A, Hoffmeister M, (2011) Protection from colorectal cancer after colonoscopy: a population-based, case-control study. Annals of internal medicine 154: 22-30.
46. Kury S, Buecher B, Robiou-du-Pont S, Scoul C, Sebille V, et al. (2007) Combinations of cytochrome P450 gene polymorphisms enhancing the risk for sporadic colorectal cancer related to red meat consumption. Cancer epidemiology, biomarkers & prevention: a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 16: 1460-1467.
47. Colditz GA, Hankinson SE, (2005) The Nurses' Health Study: lifestyle and health among women. Nature reviews Cancer 5: 388-396.
48. Giovannucci E, Rimm EB, Stampfer MJ, Colditz GA, Ascherio A, et al. (1994) Aspirin use and the risk for colorectal cancer and adenoma in male health professionals. Annals of internal medicine 121: 241-246.
49. Jiao S, Hsu L, Hutter CM, Peters U, (2011) The use of imputed values in the meta-analysis of genome-wide association studies. Genetic epidemiology 35: 597-605.
50. Woolf B, (1955) On estimating the relation between blood group and disease. Ann Hum Genet 19: 251-253.
51. Risch N, Merikangas K, (1996) The future of genetic studies of complex human diseases. Science 273: 1516-1517.
52. A haplotype map of the human genome. Nature 437: 1299-1320.
53. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
54. Hoggart CJ, Clark TG, De Iorio M, Whittaker JC, Balding DJ, (2008) Genome-wide significance for dense SNP and resequencing data. Genetic epidemiology 32: 179-185.
55. Pe'er I, Yelensky R, Altshuler D, Daly MJ, (2008) Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genetic epidemiology 32: 381-385.
56. Dudbridge F, Gusnanto A, (2008) Estimation of significance thresholds for genomewide association scans. Genetic epidemiology 32: 227-234.
57. Mukherjee B, Chatterjee N, (2008) Exploiting gene-environment independence for analysis of case-control studies: an empirical Bayes-type shrinkage estimator to trade-off between bias and efficiency. Biometrics 64: 685-694.
58. Kooperberg C, Leblanc M, (2008) Increasing the power of identifying gene×gene interactions in genome-wide association studies. Genetic epidemiology 32: 255-263.
59. Murcray CE, Lewinger JP, Gauderman WJ, (2009) Gene-environment interaction in genome-wide association studies. Am J Epidemiol 169: 219-226.
60. Roeder K, Wasserman L, (2009) Genome-Wide Significance Levels and Weighted Hypothesis Testing. Statistical science: a review journal of the Institute of Mathematical Statistics 24: 398-413.
61. Ionita-Laza I, McQueen MB, Laird NM, Lange C, (2007) Genomewide weighted hypothesis testing in family-based association studies, with an application to a 100K scan. American journal of human genetics 81: 607-614.
62. Piegorsch WW, Weinberg CR, Taylor JA, (1994) Non-hierarchical logistic models and case-only designs for assessing susceptibility in population-based case-control studies. Statistics in medicine 13: 153-162.
63. Dai JY, Kooperberg C, Leblanc M, (submitted) On two-stage hypothesis testing procedures via asymptotically independent statistics. J R Stat Soc Series B Stat Methodol.
64. R Development Core Team. 2010. R: A Language and Environment for Statistical Computing. Vienna, Austria.