Exploring multilocus associations of inflammation genes and colorectal cancer risk using hapConstructor

BMC Medical Genetics

Volumn 11, Issue 1, 2010, Pages

  Curtin, Karen ^a   Wolff, Roger K ^a   Herrick, Jennifer S ^a   Abo, Ryan ^a   Slattery, Martha L ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

I KAPPA B KINASE BETA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERLEUKIN 6; I KAPPA B KINASE; NFKB1 PROTEIN, HUMAN;

ADULT; AGED; ALLELE; ARTICLE; CANCER RISK; COLON CANCER; COLORECTAL CANCER; COMPUTER PROGRAM; CONTROLLED STUDY; CYTOKINE PRODUCTION; DISEASE ASSOCIATION; FEMALE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENOTYPE; HAPLOTYPE; HUMAN; INFLAMMATION; LOGISTIC REGRESSION ANALYSIS; MAJOR CLINICAL STUDY; MALE; MULTILOCUS ANALYSIS; RECTUM CANCER; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; CASE CONTROL STUDY; CLINICAL TRIAL; COLON TUMOR; GENE LOCUS; GENETICS; INTERVIEW; METABOLISM; MIDDLE AGED; MONTE CARLO METHOD; MULTICENTER STUDY; RECTUM TUMOR; RISK FACTOR; STATISTICAL MODEL;

ADULT; AGED; CASE-CONTROL STUDIES; COLONIC NEOPLASMS; FEMALE; GENETIC ASSOCIATION STUDIES; GENETIC LOCI; GENOTYPE; HAPLOTYPES; HUMANS; I-KAPPA B KINASE; INFLAMMATION; INTERLEUKIN-6; INTERVIEWS AS TOPIC; LOGISTIC MODELS; MALE; MIDDLE AGED; MONTE CARLO METHOD; NF-KAPPA B P50 SUBUNIT; POLYMORPHISM, SINGLE NUCLEOTIDE; RECTAL NEOPLASMS; RISK FACTORS; SOFTWARE;

EID: 78649537944     PISSN: None     EISSN: 14712350     Source Type: Journal    
DOI: 10.1186/1471-2350-11-170     Document Type: Article

References (32)

1. Abo R, Knight S, Wong J, Cox A, Camp NJ. hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework. Bioinformatics (Oxford, England) 2008, 24(18):2105-2107. 10.1093/bioinformatics/btn359, 2530882, 18653522.
2. hapConstructor Home Page. , http://www-genepi.med.utah.edu/Genie/hapConstructor.html
3. Slattery ML, Wolff RK, Herrick JS, Caan BJ, Potter JD. IL6 genotypes and colon and rectal cancer. Cancer Causes Control 2007, 18(10):1095-1105. 10.1007/s10552-007-9049-x, 2442470, 17694420.
4. Hussain SP, Harris CC. Inflammation and cancer: an ancient link with novel potentials. International journal of cancer 2007, 121(11):2373-2380.
5. Landi S, Moreno V, Gioia-Patricola L, Guino E, Navarro M, de Oca J, Capella G, Canzian F. Association of common polymorphisms in inflammatory genes interleukin (IL)6, IL8, tumor necrosis factor alpha, NFKB1, and peroxisome proliferator-activated receptor gamma with colorectal cancer. Cancer Res 2003, 63(13):3560-3566.
6. Slattery ML, Edwards S, Curtin K, Schaffer D, Neuhausen S. Associations between smoking, passive smoking, GSTM-1, NAT2, and rectal cancer. Cancer Epidemiol Biomarkers Prev 2003, 12(9):882-889.
7. Slattery ML, Potter J, Caan B, Edwards S, Coates A, Ma KN, Berry TD. Energy balance and colon cancer--beyond physical activity. Cancer Res 1997, 57(1):75-80.
8. Edwards S, Slattery ML, Mori M, Berry TD, Caan BJ, Palmer P, Potter JD. Objective system for interviewer performance evaluation for use in epidemiologic studies. American journal of epidemiology 1994, 140(11):1020-1028.
9. Zhang P, Sheng H, Uehara R. A double classification tree search algorithm for index SNP selection. BMC Bioinformatics 2004, 5:89. 10.1186/1471-2105-5-89, 476734, 15238162.
10. Laramie JM, Wilk JB, DeStefano AL, Myers RH. HaploBuild: an algorithm to construct non-contiguous associated haplotypes in family based genetic studies. Bioinformatics 2007, 23(16):2190-2192. 10.1093/bioinformatics/btm316, 2665175, 17586827.
11. Piccolo SR, Abo RP, Allen-Brady K, Camp NJ, Knight S, Anderson JL, Horne BD. Evaluation of genetic risk scores for lipid levels using genome-wide markers in the Framingham Heart Study. BMC proceedings 2009, 3(Suppl 7):S46. 10.1186/1753-6561-3-s7-s46, 2795945, 20018038.
12. Shephard ND, Abo R, Rigas SH, Frank B, Lin WY, Brock IW, Shippen A, Balasubramanian SP, Reed MW, Bartram CR, et al. A breast cancer risk haplotype in the caspase-8 gene. Cancer Res 2009, 69(7):2724-2728. 10.1158/0008-5472.CAN-08-4266, 2730164, 19318553.
13. Slattery ML, Herrick JS, Lundgreen A, Fitzpatrick FA, Curtin K, Wolff RK. Genetic variation in a metabolic signaling pathway and colon and rectal cancer risk: mTOR, PTEN, STK11, RPKAA1, PRKAG2, TSC1, TSC2, PI3K and Akt1. Carcinogenesis 31(9):1604-1611. 10.1093/carcin/bgq142, 20622004.
14. Thomas A. GCHap: fast MLEs for haplotype frequencies by gene counting. Bioinformatics 2003, 19(15):2002-2003. 10.1093/bioinformatics/btg254, 14555636.
15. Allen-Brady K, Wong J, Camp NJ. PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size. BMC Bioinformatics 2006, 7:209. 10.1186/1471-2105-7-209, 1459209, 16620382.
16. Curtin K, Wong J, Allen-Brady K, Camp NJ. PedGenie: meta genetic association testing in mixed family and case-control designs. BMC Bioinformatics 2007, 8:448. 10.1186/1471-2105-8-448, 2200673, 18005446.
17. Bland JM, Altman DG. Matching. Bmj 1994, 309(6962):1128. 2541945, 7987107.
18. Agresti A. An introduction to categorical data analysis 1996, New York: John Wiley & Sons, Inc.
19. Lawrence T, Willoughby DA, Gilroy DW. Anti-inflammatory lipid mediators and insights into the resolution of inflammation. Nat Rev Immunol 2002, 2(10):787-795. 10.1038/nri915, 12360216.
20. Kandel ES. NFkappaB inhibition and more: a side-by-side comparison of the inhibitors of IKK and proteasome. Cell cycle (Georgetown, Tex 2009, 8(12):1819-1820.
21. Parker KM, Ma MH, Manyak S, Altamirano CV, Tang YM, Frantzen M, Mikail A, Roussos E, Sjak-Shie N, Vescio RA, et al. Identification of polymorphisms of the IkappaBalpha gene associated with an increased risk of multiple myeloma. Cancer genetics and cytogenetics 2002, 137(1):43-48. 10.1016/S0165-4608(02)00541-1, 12377412.
22. Slattery ML, Herrick J, Wolff RK, Caan BJ, Potter JD, Sweeney C. CDX2 VDR polymorphism and colorectal cancer. Cancer Epidemiol Biomarkers Prev 2007, 16(12):2752-2755. 10.1158/1055-9965.EPI-07-2611, 2659563, 18086783.
23. Slattery ML, Murtaugh M, Caan B, Ma KN, Neuhausen S, Samowitz W. Energy balance, insulin-related genes and risk of colon and rectal cancer. International journal of cancer 2005, 115(1):148-154.
24. Slattery ML, Neuhausen SL, Hoffman M, Caan B, Curtin K, Ma KN, Samowitz W. Dietary calcium, vitamin D, VDR genotypes and colorectal cancer. International journal of cancer 2004, 111(5):750-756.
25. Ferrari SL, Ahn-Luong L, Garnero P, Humphries SE, Greenspan SL. Two promoter polymorphisms regulating interleukin-6 gene expression are associated with circulating levels of C-reactive protein and markers of bone resorption in postmenopausal women. The Journal of clinical endocrinology and metabolism 2003, 88(1):255-259. 10.1210/jc.2002-020092, 12519862.
26. Curtin K, Lin WY, George R, Katory M, Shorto J, Cannon-Albright LA, Bishop DT, Cox A, Camp NJ. Meta association of colorectal cancer confirms risk alleles at 8q24 and 18q21. Cancer Epidemiol Biomarkers Prev 2009, 18(2):616-621. 10.1158/1055-9965.EPI-08-0690, 2729170, 19155440.
27. Curtin K, Lin WY, George R, Katory M, Shorto J, Cannon-Albright LA, Smith G, Bishop DT, Cox A, Camp NJ. Genetic variants in XRCC2: new insights into colorectal cancer tumorigenesis. Cancer Epidemiol Biomarkers Prev 2009, 18(9):2476-2484. 10.1158/1055-9965.EPI-09-0187, 2742634, 19690184.
28. Yang Y, Li SS, Chien JW, Andriesen J, Zhao LP. A systematic search for SNPs/haplotypes associated with disease phenotypes using a haplotype-based stepwise procedure. BMC Genet 2008, 9:90. 10.1186/1471-2156-9-90, 2680203, 19102730.
29. Wang K, Abbott D. A principal components regression approach to multilocus genetic association studies. Genet Epidemiol 2008, 32(2):108-118. 10.1002/gepi.20266, 17849491.
30. Gauderman WJ, Murcray C, Gilliland F, Conti DV. Testing association between disease and multiple SNPs in a candidate gene. Genet Epidemiol 2007, 31(5):383-395. 10.1002/gepi.20219, 17410554.
31. Mei H, Ma D, Ashley-Koch A, Martin ER. Extension of multifactor dimensionality reduction for identifying multilocus effects in the GAW14 simulated data. BMC Genet 2005, 6(Suppl 1):S145. 10.1186/1471-2156-6-S1-S145, 1866790, 16451605.
32. Greene CS, Penrod NM, Kiralis J, Moore JH. Spatially Uniform ReliefF (SURF) for Computationally-Efficient Filtering of Gene-Gene Interactions. BioData mining 2009, 2(1):5. 10.1186/1756-0381-2-5, 2761303, 19772641.