Correlating observed odds ratios from lung cancer case-control studies to SNP functional scores predicted by bioinformatic tools

Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis

Volumn 639, Issue 1-2, 2008, Pages 80-88

  Zhu, Yong ^a   Hoffman, Aaron ^a   Wu, Xifeng ^b   Zhang, Heping ^a   Zhang, Yawei ^a   Leaderer, Derek ^a   Zheng, Tongzhang ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

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

Author keywords

Pmut; PolyPhen; SIFT; SNP; SNPs3D

Indexed keywords

ARTICLE; BIOINFORMATICS; CANCER RISK; CASE CONTROL STUDY; COMPUTER PROGRAM; CORRELATION COEFFICIENT; CORRELATIONAL STUDY; GENETIC ASSOCIATION; GENETIC EPIDEMIOLOGY; GENETIC VARIABILITY; GENOTYPE; HUMAN; INFORMATION PROCESSING; INFORMATION RETRIEVAL; LUNG CANCER; PMUTT SOFTWARE; POLYPHEN SOFTWARE; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; SCORING SYSTEM; SIFT SOFTWARE; SINGLE NUCLEOTIDE POLYMORPHISM; SNPS3D SOFTWARE; STATISTICAL SIGNIFICANCE;

CASE-CONTROL STUDIES; COMPUTATIONAL BIOLOGY; LUNG NEOPLASMS; ODDS RATIO; POLYMORPHISM, SINGLE NUCLEOTIDE; PUBMED; RESEARCH DESIGN; RISK FACTORS;

EID: 39249084312     PISSN: 00275107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mrfmmm.2007.11.005     Document Type: Article

References (66)

1. Schork N.J., Fallin D., and Lanchbury J.S. Single nucleotide polymorphisms and the future of genetic epidemiology. Clin. Genet. 58 (2000) 250-264
2. Imyanitov E.N., Togo A.V., and Hanson K.P. Searching for cancer-associated gene polymorphisms: promises and obstacles. Cancer Lett. 204 (2004) 3-14
3. Sunyaev S., Ramensky V., Koch I., Lathe III W., Kondrashov A.S., and Bork P. Prediction of deleterious human alleles. Hum. Mol. Genet. 10 (2001) 591-597
4. Cartegni L., Wang J., Zhu Z., Zhang M.Q., and Krainer A.R. ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res. 31 (2003) 3568-3571
5. Ng P.C., and Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids. Res. 31 (2003) 3812-3814
6. Yue P., Melamud E., and Moult J. SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinform. 7 (2006) 166
7. Ferrer-Costa C., Gelpi J.L., Zamakola L., Parraga I., de la Cruz X., and Orozco M. PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinformatics 21 (2005) 3176-3178
8. Yue P., Li Z., and Moult J. Loss of protein structure stability as a major causative factor in monogenic disease. J. Mol. Biol. 353 (2005) 459-473
9. Yue P., and Moult J. Identification and analysis of deleterious human SNPs. J. Mol. Biol. 356 (2006) 1263-1274
10. Ferrer-Costa C., Orozco M., and de la Cruz X. Sequence-based prediction of pathological mutations. Proteins 57 (2004) 811-819
11. Laird N.M., and Mosteller F. Some statistical methods for combining experimental results. Int. J. Technol. Assess. Health Care 6 (1990) 5-30
12. Zhu Y., Spitz M.R., Amos C.I., Lin J., Schabath M.B., and Wu X. An evolutionary perspective on single-nucleotide polymorphism screening in molecular cancer epidemiology. Cancer Res. 64 (2004) 2251-2257
13. Ng P.C., and Henikoff S. Accounting for human polymorphisms predicted to affect protein function. Genome Res. 12 (2002) 436-446
14. Mathe E., Olivier M., Kato S., Ishioka C., Hainaut P., and Tavtigian S.V. Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods. Nucleic Acids Res. 34 (2006) 1317-1325
15. Xi T., Jones I.M., and Mohrenweiser H.W. Many amino acid substitution variants identified in DNA repair genes during human population screenings are predicted to impact protein function. Genomics 83 (2004) 970-979
16. Wang H., Hao B., Chen X., Zhao N., Cheng G., Jiang Y., Liu Y., Lin C., Tan W., Lu D., Wei Q., Jin L., Lin D., and He F. Beta-2 adrenergic receptor gene (ADRB2) polymorphism and risk for lung adenocarcinoma: a case-control study in a Chinese population. Cancer Lett. (2005)
17. Zienolddiny S., Campa D., Lind H., Ryberg D., Skaug V., Stangeland L., Phillips D.H., Canzian F., and Haugen A. Polymorphisms of DNA repair genes and risk of non-small cell lung cancer. Carcinogenesis 27 (2006) 560-567
18. Ito H., Matsuo K., Hamajima N., Mitsudomi T., Sugiura T., Saito T., Yasue T., Lee K.M., Kang D., Yoo K.Y., Sato S., Ueda R., and Tajima K. Gene-environment interactions between the smoking habit and polymorphisms in the DNA repair genes, APE1 Asp148Glu and XRCC1 Arg399Gln, in Japanese lung cancer risk. Carcinogenesis 25 (2004) 1395-1401 Epub March, 2004, 1325
19. Popanda O., Schattenberg T., Phong C.T., Butkiewicz D., Risch A., Edler L., Kayser K., Dienemann H., Schulz V., Drings P., Bartsch H., and Schmezer P. Specific combinations of DNA repair gene variants and increased risk for non-small cell lung cancer. Carcinogenesis 25 (2004) 2433-2441
20. Popanda O., Edler L., Waas P., Schattenberg T., Butkiewicz D., Muley T., Dienemann H., Risch A., Bartsch H., and Schmezer P. Elevated risk of squamous-cell carcinoma of the lung in heavy smokers carrying the variant alleles of the TP53 Arg72Pro and p21 Ser31Arg polymorphisms. Lung Cancer 55 (2007) 25-34
21. Hamada G.S., Sugimura H., Suzuki I., Nagura K., Kiyokawa E., Iwase T., Tanaka M., Takahashi T., Watanabe S., Kino I., et al. The heme-binding region polymorphism of cytochrome P450IA1 (CypIA1), rather than the RsaI polymorphism of IIE1 (CypIIE1), is associated with lung cancer in Rio de Janeiro. Cancer Epidemiol. Biomarkers Prev. 4 (1995) 63-67
22. Larsen J.E., Colosimo M.L., Yang I.A., Bowman R., Zimmerman P.V., and Fong K.M. Risk of non-small cell lung cancer and the cytochrome P4501A1 Ile462Val polymorphism. Cancer Causes Control 16 (2005) 579-585
23. London S.J., Yuan J.M., Coetzee G.A., Gao Y.T., Ross R.K., and Yu M.C. CYP1A1 I462V genetic polymorphism and lung cancer risk in a cohort of men in Shanghai, China. Cancer Epidemiol. Biomarkers Prev. 9 (2000) 987-991
24. Ng D.P., Tan K.W., Zhao B., and Seow A. CYP1A1 polymorphisms and risk of lung cancer in non-smoking Chinese women: influence of environmental tobacco smoke exposure and GSTM1/T1 genetic variation. Cancer Causes Control 16 (2005) 399-405
25. Song N., Tan W., Xing D., and Lin D. CYP 1A1 polymorphism and risk of lung cancer in relation to tobacco smoking: a case-control study in China. Carcinogenesis 22 (2001) 11-16
26. Sugimura H., Wakai K., Genka K., Nagura K., Igarashi H., Nagayama K., Ohkawa A., Baba S., Morris B.J., Tsugane S., Ohno Y., Gao C., Li Z., Takezaki T., Tajima K., and Iwamasa T. Association of Ile462Val (Exon 7) polymorphism of cytochrome P450 IA1 with lung cancer in the Asian population: further evidence from a case-control study in Okinawa. Cancer Epidemiol. Biomarkers Prev. 7 (1998) 413-417
27. Wenzlaff A.S., Cote M.L., Bock C.H., Land S.J., Santer S.K., Schwartz D.R., and Schwartz A.G. CYP1A1 and CYP1B1 polymorphisms and risk of lung cancer among never smokers: a population-based study. Carcinogenesis 26 (2005) 2207-2212
28. Yang X.R., Wacholder S., Xu Z., Dean M., Clark V., Gold B., Brown L.M., Stone B.J., Fraumeni Jr. J.F., and Caporaso N.E. CYP1A1 and GSTM1 polymorphisms in relation to lung cancer risk in Chinese women. Cancer Lett. 214 (2004) 197-204
29. Liang G., Pu Y., and Yin L. Rapid detection of single nucleotide polymorphisms related with lung cancer susceptibility of Chinese population. Cancer Lett. 223 (2005) 265-274
30. To-Figueras J., Gene M., Gomez-Catalan J., Pique E., Borrego N., and Corbella J. Lung cancer susceptibility in relation to combined polymorphisms of microsomal epoxide hydrolase and glutathione S-transferase P1. Cancer Lett. 173 (2001) 155-162
31. Voho A., Metsola K., Anttila S., Impivaara O., Jarvisalo J., Vainio H., Husgafvel-Pursiainen K., and Hirvonen A. EPHX1 gene polymorphisms and individual susceptibility to lung cancer. Cancer Lett. 237 (2006) 102-108
32. Shen M., Berndt S.I., Rothman N., Demarini D.M., Mumford J.L., He X., Bonner M.R., Tian L., Yeager M., Welch R., Chanock S., Zheng T., Caporaso N., and Lan Q. Polymorphisms in the DNA nucleotide excision repair genes and lung cancer risk in Xuan Wei, China. Int. J. Cancer 116 (2005) 768-773
33. Hu Z., Xu L., Shao M., Yuan J., Wang Y., Wang F., Yuan W., Qian J., Ma H., Liu H., Chen W., Yang L., Jing G., Huo X., Chen F., Jin L., Wei Q., Wu T., Lu D., Huang W., and Shen H. Polymorphisms in the two helicases ERCC2/XPD and ERCC3/XPB of the transcription factor IIH complex and risk of lung cancer: a case-control analysis in a Chinese population. Cancer Epidemiol. Biomarkers Prev. 15 (2006) 1336-1340
34. Yin J., Vogel U., Ma Y., Guo L., Wang H., and Qi R. Polymorphism of the DNA repair gene ERCC2 Lys751Gln and risk of lung cancer in a northeastern Chinese population. Cancer Genet. Cytogenet. 169 (2006) 27-32
35. Sakiyama T., Kohno T., Mimaki S., Ohta T., Yanagitani N., Sobue T., Kunitoh H., Saito R., Shimizu K., Hirama C., Kimura J., Maeno G., Hirose H., Eguchi T., Saito D., Ohki M., and Yokota J. Association of amino acid substitution polymorphisms in DNA repair genes TP53, POLI, REV1 and LIG4 with lung cancer risk. Int. J. Cancer 114 (2005) 730-737
36. Cui Y., Morgenstern H., Greenland S., Tashkin D.P., Mao J., Cao W., Cozen W., Mack T.M., and Zhang Z.F. Polymorphism of xeroderma pigmentosum group G and the risk of lung cancer and squamous cell carcinomas of the oropharynx, larynx and esophagus. Int. J. Cancer 118 (2006) 714-720
37. Larsen J.E., Colosimo M.L., Yang I.A., Bowman R., Zimmerman P.V., and Fong K.M. CYP1A1 Ile462Val and MPO G-463A interact to increase risk of adenocarcinoma but not squamous cell carcinoma of the lung. Carcinogenesis 27 (2006) 525-532
38. Lewis S.J., Cherry N.M., Niven R.M., Barber P.V., and Povey A.C. GSTM1, GSTT1 and GSTP1 polymorphisms and lung cancer risk. Cancer Lett. 180 (2002) 165-171
39. Schneider J., Bernges U., Philipp M., and Woitowitz H.J. GSTM1, GSTT1, and GSTP1 polymorphism and lung cancer risk in relation to tobacco smoking. Cancer Lett. 208 (2004) 65-74
40. Wang Y., Spitz M.R., Schabath M.B., Ali-Osman F., Mata H., and Wu X. Association between glutathione S-transferase p1 polymorphisms and lung cancer risk in Caucasians: a case-control study. Lung Cancer 40 (2003) 25-32
41. Wenzlaff A.S., Cote M.L., Bock C.H., Land S.J., and Schwartz A.G. GSTM1, GSTT1 and GSTP1 polymorphisms, environmental tobacco smoke exposure and risk of lung cancer among never smokers: a population-based study. Carcinogenesis 26 (2005) 395-401
42. Park J.M., Lee G.Y., Choi J.E., Kang H.G., Jang J.S., Cha S.I., Lee E.B., Kim S.G., Kim C.H., Lee W.K., Kam S., Kim D.S., Jung T.H., and Park J.Y. No association between polymorphisms in the histone deacetylase genes and the risk of lung cancer. Cancer Epidemiol. Biomarkers Prev. 14 (2005) 1841-1843
43. Spinola M., Conti B., Ravagnani F., Fabbri A., Incarbone M., Cataldo I., Pira E., Pelucchi C., La Vecchia C., and Dragani T.A. A new polymorphism (Ser362Thr) of the l-myc gene is not associated with lung adenocarcinoma risk and prognosis. Eur. J. Cancer Prev. 13 (2004) 87-89
44. Jang J.S., Lee S.J., Choi J.E., Cha S.I., Lee E.B., Park T.I., Kim C.H., Lee W.K., Kam S., Choi J.Y., Kang Y.M., Park R.W., Kim I.S., Cho Y.L., Jung T.H., Han S.B., and Park J.Y. Methyl-CpG binding domain 1 gene polymorphisms and risk of primary lung cancer. Cancer Epidemiol. Biomarkers Prev. 14 (2005) 2474-2480
45. Chae M.H., Jang J.S., Kang H.G., Park J.H., Park J.M., Lee W.K., Kam S., Lee E.B., Son J.W., and Park J.Y. O6-alkylguanine-DNA alkyltransferase gene polymorphisms and the risk of primary lung cancer. Mol. Carcinog. 45 (2006) 239-249
46. Cohet C., Borel S., Nyberg F., Mukeria A., Bruske-Hohlfeld I., Constantinescu V., Benhamou S., Brennan P., Hall J., and Boffetta P. Exon 5 polymorphisms in the O6-alkylguanine DNA alkyltransferase gene and lung cancer risk in non-smokers exposed to second-hand smoke. Cancer Epidemiol. Biomarkers Prev. 13 (2004) 320-323
47. Jang J.-S., Lee S.J., Choi J.E., Cha S.I., Lee E.B., Park T.I., Kim C.H., Lee W.K., Kam S., Choi J.-Y., Kang Y.M., Park R.-W., Kim I.-S., Cho Y.L., Jung T.H., Han S.B., and Park J.Y. Methyl-CpG binding domain 1 gene polymorphisms and risk of primary lung cancer 10.1158/1055-9965.EPI-05-0423. Cancer Epidemiol. Biomarkers Prev. 14 (2005) 2474-2480
48. Hu Z., Huo X., Lu D., Qian J., Zhou J., Chen Y., Xu L., Ma H., Zhu J., Wei Q., and Shen H. Functional polymorphisms of matrix metalloproteinase-9 are associated with risk of occurrence and metastasis of lung cancer. Clin. Cancer Res. 11 (2005) 5433-5439
49. Shi Q., Zhang Z., Li G., Pillow P.C., Hernandez L.M., Spitz M.R., and Wei Q. Polymorphisms of methionine synthase and methionine synthase reductase and risk of lung cancer: a case-control analysis. Pharmacogenet. Genomics 15 (2005) 547-555
50. Lan Q., Shen M., Berndt S.I., Bonner M.R., He X., Yeager M., Welch R., Keohavong P., Donahue M., Hainaut P., and Chanock S. Smoky coal exposure, NBS1 polymorphisms, p53 protein accumulation, and lung cancer risk in Xuan Wei, China. Lung Cancer 49 (2005) 317-323
51. Ryk C., Kumar R., Sanyal S., de Verdier P.J., Hemminki K., Larsson P., Steineck G., and Hou S.M. Influence of polymorphism in DNA repair and defence genes on p53 mutations in bladder tumours. Cancer Lett. 241 (2006) 142-149
52. Alexandrie A.K., Nyberg F., Warholm M., and Rannug A. Influence of CYP1A1, GSTM1, GSTT1, and NQO1 genotypes and cumulative smoking dose on lung cancer risk in a Swedish population. Cancer Epidemiol. Biomarkers Prev. 13 (2004) 908-914
53. Bock C.H., Wenzlaff A.S., Cote M.L., Land S.J., and Schwartz A.G. NQO1 T allele associated with decreased risk of later age at diagnosis lung cancer among never smokers: results from a population-based study. Carcinogenesis 26 (2005) 381-386 Epub October, 2004, 2021
54. Lawson K.A., Woodson K., Virtamo J., and Albanes D. Association of the NAD(P)H:quinone oxidoreductase (NQO1) 609C → T polymorphism with lung cancer risk among male smokers. Cancer Epidemiol. Biomarkers Prev. 14 (2005) 2275-2276
55. Saldivar S.J., Wang Y., Zhao H., Shao L., Lin J., Spitz M.R., and Wu X. An association between a NQO1 genetic polymorphism and risk of lung cancer. Mutat. Res. 582 (2005) 71-78
56. Park J., Chen L., Tockman M.S., Elahi A., and Lazarus P. The human 8-oxoguanine DNA N-glycosylase 1 (hOGG1) DNA repair enzyme and its association with lung cancer risk. Pharmacogenetics 14 (2004) 103-109
57. Jain N., Singh V., Hedau S., Kumar S., Daga M.K., Dewan R., Murthy N.S., Husain S.A., and Das B.C. Infection of human papillomavirus type 18 and p53 codon 72 polymorphism in lung cancer patients from India. Chest 128 (2005) 3999-4007
58. Liu G., Zhou W., Park S., Wang L.I., Miller D.P., Wain J.C., Lynch T.J., Su L., and Christiani D.C. The SOD2 Val/Val genotype enhances the risk of nonsmall cell lung carcinoma by p53 and XRCC1 polymorphisms. Cancer 101 (2004) 2802-2808
59. Schabath M.B., Wu X., Wei Q., Li G., Gu J., and Spitz M.R. Combined effects of the p53 and p73 polymorphisms on lung cancer risk. Cancer Epidemiol. Biomarkers Prev. 15 (2006) 158-161
60. Zhang X., Miao X., Liang G., Hao B., Wang Y., Tan W., Li Y., Guo Y., He F., Wei Q., and Lin D. Polymorphisms in DNA base excision repair genes ADPRT and XRCC1 and risk of lung cancer. Cancer Res. 65 (2005) 722-726
61. Gu J., Wu X., Dong Q., Romeo M.J., Lin X., Gutkind J.S., and Berman D.M. A nonsynonymous single-nucleotide polymorphism in the PDZ-Rho guanine nucleotide exchange factor (Ser1416Gly) modulates the risk of lung cancer in Mexican Americans. Cancer 106 (2006) 2707-2715
62. Liang G., Miao X., Zhou Y., Tan W., and Lin D. A functional polymorphism in the SULT1A1 gene (G638A) is associated with risk of lung cancer in relation to tobacco smoking. Carcinogenesis 25 (2004) 773-778
63. Pachouri S.S., Sobti R.C., Kaur P., Singh J., and Gupta S.K. Impact of polymorphism in sulfotransferase gene on the risk of lung cancer. Cancer Genet. Cytogenet. 171 (2006) 39-43
64. Hu Z., Wang Y., Wang X., Liang G., Miao X., Xu Y., Tan W., Wei Q., Lin D., and Shen H. DNA repair gene XPC genotypes/haplotypes and risk of lung cancer in a Chinese population. Int. J. Cancer 115 (2005) 478-483
65. Lee G.Y., Jang J.S., Lee S.Y., Jeon H.S., Kim K.M., Choi J.E., Park J.M., Chae M.H., Lee W.K., Kam S., Kim I.S., Lee J.T., Jung T.H., and Park J.Y. XPC polymorphisms and lung cancer risk. Int. J. Cancer 115 (2005) 807-813
66. Hao B., Miao X., Li Y., Zhang X., Sun T., Liang G., Zhao Y., Zhou Y., Wang H., Chen X., Zhang L., Tan W., Wei Q., Lin D., and He F. A novel T-77C polymorphism in DNA repair gene XRCC1 contributes to diminished promoter activity and increased risk of non-small cell lung cancer. Oncogene 25 (2006) 3613-3620