Genome-wide association study identifies multiple loci associated with bladder cancer risk

Human Molecular Genetics

Volumn 23, Issue 5, 2014, Pages

  Figueroa, Jonine D ^a   Ye, Yuanqing ^b   Siddiq, Afshan ^c,d   Garcia closas, Montserrat ^a,d   Chatterjee, Nilanjan ^a   Prokunina olsson, Ludmila ^a   Cortessis, Victoria K ^e   Kooperberg, Charles ^f   Cussenot, Olivier ^g,h   Benhamou, Simone ^i,j   Prescott, Jennifer ^k,l   Porru, Stefano ^m   Dinney, Colin P ^b   Malats, Núria ⁿ   Baris, Dalsu ^a   Purdue, Mark ^a   Jacobs, Eric J ^o   Albanes, Demetrius ^a   Wang, Zhaoming ^p   Deng, Xiang ^p   Chung, Charles C ^p   Tang, Wei ^a   Bas bueno de mesquita, H ^q,r   Trichopoulos, Dimitrios ^l,s,t   Ljungberg, Börje ^u   Clavel chapelon, Françoise ^v   Weiderpass, Elisabete ^w,x,y,z   Krogh, Vittorio ^aa   Dorronsoro, Miren ^ab,ac   Travis, Ruth ^ad   Tjønneland, Anne ^ae   Brenan, Paul ^af   Chang claude, Jenny ^ag   Riboli, Elio ^c,d   Conti, David ^e   Gago dominguez, Manuela ^ah   Stern, Mariana C ^e   Pike, Malcolm C ^ai   Van den berg, David ^e   Yuan, Jian Min ^aj   Hohensee, Chancellor ^e   Rodabough, Rebecca ^e   Cancel tassin, Geraldine ^f,g,ak   Roupret, Morgan ^f,g,ak   Comperat, Eva ^f,g,ak   Chen, Constance ^k,l   De vivo, Immaculata ^j,k,l   Giovannucci, Edward ^k,l   Hunter, David J ^j,k,l,al   Kraft, Peter ^k,l   Lindstrom, Sara ^k,l   Carta, Angela ^l   Pavanello, Sofia ^am   Arici, Cecilia ^l   Mastrangelo, Giuseppe ^am   Kamat, Ashish M ^b   Lerner, Seth P ^an   Barton grossman, H ^l   Lin, Jie ^b   Gu, Jian ^b   Pu, Xia ^b   Hutchinson, Amy ^o   Burdette, Laurie ^o   Wheeler, William ^ao   Kogevinas, Manolis ^ab,ap,aq,ar   Tardón, Adonina ^as   Serra, Consol ^at   Carrato, Alfredo ^au   García closas, Reina ^av   Lloreta, Josep ^ac   Schwenn, Molly ^aw   Karagas, Margaret R ^ax   Johnson, Alison ^ay   Schned, Alan ^ax   Armenti, Karla R ^az   Hosain, G M ^az   Andriole, Gerald ^ba   Grubb, Robert ^ba   Black, Amanda ^a   Ryan Diver, W ^o   Gapstur, Susan M ^o   Weinstein, Stephanie J ^a   Virtamo, Jarmo ^bb   Haiman, Chris A ^e   Landi, Maria T ^a   Caporaso, Neil ^a   Fraumeni, Joseph F ^a   Vineis, Paolo ^c,d   Wu, Xifeng ^b   Silverman, Debra T ^a   Chanock, Stephen ^a   Rothman, Nathaniel ^a   more..

^a NATIONAL CANCER INSTITUTE   (United States)

^b UNIVERSITY OF TEXAS   (United States)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d INSTITUTE OF CANCER RESEARCH   (United Kingdom)

^e UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^f Fred Hutchinson Cancer Research Center   (United States)

^g HÔPITAL TENON   (France)

^h CeRePP Group   (France)

ⁱ FONDATION JEAN DAUSSET CEPH   (France)

^j Gustave Roussy Comprehensive Cancer Institute   (France)

^k BRIGHAM AND WOMEN S HOSPITAL   (United States)

^l HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^m UNIVERSITY OF BRESCIA   (Italy)

ⁿ Centro Nacional de Investigaciones Oncológicas   (Spain)

^o AMERICAN CANCER SOCIETY   (United States)

^p SAIC FREDERICK INC   (United States)

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

^r UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^s BIOMEDICAL RESEARCH FOUNDATION   (Greece)

^t HELLENIC HEALTH FOUNDATION   (Greece)

^u UMEÅ UNIVERSITY   (Sweden)

^v CENTRE FOR RESEARCH IN EPIDEMIOLOGY AND POPULATION HEALTH   (France)

^w UNIVERSITY OF TROMSØ   (Norway)

^x CANCER REGISTRY OF NORWAY   (Norway)

^y KAROLINSKA INSTITUTE   (Sweden)

^z FOLKHÄLSAN RESEARCH CENTER   (Finland)

^aa NATIONAL CANCER INSTITUTE   (Italy)

^ab BIODONOSTIA HEALTH RESEARCH INSTITUTE   (Spain)

^ac CIBER EPIDEMIOLOGÍA Y SALUD PÚBLICA CIBERESP   (Spain)

^ad UNIVERSITY OF OXFORD   (United Kingdom)

^ae DANISH CANCER SOCIETY RESEARCH CENTER   (Denmark)

^af INTERNATIONAL AGENCY FOR RESEARCH ON CANCER   (France)

^ag GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^ah HOSPITAL CLÍNICO UNIVERSITARIO   (Spain)

^ai MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^aj UNIVERSITY OF PITTSBURGH CANCER INSTITUTE   (United States)

^ak SORBONNE UNIVERSITÉ   (France)

^al BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^am UNIVERSITY OF PADOVA   (Italy)

^an BAYLOR COLLEGE OF MEDICINE   (United States)

^ao INFORMATION MANAGEMENT SERVICES INC   (United States)

^ap CENTRE FOR RESEARCH IN ENVIRONMENTAL EPIDEMIOLOGY CREAL   (Spain)

^aq INST MUNIC D INVESTIGACIO MEDICA   (Spain)

^ar NATIONAL SCHOOL OF PUBLIC HEALTH   (Greece)

^as UNIVERSITY OF OVIEDO   (Spain)

^at UNIVERSITAT POMPEU FABRA   (Spain)

^au HOSPITAL RAMÓN Y CAJAL   (Spain)

^av HOSPITAL UNIVERSITARIO DE CANARIAS   (Spain)

^aw Maine Cancer Registry   (United States)

^ax DARTMOUTH MEDICAL SCHOOL   (United States)

^ay Vermont Cancer Registry   (United States)

^az NEW HAMPSHIRE DEPARTMENT OF HEALTH AND HUMAN SERVICES   (United States)

^ba WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^bb NATIONAL PUBLIC HEALTH INSTITUTE   (Finland)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BLADDER TUMOR; CASE CONTROL STUDY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC PREDISPOSITION; GENETICS; GENOTYPE; HUMAN; META ANALYSIS (TOPIC); PATHOLOGY; RISK; SINGLE NUCLEOTIDE POLYMORPHISM;

CASE-CONTROL STUDIES; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; META-ANALYSIS AS TOPIC; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK; URINARY BLADDER NEOPLASMS;

EID: 84894054918     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddt519     Document Type: Article

References (58)

1. Ferlay, J., Shin, H.R., Bray, F., Forman, D., Mathers, C. and Parkin, D.M. (2010) Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int. J. Cancer, 127, 2893-2917.
2. Silverman, D.T., Devessa, S.S., Moore, L. and Rothman, N. (2006) In Fraumeni, J.F. Jr and Schottenfeld, D. (eds), Cancer Epidemiology and Prevention, 3rd edn. Oxford University Press, New York, NY, pp. 1101-1127.
3. Kantor, A.F., Hartge, P., Hoover, R.N. and Fraumeni, J.F. Jr (1985) Familial and environmental interactions in bladder cancer risk. Int. J. Cancer, 35, 703-706.
4. Murta-Nascimento, C., Silverman, D.T., Kogevinas, M., Garcia-Closas, M., Rothman, N., Tardon, A., Garcia-Closas, R., Serra, C., Carrato, A., Villanueva, C. et al. (2007) Risk of bladder cancer associated with family history of cancer: do low-penetrance polymorphisms account for the increase in risk? Cancer Epidemiol. Biomarkers Prev., 16, 1595-1600.
5. Garcia-Closas, M., Malats, N., Silverman, D.,Dosemeci, M., Kogevinas, M., Hein, D.W., Tardon, A., Serra, C., Carrato, A., Garcia-Closas, R. et al. (2005) NAT2 slow acetylation, GSTM1 null genotype, and risk of bladder cancer: results from the Spanish Bladder Cancer Study and meta-analyses. Lancet, 366, 649-659.
6. Garcia-Closas, M., Ye, Y., Rothman, N., Figueroa, J.D., Malats, N., Dinney, C.P., Chatterjee, N., Prokunina-Olsson, L., Wang, Z., Lin, J. et al. (2011) A genome-wide association study of bladder cancer identifies a new susceptibility locus within SLC14A1, a urea transporter gene on chromosome 18q12.3. Hum. Mol. Genet., 20, 4282-4289.
7. Kiemeney, L.A., Thorlacius, S., Sulem, P., Geller, F., Aben, K.K., Stacey, S.N., Gudmundsson, J., Jakobsdottir, M., Bergthorsson, J.T., Sigurdsson,A. et al. (2008) Sequence variant on 8q24 confers susceptibility to urinary bladder cancer. Nat. Genet., 40, 1307-1312.
8. Moore, L.E., Baris, D.R., Figueroa, J.D., Garcia-Closas, M., Karagas, M.R., Schwenn, M.R., Johnson, A.T., Lubin, J.H., Hein, D.W., Dagnall, C.L. et al. (2011) GSTM1 null and NAT2 slow acetylation genotypes, smoking intensity and bladder cancer risk: results from the New England bladder cancer study and NAT2 meta-analysis. Carcinogenesis, 32, 182-189.
9. Rothman, N., Garcia-Closas, M., Chatterjee, N., Malats, N., Wu, X., Figueroa, J.D., Real, F.X., Van Den Berg, D., Matullo, G., Baris, D. et al. (2010) A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci. Nat. Genet., 42, 978-984.
10. Wu, X., Ye, Y., Kiemeney, L.A., Sulem, P., Rafnar, T., Matullo, G., Seminara, D., Yoshida, T., Saeki, N., Andrew, A.S. et al. (2009) Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibility to urinary bladder cancer. Nat. Genet., 41, 991-995.
11. Kiemeney, L.A., Sulem, P., Besenbacher, S., Vermeulen, S.H., Sigurdsson, A., Thorleifsson, G., Gudbjartsson, D.F., Stacey, S.N., Gudmundsson, J., Zanon, C. et al. (2010)Asequence variant at 4p16.3 confers susceptibility to urinary bladder cancer. Nat. Genet., 42, 415-419.
12. Rafnar, T., Vermeulen, S.H., Sulem, P., Thorleifsson, G., Aben, K.K., Witjes, J.A., Grotenhuis, A.J., Verhaegh, G.W., Hulsbergen-van de Kaa, C.A., Besenbacher, S. et al. (2011) Europeangenome-wide association study identifies SLC14A1 as a new urinary bladder cancer susceptibility gene. Hum. Mol. Genet., 20, 4268-4281.
13. Tang, W., Fu, Y.P., Figueroa, J.D., Malats, N., Garcia-Closas, M., Chatterjee, N., Kogevinas, M., Baris, D., Thun, M., Hall, J.L. et al. (2012) Mapping of the UGT1A locus identifies an uncommon coding variant that affects mRNA expression and protects from bladder cancer. Hum. Mol. Genet., 21, 1918-1930.
14. Rafnar, T., Sulem, P., Stacey, S.N., Geller, F., Gudmundsson, J., Sigurdsson, A., Jakobsdottir, M., Helgadottir, H., Thorlacius, S., Aben, K.K. et al. (2009) Sequence variants at theTERT-CLPTM1Llocus associate withmanycancer types. Nat. Genet., 41, 221-227.
15. Park, J.H., Wacholder, S., Gail, M.H., Peters, U., Jacobs, K.B., Chanock, S.J. and Chatterjee, N. (2010) Estimation of effect size distribution from genome-wide association studies and implications for future discoveries. Nat. Genet., 42, 570-575.
16. Hunter, D.J., Kraft, P., Jacobs, K.B., Cox, D.G., Yeager, M., Hankinson, S.E., Wacholder, S., Wang, Z., Welch, R., Hutchinson, A. et al. (2007) A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat. Genet., 39, 870-874.
17. Landi, M.T., Chatterjee, N., Yu, K., Goldin, L.R., Goldstein, A.M., Rotunno, M., Mirabello, L., Jacobs, K., Wheeler, W., Yeager, M. et al. (2009) A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. Am. J. Hum. Genet., 85, 679-691.
18. Landi, M.T., Consonni, D., Rotunno, M., Bergen, A.W., Goldstein, A.M., Lubin, J.H., Goldin, L., Alavanja, M., Morgan, G., Subar, A.F. et al. (2008) Environment And Genetics in Lung cancer Etiology (EAGLE) study: an integrative population-based case-control study of lung cancer.BMCPublic Health, 8, 203.
19. Michiels, S., Laplanche, A., Boulet, T., Dessen, P., Guillonneau, B., Mejean, A., Desgrandchamps, F., Lathrop, M., Sarasin, A. and Benhamou, S. (2009) Genetic polymorphisms in 85 DNA repair genes and bladder cancer risk. Carcinogenesis, 30, 763-768.
20. Siddiq, A., Couch, F.J., Chen, G.K., Lindstrom, S., Eccles, D., Millikan, R.C., Michailidou, K., Stram, D.O., Beckmann, L., Rhie, S.K. et al. (2012) A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11. Hum. Mol. Genet., 21, 5373-5384.
21. Schumacher, F.R., Berndt, S.I., Siddiq, A., Jacobs, K.B., Wang, Z., Lindstrom, S., Stevens, V.L., Chen, C., Mondul, A.M., Travis, R.C. et al. (2011) Genome-wide association study identifies new prostate cancer susceptibility loci. Hum. Mol. Genet., 20, 3867-3875.
22. Gerstein, M.B., Kundaje, A., Hariharan, M., Landt, S.G., Yan, K.K., Cheng, C., Mu, X.J., Khurana, E., Rozowsky, J., Alexander, R. et al. (2012) Architecture of the human regulatory network derived from ENCODE data. Nature, 489, 91-100.
23. Ward, L.D. and Kellis, M. (2012) HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res., 40, D930-D934.
24. Boyle, A.P., Hong, E.L., Hariharan, M., Cheng, Y., Schaub, M.A., Kasowski, M., Karczewski, K.J., Park, J., Hitz, B.C., Weng, S. et al. (2012) Annotation of functional variation in personal genomes using RegulomeDB. Genome Res., 22, 1790-1797.
25. Garcia-Closas, M., Rothman, N., Figueroa, J.D., Prokunina-Olsson, L., Han, S.S., Baris, D., Jacobs, E.J., Malats, N., De Vivo, I., Albanes, D. et al. (2013) Common genetic polymorphisms modify the effect of smoking on absolute risk of bladder cancer. Cancer Res., 73, 2211-2220.
26. Houlston, R.S., Cheadle, J., Dobbins, S.E., Tenesa, A., Jones, A.M., Howarth, K., Spain, S.L., Broderick, P., Domingo, E., Farrington, S. et al. (2010) Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33. Nat. Genet., 42, 973-977.
27. Sawcer, S., Hellenthal, G., Pirinen, M., Spencer, C.C., Patsopoulos, N.A., Moutsianas, L., Dilthey, A., Su, Z., Freeman, C., Hunt, S.E. et al. (2011) Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature, 476, 214-219.
28. Jones, A.M., Beggs, A.D., Carvajal-Carmona, L., Farrington, S., Tenesa, A., Walker, M., Howarth, K., Ballereau, S., Hodgson, S.V., Zauber, A. et al. (2012) TERC polymorphisms are associated both with susceptibility to colorectal cancer and with longer telomeres. Gut, 61, 248-254.
29. Mirabello, L., Yu, K., Kraft, P., De Vivo, I., Hunter, D.J., Prescott, J., Wong, J.Y., Chatterjee, N., Hayes, R.B. and Savage, S.A. (2010) The association of telomere length and genetic variation in telomere biology genes. Hum. Mutat., 31, 1050-1058.
30. Blasco, M.A. (2007) Telomere length, stem cells and aging. Nat. Chem. Biol., 3, 640-649.
31. Takihana, Y., Tsuchida, T., Fukasawa, M., Araki, I., Tanabe, N. and Takeda, M. (2006) Real-time quantitative analysis for human telomerase reverse transcriptase mRNA and human telomerase RNA component mRNA expressions as markers for clinicopathologic parameters in urinary bladder cancer. Int. J. Urol., 13, 401-408.
32. Jongstra-Bilen, J. and Jongstra, J. (2006) Leukocyte-specific protein 1 (LSP1): a regulator of leukocyte emigration in inflammation. Immunol. Res., 35, 65-74.
33. Zheng, Y.L.,Amr,S., Saleh, D.A., Dash, C., Ezzat, S., Mikhail, N.N., Gouda, I., Loay, I., Hifnawy, T., Abdel-Hamid, M. et al. (2012) Urinary bladder cancer risk factors in Egypt: a multicenter case-control study. Cancer Epidemiol. Biomarkers Prev., 21, 537-546.
34. Anderson, C.A., Boucher, G., Lees, C.W., Franke, A., D'Amato, M., Taylor, K.D., Lee, J.C., Goyette, P., Imielinski, M., Latiano, A. et al. (2011) Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat. Genet., 43, 246-252.
35. Easton, D.F., Pooley, K.A., Dunning, A.M., Pharoah, P.D., Thompson, D., Ballinger, D.G., Struewing, J.P., Morrison, J., Field, H., Luben, R. et al. (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature, 447, 1087-1093.
36. Calin, G.A. and Croce, C.M. (2006) MicroRNA-cancer connection: the beginning of a new tale. Cancer Res., 66, 7390-7394.
37. Kim, H.K., Prokunina-Olsson, L. and Chanock, S.J. (2012)Common genetic variants in miR-1206 (8q24.2) and miR-612 (11q13.3) affect biogenesis of mature miRNA forms. PLoS ONE, 7, e47454.
38. Steinthorsdottir, V., Thorleifsson, G., Reynisdottir, I., Benediktsson, R., Jonsdottir, T., Walters, G.B., Styrkarsdottir, U., Gretarsdottir, S., Emilsson, V., Ghosh, S. et al. (2007)Avariant inCDKAL1influences insulin response and risk of type 2 diabetes. Nat. Genet., 39, 770-775.
39. Pascoe, L., Tura, A., Patel, S.K., Ibrahim, I.M., Ferrannini, E., Zeggini, E., Weedon, M.N., Mari, A., Hattersley, A.T., McCarthy, M.I. et al. (2007) Common variants of the novel type 2 diabetes genes CDKAL1 and HHEX/ IDE are associated with decreased pancreatic beta-cell function. Diabetes, 56, 3101-3104.
40. Franke, A., McGovern, D.P., Barrett, J.C., Wang, K., Radford-Smith, G.L., Ahmad, T., Lees, C.W., Balschun, T., Lee, J., Roberts, R. et al. (2010) Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat. Genet., 42, 1118-1125.
41. Barrett, J.C., Hansoul, S., Nicolae, D.L., Cho, J.H., Duerr, R.H., Rioux, J.D., Brant, S.R., Silverberg, M.S., Taylor, K.D., Barmada, M.M. et al. (2008) Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat. Genet., 40, 955-962.
42. Hancock, D.B., Artigas, M.S., Gharib, S.A., Henry, A., Manichaikul, A., Ramasamy, A., Loth, D.W., Imboden, M., Koch, B., McArdle, W.L. et al. (2012) Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. PLoS Genet., 8, e1003098.
43. Frazer, K.A., Ballinger, D.G., Cox, D.R., Hinds, D.A., Stuve, L.L., Gibbs, R.A., Belmont, J.W., Boudreau, A., Hardenbol, P., Leal, S.M. et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449, 851-861.
44. Patterson, N., Price, A.L. and Reich, D. (2006) Population structure and eigenanalysis. PLoS Genet., 2, e190.
45. Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A. and Reich, D. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet., 38, 904-909.
46. Yu, K., Wang, Z., Li, Q., Wacholder, S., Hunter, D.J., Hoover, R.N., Chanock, S. and Thomas, G. (2008) Population substructure and control selection in genome-wide association studies. PLoS ONE, 3, e2551.
47. Berndt, S.I., Skibola, C.F., Joseph, V., Camp, N.J., Nieters, A., Wang, Z., Cozen, W., Monnereau, A., Wang, S.S., Kelly, R.S. et al. (2013) Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia. Nat. Genet., 45, 868-876.
48. Lan, Q., Hsiung, C.A., Matsuo, K., Hong, Y.C., Seow, A., Wang, Z., Hosgood, H.D. III, Chen, K., Wang, J.C., Chatterjee, N. et al. (2012) Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia. Nat. Genet., 44, 1330-1335.
49. Savage, S.A., Mirabello, L., Wang, Z., Gastier-Foster, J.M., Gorlick, R., Khanna, C., Flanagan, A.M., Tirabosco, R., Andrulis, I.L., Wunder,J.S. et al. (2013) Genome-wide association study identifies two susceptibility loci for osteosarcoma. Nat. Genet., 45, 799-803.
50. de Bakker, P.I., Ferreira, M.A., Jia, X., Neale, B.M., Raychaudhuri, S. and Voight, B.F. (2008) Practical aspects of imputation-driven meta-analysis of genome-wide association studies. Hum. Mol. Genet., 17, R122-R128.
51. Clayton, D. (2008) Testing for association on the X chromosome. Biostatistics, 9, 593-600.
52. Chen, Y.H., Chatterjee, N. and Carroll, R.J. (2009) Shrinkage estimators for robust and efficient inference in haplotype-based case-control studies. J. Am. Stat. Assoc., 104, 220-233.
53. Mukherjee, B. and 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.
54. Han, S.S., Rosenberg, P.S., Garcia-Closas, M., Figueroa, J.D., Silverman, D., Chanock, S.J., Rothman, N. and Chatterjee, N. (2012) Likelihood ratio test for detecting gene (G)-environment (E) interactions under an additive risk model exploiting G-E independence for case-control data. Am. J. Epidemiol., 176, 1060-1067.
55. Fearnhead, P. (2006) SequenceLDhot: detecting recombination hotspots. Bioinformatics, 22, 3061-3066.
56. Fearnhead, P., Harding, R.M., Schneider, J.A., Myers, S. and Donnelly, P. (2004) Application of coalescent methods to reveal fine-scale rate variation and recombination hotspots. Genetics, 167, 2067-2081.
57. Howie, B.N., Donnelly, P. and Marchini, J. (2009) A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet., 5, e1000529.
58. Fu, Y.P., Kohaar, I., Rothman, N., Earl, J., Figueroa, J.D., Ye, Y., Malats, N., Tang, W., Liu, L., Garcia-Closas, M. et al. (2012) Common genetic variants in the PSCA gene influence gene expression and bladder cancer risk. Proc. Natl. Acad. Sci. USA, 109, 4974-4979.