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1 Supplementary webappendix This webappendix formed part of the original submission and has been peer reviewed. We post it as supplied by the authors. Supplement to: Hartman M, Loy EY, Ku CS, Chia KS. Molecular epidemiology and its current clinical use in cancer management. Lancet Oncol 2010; 11:
2 Table 1: List of cancer GWAS publications No. Cancer Reference Initial Sample Size Replication Sample Size Number of SNP tested 1 Colorectal Nat Genet. 2007;39: cases, 960 7,334 cases, 5,246 [547,647] 2 Colorectal Nat Genet. 2007;39: ,257 cases, 1,336 6,223 cases, 6,443 [99,632] 3 Colorectal Nat Genet. 2007;39: cases, 965 7,473 cases, 5,984 [547,647] 4 Colorectal Nat Genet. 2008;40: cases, ,872 cases, 17,526 [547,647] 5 Colorectal Nat Genet. 2008;40: cases, 1,002 16,476 cases, 15,351 [541,628] 6 Colorectal Nat Genet. 2008;40: ,902 cases, 1,929 4,878 cases, 4,914 [up to 548,586] 7 Breast Nat Genet. 2007;39: ,599 cases, 11,546 2,934 cases, 5,967 [311,524] 8 Breast Nat Genet. 2007;39: ,145 cases, 1,142 1,176 cases, 2,072 [528,173] 9 Breast Nature. 2007;447: cases, ,646 cases, 24,889 [205,586] 10 Breast BMC Med Genet. 1,345 individuals [70,897] 2007;19:Suppl 1:S6 (Framingham) 11 Breast Proc Natl Acad Sci U S A. 249 cases, 299 1,193 cases, 1,166 [150,080] 2008;105: Breast Breast Cancer Res Treat. 30 cases, 30 [200,220] 2009;114: Breast Nat Genet. 2009;41: ,505 cases, 1,522 1,554 cases, 1,576 [up to 607,728] 14 Breast Nat Genet. 2009;41: ,145 cases, 1,142 8,625 cases, 9,657 [528,173] 15 Prostate Nat Genet. 2007; 39: ,172 cases, 1,157 3,124 cases, 3,142 [538,548] 16 Prostate Nat Genet. 2007;39: ,453 cases, 3,064 1,583 cases, 2,817 [316,515] 17 Prostate Nat Genet. 2007;39: ,501 cases, 11,290 1,992 cases, 3,058 [310,520] 18 Prostate BMC Med Genet. 2007;8 Suppl 1,345 individuals [70,897]
3 1:S6 (Framingham) 19 Prostate J Natl Cancer Inst. 1,235 cases, 1,599 1,242 cases, 917 [60,275] 2007;99: Prostate Nat Genet. 2008;40: ,172 cases, 1,157 3,941 cases, 3,964 [527,869] 21 Prostate Nat Genet. 2008;40: ,854 cases, 21,372 8,239 cases, 7,590 [310,520] 22 Prostate Nat Genet. 2008;40: ,854 cases, 1,894 3,268 cases, 3,366 [541,129] 23 Prostate Cancer Res. 2009;69: ,235 aggressive cases, 1,599 3,629 aggressive cases, 4,255 non-aggressive cases, [~2 million] (imputed) 5, Lung Cancer Lett. 2007;251: cases, cases, 356 [~116,204] (pooled) 25 Lung Nature. 2008;452: ,926 cases, 2,522 2,513 cases, 4,752 [310,023] 26 Lung Nat Genet. 2008;40: ,154 cases, 1,137 2,724 cases, 3,694 [317,498] 27 Neuroblastoma N Engl J Med. 2008;358:2585-1,032 cases, 2, cases, 2,128 [464,934] Melanoma Nat Genet. 2008;40: cases, 864 1,230 cases 1,251 [535,150] (pooled) 29 Lung Adenocarcinoma Int J Cancer. 2008;123: cases, 522 [~318,000] (pooled) 30 Chronic Lymphocytic Leukemia Nat Genet. 2008;40: cases, 1,438 1,024 cases, 1,677 [345,665] 31 Bladder Nat Genet. 2008;40: ,803 cases, 2,165 cases, 3,800 [302,140] 34, Basal Cell Carcinoma Nat Genet. 2008;40: cases, 33,117 1,216 cases, 2,844 [304,083] 33 Lung J Natl Cancer Inst. 194 cases, 219 3,878 cases, 4,831 [up to 722,376] 2008;100: Lung Nat Genet. 2008;40: ,952 cases, 1,438 7,579 cases, 8,236 [223,891] 35 Lung Nat Genet. 2008;40: ,971 cases, 3,746 2,899 cases, 5,573 [315,194] 36 Thyroid Nat Genet. 2009;41: cases, 37, cases, 1,727 [304,083] 37 Neuroblastoma Nat Genet. 2009;41: cases, 2, cases, 1,178 [462,866]
4 38 Nasopharyngeal J Hum Genet [Epub] 111 cases, cases, 252 [533,048] 39 Testicular Nat Genet [Epub] 277 cases, cases, 860, [611,254] 204 sets of parents 40 Childhood acute lymphoblastic leukemia (treatment) JAMA 2009;301: children [476,796] Webreferences 1 Tomlinson I, Webb E, Carvajal-Carmona L, et al. A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q Nat Genet 2007; 39: Zanke BW, Greenwood CM, Rangrej J, et al. Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. Nat Genet 2007; 39: Broderick P, Carvajal-Carmona L, Pittman AM, et al. A genome-wide association study shows that common alleles of SMAD7 influence colorectal cancer risk. Nat Genet 2007; 39: Tomlinson IP, Webb E, Carvajal-Carmona L, et al. A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3. Nat Genet 2008; 40: Tenesa A, Farrington SM, Prendergast JG, et al. Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. Nat Genet 2008; 40: Houlston RS, Webb E, Broderick P, et al. Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. Nat Genet 2008; 40: Stacey SN, Manolescu A, Sulem P, et al. Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet 2007; 39: Hunter DJ, Kraft P, Jacobs KB, et al. A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 2007; 39: Easton DF, Pooley KA, Dunning AM, et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 2007; 447: Murabito JM, Rosenberg CL, Finger D, et al. A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study. BMC Med Genet 2007; 8: S6. 11 Gold B, Kirchhoff T, Stefanov S, et al. Genome-wide association study provides evidence for a breast cancer risk locus at 6q Proc Natl Acad Sci USA 2008; 105: Kibriya MG, Jasmine F, Argos M, et al. A pilot genome-wide association study of early-onset breast cancer. Breast Cancer
5 Res Treat 2009; 114: Zheng W, Long J, Gao YT, et al. Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1. Nat Genet 2009; 41: Thomas G, Jacobs KB, Kraft P, et al. A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). Nat Genet 2009; 41: Yeager M, Orr N, Hayes RB, et al. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 2007; 39: Gudmundsson J, Sulem P, Manolescu A, et al. Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat Genet 2007; 39: Gudmundsson J, Sulem P, Steinthorsdottir V, et al. Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes. Nat Genet 2007; 39: Murabito JM, Rosenberg CL, Finger D, et al. A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study. BMC Med Genet 2007; 8: S6. 19 Duggan D, Zheng SL, Knowlton M, et al. Two genome-wide association studies of aggressive prostate cancer implicate putative prostate tumor suppressor gene DAB2IP. J Natl Cancer Inst 2007; 99: Thomas G, Jacobs KB, Yeager M, et al. Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet 2008; 40: Gudmundsson J, Sulem P, Rafnar T, et al. Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer. Nat Genet 2008; 40: Eeles RA, Kote-Jarai Z, Giles GG, et al. Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet 2008; 40: Sun J, Zheng SL, Wiklund F, et al. Sequence variants at 22q13 are associated with prostate cancer risk. Cancer Res 2009; 69: Spinola M, Leoni VP, Galvan A, et al. Genome-wide single nucleotide polymorphism analysis of lung cancer risk detects the KLF6 gene. Cancer Lett 2007; 251: Hung RJ, McKay JD, Gaborieau V, et al. A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. Nature 2008; 452: Amos CI, Wu X, Broderick P, et al. Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. Nat Genet 2008; 40: Liu P, Vikis HG, Wang D, et al. Familial aggregation of common sequence variants on 15q in lung cancer. J Natl
6 Cancer Inst 2008; 100: Wang Y, Broderick P, Webb E, et al. Common 5p15.33 and 6p21.33 variants influence lung cancer risk. Nat Genet 2008; 40: McKay JD, Hung RJ, Gaborieau V, et al. Lung cancer susceptibility locus at 5p Nat Genet 2008; 40: Galvan A, Falvella FS, Spinola M, et al. A polygenic model with common variants may predict lung adenocarcinoma risk in humans. Int J Cancer 2008; 123: Brown KM, Macgregor S, Montgomery GW, et al. Common sequence variants on 20q11.22 confer melanoma susceptibility. Nat Genet 2008; 40: Kiemeney LA, Thorlacius S, Sulem P, et al. Sequence variant on 8q24 confers susceptibility to urinary bladder cancer. Nat Genet 2008; 40: Stacey SN, Gudbjartsson DF, Sulem P, et al. Common variants on 1p36 and 1q42 are associated with cutaneous basal cell carcinoma but not with melanoma or pigmentation traits. Nat Genet 2008; 40: Maris JM, Mosse YP, Bradfield JP, et al. Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. N Engl J Med 2008; 358: Capasso M, Devoto M, Hou C, et al. Common variations in BARD1 influence susceptibility to high-risk neuroblastoma. Nat Genet 2009; 41: Ng CC, Yew PY, Puah SM, et al. A genome-wide association study identifies ITGA9 conferring risk of nasopharyngeal carcinoma. J Hum Genet 2009; 54: Kanetsky PA, Mitra N, Vardhanabhuti S, et al. Common variation in KITLG and at 5q31.3 predisposes to testicular germ cell cancer. Nat Genet 2009; 41: Gudmundsson J, Sulem P, Gudbjartsson DF, et al. Common variants on 9q22.33 and 14q13.3 predispose to thyroid cancer in European populations. Nat Genet 2009; 41: Di Bernardo MC, Crowther-Swanepoel D, Broderick P, et al. A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia. Nat Genet 2008; 40: Yang JJ, Cheng C, Yang W, et al. Genome-wide interrogation of germline genetic variation associated with treatment response in childhood acute lymphoblastic leukemia. JAMA 2009; 301:
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Supplementary Figure S1A
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