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Deciphering the Impact of Common Genetic Variation on Lung Cancer Risk: A Genome-Wide Association Study

¹ Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey, United Kingdom; ² Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, Texas; and ³ Department of Oncology, University of Cambridge, Cambridge, United Kingdom

Requests for reprints: Richard Houlston, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, United Kingdom. Phone: 44-0-208-722-4175; Fax: 44-0-208-722-4359; E-mail: richard.houlston{at}icr.ac.uk.

Key Words: lung cancer • genome-wide association

To explore the impact of common variation on the risk of developing lung cancer, we conducted a two-phase genome-wide association (GWA) study. In phase 1, we compared the genotypes of 511,919 tagging single nucleotide polymorphisms (SNP) in 1,952 cases and 1,438 controls; in phase 2, 30,568 SNPs were genotyped in 2,465 cases and 3,005 controls. SNP selection was based on best supported P values from phase 1 and two other GWA studies of lung cancer. In the combined analysis of phases 1 and 2, the strongest associations identified were defined by SNPs mapping to 15q25.1 (rs12914385; P = 3.19 x 10^–16), 5p15.33 (rs4975616; P = 6.66 x 10^–7), and 6p21.33 (rs3117582; P = 9.13 x 10^–7). Variation at 15q25.1, but not 5p15.33 or 6p21.33, was strongly associated with smoking behavior with risk alleles correlated to higher consumption. Variation at 5p15.33 was shown to significantly influence induction of lung cancer histology. Pooling data from the four series provided 21,620 genotypes for 7,560 cases and 8,205 controls. A meta-analysis provided increased support that variation at 15q25.1 (rs8034191; P = 3.24 x 10^–26), 5p15.33 (rs4975616; P = 2.99 x 10^–9), and 6p21.33 (rs3117582; P = 4.46 x 10^–10) influences lung cancer risk. The next best-supported associations were attained at 15q15.2 (rs748404: P = 1.08 x 10^–6) and 10q23.31 (rs1926203; P = 1.28 x 10^–6). These data indicate few common variants account for 1% of the excess familial risk underscoring the necessity of having additional large sample series for gene discovery. [Cancer Res 2009;69(16):6633–41]