Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia

Abstract

To identify common genetic variants that contribute to lung cancer susceptibility, we conducted a multistage genome-wide association study of lung cancer in Asian women who never smoked. We scanned 5,510 never-smoking female lung cancer cases and 4,544 controls drawn from 14 studies from mainland China, South Korea, Japan, Singapore, Taiwan and Hong Kong. We genotyped the most promising variants (associated at P < 5 × 10(-6)) in an additional 1,099 cases and 2,913 controls. We identified three new susceptibility loci at 10q25.2 (rs7086803, P = 3.54 × 10(-18)), 6q22.2 (rs9387478, P = 4.14 × 10(-10)) and 6p21.32 (rs2395185, P = 9.51 × 10(-9)). We also confirmed associations reported for loci at 5p15.33 and 3q28 and a recently reported finding at 17q24.3. We observed no evidence of association for lung cancer at 15q25 in never-smoking women in Asia, providing strong evidence that this locus is not associated with lung cancer independent of smoking.

Figure 1. Association results from a GWAS of never-smoking women in Asia

Manhattan plot based on P values derived from 1-degree-of-freedom tests of genotype trend effect in an unconditional logistic regression analysis adjusted for study, age and three eigenvectors in a GWAS of lung cancer in never-smoking Asian females, including 5,510 lung cancer cases and 4,544 controls. The x axis represents chromosomal location, and the y axis shows P values on a negative logarithmic scale. The red horizontal line represents the genome-wide significance threshold of P = 5 × 10^-8. Labeled are two previously associated loci (TERT at 5p15.33 and TP63 at 3q28) together with three newly identified loci (VTI1A on chromosome 10 and ROS1-DCBLD1 and the HLA Class II region on chromosome 6).

Figure 2. Association results, recombination hot-spots, and linkage disequilibrium plots for the regions newly associated with lung cancer in never-smoking Asian females

Top, association results of GWAS data (grey diamonds), TaqMan data (blue diamonds) and combined data (red diamonds) are shown in the top panel with −log₁₀(P) values (left y axis). Overlaid are the likelihood ratio statistics (right y axis) to estimate putative recombination hotspots across the region on the basis of 3 sets of 100 randomly selected control samples representing Han Chinese, Japanese and Korean (connected lines in green, blue, and red, respectively) individuals. Bottom, LD heatmap based on pairwise r² values from total control populations for all SNPs included in the GWAS. (a) A 229.7- kb region at 10q25.2 spanning the VTI1A gene. (b) A 223.4- kb region at 6q22.2 spanning the ROS1, DCBLD1 and GOPC genes. (c) A 279.6- kb region at 6p21.32 spanning multiple genes in the HLA class II region. Because a Taqman assay could not be designed for rs2395185, we instead genotyped rs28366298, its perfect surrogate (r² = 1.0), by TaqMan. The reported P value is based on meta-analysis of the rs2395185 results in the GWAS and the rs28366298 results in the TaqMan set. Genomic coordinates are based on NCBI Human Genome Build 36. Schematic gene structures are taken from the UCSC Genome Browser and are scaled to the x-axis.

Figure 2. Association results, recombination hot-spots, and linkage disequilibrium plots for the regions newly associated with lung cancer in never-smoking Asian females

Top, association results of GWAS data (grey diamonds), TaqMan data (blue diamonds) and combined data (red diamonds) are shown in the top panel with −log₁₀(P) values (left y axis). Overlaid are the likelihood ratio statistics (right y axis) to estimate putative recombination hotspots across the region on the basis of 3 sets of 100 randomly selected control samples representing Han Chinese, Japanese and Korean (connected lines in green, blue, and red, respectively) individuals. Bottom, LD heatmap based on pairwise r² values from total control populations for all SNPs included in the GWAS. (a) A 229.7- kb region at 10q25.2 spanning the VTI1A gene. (b) A 223.4- kb region at 6q22.2 spanning the ROS1, DCBLD1 and GOPC genes. (c) A 279.6- kb region at 6p21.32 spanning multiple genes in the HLA class II region. Because a Taqman assay could not be designed for rs2395185, we instead genotyped rs28366298, its perfect surrogate (r² = 1.0), by TaqMan. The reported P value is based on meta-analysis of the rs2395185 results in the GWAS and the rs28366298 results in the TaqMan set. Genomic coordinates are based on NCBI Human Genome Build 36. Schematic gene structures are taken from the UCSC Genome Browser and are scaled to the x-axis.

Figure 2. Association results, recombination hot-spots, and linkage disequilibrium plots for the regions newly associated with lung cancer in never-smoking Asian females

Top, association results of GWAS data (grey diamonds), TaqMan data (blue diamonds) and combined data (red diamonds) are shown in the top panel with −log₁₀(P) values (left y axis). Overlaid are the likelihood ratio statistics (right y axis) to estimate putative recombination hotspots across the region on the basis of 3 sets of 100 randomly selected control samples representing Han Chinese, Japanese and Korean (connected lines in green, blue, and red, respectively) individuals. Bottom, LD heatmap based on pairwise r² values from total control populations for all SNPs included in the GWAS. (a) A 229.7- kb region at 10q25.2 spanning the VTI1A gene. (b) A 223.4- kb region at 6q22.2 spanning the ROS1, DCBLD1 and GOPC genes. (c) A 279.6- kb region at 6p21.32 spanning multiple genes in the HLA class II region. Because a Taqman assay could not be designed for rs2395185, we instead genotyped rs28366298, its perfect surrogate (r² = 1.0), by TaqMan. The reported P value is based on meta-analysis of the rs2395185 results in the GWAS and the rs28366298 results in the TaqMan set. Genomic coordinates are based on NCBI Human Genome Build 36. Schematic gene structures are taken from the UCSC Genome Browser and are scaled to the x-axis.