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Comparative Study
, 39 (3), 197-206

Informed Genome-Wide Association Analysis With Family History as a Secondary Phenotype Identifies Novel Loci of Lung Cancer

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Comparative Study

Informed Genome-Wide Association Analysis With Family History as a Secondary Phenotype Identifies Novel Loci of Lung Cancer

Julia G Poirier et al. Genet Epidemiol.

Abstract

Lung cancer is the leading cause of cancer death worldwide. Although several genetic variants associated with lung cancer have been identified in the past, stringent selection criteria of genome-wide association studies (GWAS) can lead to missed variants. The objective of this study was to uncover missed variants by using the known association between lung cancer and first-degree family history of lung cancer to enrich the variant prioritization for lung cancer susceptibility regions. In this two-stage GWAS study, we first selected a list of variants associated with both lung cancer and family history of lung cancer in four GWAS (3,953 cases, 4,730 controls), then replicated our findings for 30 variants in a meta-analysis of four additional studies (7,510 cases, 7,476 controls). The top ranked genetic variant rs12415204 in chr10q23.33 encoding FFAR4 in the Discovery set was validated in the Replication set with an overall OR of 1.09 (95% CI=1.04, 1.14, P=1.63×10(-4)). When combining the two stages of the study, the strongest association was found in rs1158970 at Ch4p15.2 encoding KCNIP4 with an OR of 0.89 (95% CI=0.85, 0.94, P=9.64×10(-6)). We performed a stratified analysis of rs12415204 and rs1158970 across all eight studies by age, gender, smoking status, and histology, and found consistent results across strata. Four of the 30 replicated variants act as expression quantitative trait loci (eQTL) sites in 1,111 nontumor lung tissues and meet the genome-wide 10% FDR threshold.

Keywords: eQTL; family history; genetic susceptibility; genome-wide association studies; lung cancer; secondary phenotype.

Figures

Figure 1
Figure 1
Flow chart of Discovery and Replication study design. The Discovery stage includes primary (lung cancer) and secondary (family history of lung cancer) phenotype analysis of four GWASs, with a meta-analysis for each phenotype. The Replication stage includes four additional studies which were used to validate associations between SNPs and lung cancer.
Figure 2
Figure 2
Forest plot of the association between rs12415204 with lung cancer across eight studies, stratified by age, gender, smoking, and histology.
Figure 3
Figure 3
Forest plot of the association between rs1158970 with lung cancer across eight studies, stratified by age, gender, smoking, and histology.
Figure 4
Figure 4
Boxplots of gene expression levels in the lung for CEP57 according to genotype groups for SNP rs10831422. The left y-axis shows the mRNA expression levels for CEP57. The x-axis represents the three genotyped groups for SNP rs10831422. The right y-axis shows the proportion of the gene expression variance explained by the SNP (gray bar). Each panel represents a different cohort: Laval (n = 408), UBC (n = 349), Groningen (n = 362). The eQTL P values were 6.2 × 10−05, 4.9 × 10−07, and 1.7 × 10−07, respectively.

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