Utation procedure. Meanwhile, P value of each pathway and the false

Utation procedure. Meanwhile, P value of each pathway and the false discovery rate (FDR) to keep the proportion of expected false positive findings were derived. The significance level of pathways analysis was set to be P#0.05 and FDR #0.5.Materials and Methods Ethics StatementThis collaborative study was approved by the institutional review boards of China Medical University, Tongji Medical College, Fudan University, Nanjing Medical University and Guangzhou Medical College with written informed consent from all participants [27,28,29,30].Study ParticipantsThe study subjects were from an ongoing two-center GWAS of lung cancer in China, including Nanjing study and Beijing study. The details of population have been described elsewhere [3]. Briefly, there were 1,473 cases and 1,962 controls in Nanjing study, 858 cases and 1,115 controls in Beijing study after quality control. All lung cancer cases were histopathologically or cytologically confirmed by at least two local purchase LY-2409021 pathologists. All controls were selected from those receiving routine physical examinations in local hospitals or those participating in the community screening of noncommunicable diseases and frequency-matched for age, gender and geographic regions to each set of the lung cancer cases.Results Genetic Information and Prior Biological Information used in Pathway AnalysisOf the total 570,373 genotyped SNPs, 340,060 SNPs were mapped into 17,225 genes within 50 kb upstream or downstream. Among them, 135,160 SNPs were ultimately assigned to 3,514 genes within the pre-defined pathways (41,560 SNPs to 1,003 genes in BioCarta pathways and 120,864 SNPs to 3,134 genes in KEGG pathways). All genes were assigned to 368 pathways that contained 10 to 200 genes (191 pathways used in BioCarta purchase BIBS39 database, 177 pathways used in KEGG database) in following pathway analysis.Genotyping and Quality ControlGenotyping was performed using an Affymetrix Genome-Wide Human SNP Array 6.0. A systematic quality control procedure was applied for both SNPs and individuals before pathway analysis [3]. Briefly, SNPs were excluded if they did not map on autosomal chromosomes, had a call rate ,95 , minor allele frequency (MAF) ,0.05, P,161025 for Hardy-Weinberg equilibrium (HWE) in combined samples of two studies or P,161024 forResults of Pathway Analysis using GSEA MethodAs presented in Table 1, a total 22 pathways were significant (P#0.05, FDR #0.5) in Nanjing study. Among them, five pathways were successfully replicated in Beijing study, including achPathway (P = 0.007), agrPathway (P = 0.033), At1rPathway (P = 0.003), metPathway (P = 0.007) and rac1Pathway (P = 0.041). After combining the two studies, four of five replicated pathways remained significance, including achPathwayPathway Analysis for GWAS of Lung Cancer(P = 0.012), At1rPathway (P = 0.022), metPathway (P = 0.010) and rac1Pathway (P = 0.005). While, in KEGG database, no pathway was identified (data not shown). Among the significant pathways (P#0.05) for the combined dataset of the two studies (Table S1 in File S1), these four indentified pathways were ranked in the top list (No.1 for rac1Pathway, No.3 for metPathway, No.4 for achPathway and No.5 for At1rPathway). For the achPathway, 9 of 16 ones had SNPs with P values ,0.05; similarly, 15, 14 and 18 significant genes were observed among 28 genes in the At1rPathway, 32 genes in the metPathway and 23 genes in the rac1Pathway, respectively. The representative SNPs with lung cancer risk at P values ,0.Utation procedure. Meanwhile, P value of each pathway and the false discovery rate (FDR) to keep the proportion of expected false positive findings were derived. The significance level of pathways analysis was set to be P#0.05 and FDR #0.5.Materials and Methods Ethics StatementThis collaborative study was approved by the institutional review boards of China Medical University, Tongji Medical College, Fudan University, Nanjing Medical University and Guangzhou Medical College with written informed consent from all participants [27,28,29,30].Study ParticipantsThe study subjects were from an ongoing two-center GWAS of lung cancer in China, including Nanjing study and Beijing study. The details of population have been described elsewhere [3]. Briefly, there were 1,473 cases and 1,962 controls in Nanjing study, 858 cases and 1,115 controls in Beijing study after quality control. All lung cancer cases were histopathologically or cytologically confirmed by at least two local pathologists. All controls were selected from those receiving routine physical examinations in local hospitals or those participating in the community screening of noncommunicable diseases and frequency-matched for age, gender and geographic regions to each set of the lung cancer cases.Results Genetic Information and Prior Biological Information used in Pathway AnalysisOf the total 570,373 genotyped SNPs, 340,060 SNPs were mapped into 17,225 genes within 50 kb upstream or downstream. Among them, 135,160 SNPs were ultimately assigned to 3,514 genes within the pre-defined pathways (41,560 SNPs to 1,003 genes in BioCarta pathways and 120,864 SNPs to 3,134 genes in KEGG pathways). All genes were assigned to 368 pathways that contained 10 to 200 genes (191 pathways used in BioCarta database, 177 pathways used in KEGG database) in following pathway analysis.Genotyping and Quality ControlGenotyping was performed using an Affymetrix Genome-Wide Human SNP Array 6.0. A systematic quality control procedure was applied for both SNPs and individuals before pathway analysis [3]. Briefly, SNPs were excluded if they did not map on autosomal chromosomes, had a call rate ,95 , minor allele frequency (MAF) ,0.05, P,161025 for Hardy-Weinberg equilibrium (HWE) in combined samples of two studies or P,161024 forResults of Pathway Analysis using GSEA MethodAs presented in Table 1, a total 22 pathways were significant (P#0.05, FDR #0.5) in Nanjing study. Among them, five pathways were successfully replicated in Beijing study, including achPathway (P = 0.007), agrPathway (P = 0.033), At1rPathway (P = 0.003), metPathway (P = 0.007) and rac1Pathway (P = 0.041). After combining the two studies, four of five replicated pathways remained significance, including achPathwayPathway Analysis for GWAS of Lung Cancer(P = 0.012), At1rPathway (P = 0.022), metPathway (P = 0.010) and rac1Pathway (P = 0.005). While, in KEGG database, no pathway was identified (data not shown). Among the significant pathways (P#0.05) for the combined dataset of the two studies (Table S1 in File S1), these four indentified pathways were ranked in the top list (No.1 for rac1Pathway, No.3 for metPathway, No.4 for achPathway and No.5 for At1rPathway). For the achPathway, 9 of 16 ones had SNPs with P values ,0.05; similarly, 15, 14 and 18 significant genes were observed among 28 genes in the At1rPathway, 32 genes in the metPathway and 23 genes in the rac1Pathway, respectively. The representative SNPs with lung cancer risk at P values ,0.