R GSE23546. Standard quality controls were performed as described previously and only Epigenetic Reader Domain subjects that passed genotyping and expression quality controls were included in this study with 409, 363, and 339 subjects from Laval, Groningen, and UBC, respectively [12].Study Subjects and Lung SpecimensStudy subjects and lung specimens were described previously [12,14]. Briefly subjects were from three sites, Laval University, University of British Columbia, and University of Groningen (henceforth referred to as Laval, UBC, and Groningen, respectively). At Laval, the lung specimens were provided by the IUCPQ site of the Respiratory Health Network Tissue Bank of the Fonds de recherche du Quebec ?Sante (FRQS) (www.tissuebank.ca); at ??Groningen, the lung specimens were provided by the local tissue bank of the Department of Pathology, and at UBC, the lung specimens were provided by the James Hogg Research Center Biobank at St Paul’s Hospital. COPD diagnosis and Autophagy severity were determined according to the GOLD recommendations [2]. Clinical characteristics of subjects by site are shown in Table 1.COPD Susceptibility LociLung eQTLs were overlaid onto COPD susceptibility loci identified by previous GWAS except for the 15q25-CHRNA3/ CHRNA5/IREB2 locus that we have reported on previously [15]. Three COPD loci were considered; 4q22 (FAM13A), 4q31 (HHIP) and 19q13 (RAB4B, EGLN2, MIA, CYP2A6). SNPs associated with COPD from previous GWAS were tabulated for the three loci (Table 2). SNPs genotyped in the lung eQTL consortium located 1 Mb up and downstream of the most distant associated SNPs in both directions were evaluated. Chromosomes 4q22 (88,875,90990,886,297), 4q31 (144,480,780-146,506,456) and 19q13 (40,292,404-42,302,706) include 718, 412 and 739 SNPs, respectively. Genes residing in the same regions were tested as cis-eQTLs for probe sets for 14 genes on 4q22 (SPP1, PKD2, ABCG2, PPM1K, HERC6, HERC5, PIGY, HERC3, NAP1L5, FAM13A, TIGD2, GPRIN3, SNCA, MMRN1), 9 genes on 4q31 (FREM3, GYPE, GYPB, GYPA, HHIP, ANAPC10, ABCE1, OTUD4, SMAD1) andTable 1. Clinical characteristics of patients that passed gene expression and genotyping quality control filters.Laval (n = 409) Male ( ) Age (years) Body Mass Index (kg/m ) FEV1 predicted – pre-BD* ( ) FVC predicted ?pre-BD* ( ) FEV1/FVC COPD Stage 1 : Mild Stage 2 : Moderate Stage 3 : Severe Stage 4 : Very Severe Asthma Diabetes Cardiac diseases Smoking Smoker Ex-Smoker Non-Smoker Not available Pack-years in ever-smokers FEV1 : forced expiratory volume in 1 second. FVC : forced vital capacity. [-] = missing value. *pre-BD: pre-bronchodilator. doi:10.1371/journal.pone.0070220.t001 90 (22.0 ) 283 (69.2 ) 36 (8.8 ) 0 (0.0 ) 48.5627.5 [37]UBC (n = 339) 53.7 60.2614.3 25.665.4 [56] 78.2624.4 [77] 86.9620.1 [75] 0.6760.13 [77] 115 (33.9 ) [99] 43 (37.4 ) 60 (52.2 ) 2 (1.7 ) 10 (8.7 ) 22 (6.5 ) 13 (3.8 ) 46 (13.6 )Groningen (n = 363) 53.2 51.5615.5 [9] 23.264.2 [42] 60.5630.0 [194] 75.0626.5 [208] 0.6460.19 [189] 158 (43.5 ) [120] 20 (12.6 ) 38 (23.9 ) 21 (13.2 ) 69 (43.4 ) 0 (0.0 ) 27 (7.4 ) 28 (7.7 )55.9 63.369.9 26.765.3 80.5618.9 [16] 89.8616.1 [31] 0.6760.10 [32] 211 (51.6 ) [34] 82 (38.9 ) 117 (55.4 23977191 ) 11 (5.2 ) 1 (0.5 ) 15 (3.7 ) 41 (10.0 ) 120 (29.3 )98 (28.9 ) 163 (48.1 ) 26 (7.7 ) 52 (15.3 ) 44.7628.5 [58]57 (15.7 ) 185 (51.0 ) 100 (27.5 ) 21 (5.8 ) 31.2617.4 [51]Refining COPD Susceptibility Loci with Lung eQTLsgenes on 19q13 (DYRK1B, FBL, FCGBP, PSMC4, ZNF546, ZNF780B, ZNF780A, MAP3K10, TTC9B, CNTD2, AKT2, C19orf47, P.R GSE23546. Standard quality controls were performed as described previously and only subjects that passed genotyping and expression quality controls were included in this study with 409, 363, and 339 subjects from Laval, Groningen, and UBC, respectively [12].Study Subjects and Lung SpecimensStudy subjects and lung specimens were described previously [12,14]. Briefly subjects were from three sites, Laval University, University of British Columbia, and University of Groningen (henceforth referred to as Laval, UBC, and Groningen, respectively). At Laval, the lung specimens were provided by the IUCPQ site of the Respiratory Health Network Tissue Bank of the Fonds de recherche du Quebec ?Sante (FRQS) (www.tissuebank.ca); at ??Groningen, the lung specimens were provided by the local tissue bank of the Department of Pathology, and at UBC, the lung specimens were provided by the James Hogg Research Center Biobank at St Paul’s Hospital. COPD diagnosis and severity were determined according to the GOLD recommendations [2]. Clinical characteristics of subjects by site are shown in Table 1.COPD Susceptibility LociLung eQTLs were overlaid onto COPD susceptibility loci identified by previous GWAS except for the 15q25-CHRNA3/ CHRNA5/IREB2 locus that we have reported on previously [15]. Three COPD loci were considered; 4q22 (FAM13A), 4q31 (HHIP) and 19q13 (RAB4B, EGLN2, MIA, CYP2A6). SNPs associated with COPD from previous GWAS were tabulated for the three loci (Table 2). SNPs genotyped in the lung eQTL consortium located 1 Mb up and downstream of the most distant associated SNPs in both directions were evaluated. Chromosomes 4q22 (88,875,90990,886,297), 4q31 (144,480,780-146,506,456) and 19q13 (40,292,404-42,302,706) include 718, 412 and 739 SNPs, respectively. Genes residing in the same regions were tested as cis-eQTLs for probe sets for 14 genes on 4q22 (SPP1, PKD2, ABCG2, PPM1K, HERC6, HERC5, PIGY, HERC3, NAP1L5, FAM13A, TIGD2, GPRIN3, SNCA, MMRN1), 9 genes on 4q31 (FREM3, GYPE, GYPB, GYPA, HHIP, ANAPC10, ABCE1, OTUD4, SMAD1) andTable 1. Clinical characteristics of patients that passed gene expression and genotyping quality control filters.Laval (n = 409) Male ( ) Age (years) Body Mass Index (kg/m ) FEV1 predicted – pre-BD* ( ) FVC predicted ?pre-BD* ( ) FEV1/FVC COPD Stage 1 : Mild Stage 2 : Moderate Stage 3 : Severe Stage 4 : Very Severe Asthma Diabetes Cardiac diseases Smoking Smoker Ex-Smoker Non-Smoker Not available Pack-years in ever-smokers FEV1 : forced expiratory volume in 1 second. FVC : forced vital capacity. [-] = missing value. *pre-BD: pre-bronchodilator. doi:10.1371/journal.pone.0070220.t001 90 (22.0 ) 283 (69.2 ) 36 (8.8 ) 0 (0.0 ) 48.5627.5 [37]UBC (n = 339) 53.7 60.2614.3 25.665.4 [56] 78.2624.4 [77] 86.9620.1 [75] 0.6760.13 [77] 115 (33.9 ) [99] 43 (37.4 ) 60 (52.2 ) 2 (1.7 ) 10 (8.7 ) 22 (6.5 ) 13 (3.8 ) 46 (13.6 )Groningen (n = 363) 53.2 51.5615.5 [9] 23.264.2 [42] 60.5630.0 [194] 75.0626.5 [208] 0.6460.19 [189] 158 (43.5 ) [120] 20 (12.6 ) 38 (23.9 ) 21 (13.2 ) 69 (43.4 ) 0 (0.0 ) 27 (7.4 ) 28 (7.7 )55.9 63.369.9 26.765.3 80.5618.9 [16] 89.8616.1 [31] 0.6760.10 [32] 211 (51.6 ) [34] 82 (38.9 ) 117 (55.4 23977191 ) 11 (5.2 ) 1 (0.5 ) 15 (3.7 ) 41 (10.0 ) 120 (29.3 )98 (28.9 ) 163 (48.1 ) 26 (7.7 ) 52 (15.3 ) 44.7628.5 [58]57 (15.7 ) 185 (51.0 ) 100 (27.5 ) 21 (5.8 ) 31.2617.4 [51]Refining COPD Susceptibility Loci with Lung eQTLsgenes on 19q13 (DYRK1B, FBL, FCGBP, PSMC4, ZNF546, ZNF780B, ZNF780A, MAP3K10, TTC9B, CNTD2, AKT2, C19orf47, P.
