Additional file 1: Tables S1. of Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia
Year: 2016
Type: article
Study design: Observational Study
Abstract: 205 SNPs Associated with IIP at 5 × 10−8 in Imputation Analysis. Table S2: SNPs with 5×10−8 < Pimputed-adjusted < .0001. Table S3: GWAS-Significant SNPs after Meta-Analysis in All Regions (Most Significant in Region in Bold Type). Table S4: Table of 70 SNPs (46 original, 24 from imputation) Adjusted for Top SNP in Region if More than One SNP in Region. Top SNP Defined in Bold Type in Table S3a. All Cases (Discovery and GWAS) Compared to Replication Controls. Table S5: HLA Allele Imputation Accuracy Summary. Table S6: HLA Allele Association with IIP. Table S7: Chromosome 6p21 genes studied via RNA-seq. Table S8: Differential Expression by Case–control Status. Table S9: Differential Expression by Genotype at rs7887 Among Controls. Table S10: Differential Expression by Imputed Number of Copies of DRB1*15:01 Among Cases (RNA-seq). Table S11: Differential Expression by Imputed Number of Copies of DQB1*06*02 Among Cases (RNA-seq). Table S12: 214 Novel SNPs Meeting Carry-forward Threshold at P < 1 × 10−4 in Imputation Analysis using 1000 Genomes Reference. Figure S1: Q-Q plots of P-values from SNPTest using Imputed Dosage for a) Genotyped SNPs and b) Imputed SNPs Prior to Genomic Control Adjustment Based on Genotyped SNP P-values from GEMMA analysis (see manuscript statistical methods for details). Figure S2: Q-Q plot of imputed (adjusted) p-values (inflation factor = 1.04) after genomic control correction. Figure S3: Imputation GWAS Results Fig. 1: Imputation GWAS results with 1616 cases and 4683 controls under additive model. SNPs above red line were genome-wide significant at P < 5 × 10-8. A subset of these SNPs and SNPs between red and blue lines, corresponding to 5 × 10−8 < P-value < .0001, were selected for follow-up and genotyped in 878 cases and 2017 controls. Figure S4: Histogram of. INFO Scores from SNPTest. Only SNPs with .INFO >0.5 Included. Figure S5: Comparison of SNPTest p-values after genomic control (see manuscript statistical methods) and GEMMA dosage-values. GEMMA dosage p-values computed after initial study complete. (DOCX 8917 kb)
Source: Figshare
Authors: Fingerlin, Tasha, Zhang, Weiming, Yang, Ivana, Ainsworth, Hannah, Russell, Pamela, Blumhagen, Rachel, Schwarz, Marvin, Brown, Kevin, Steele, Mark, Loyd, James, Cosgrove, Gregory, Lynch, David, Groshong, Steve, Collard, Harold, Wolters, Paul, Bradford, Williamson, Kossen, Karl, Seiwert, Scott, du Bois, Roland, Garcia, Christine, Devine, Megan, Gudmundsson, Gunnar, Isaksson, Helgi, Kaminski, Naftali, Zhang, Yingze, Gibson, Kevin, Lancaster, Lisa, Maher, Toby, Molyneaux, Philip, Wells, Athol, Moffatt, Miriam, Selman, Moises, Pardo, Annie, Kim, Dong, Crapo, James, Make, Barry, Regan, Elizabeth, Walek, Dinesha, Daniel, Jerry, Kamatani, Yoichiro, Zelenika, Diana, Murphy, Elissa, Smith, Keith, McKean, David, Pedersen, Brent, Talbert, Janet, Powers, Julia, Markin, Cheryl, Beckman, Kenneth, Lathrop, Mark, Freed, Brian, Langefeld, Carl, Schwartz, David
Language: English
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W7137860088