Materials for : Host-microbe interactions shape genetic risk for inflammatory bowel disease
Materials for : Host-microbe interactions shape genetic risk for inflammatory bowel disease
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2012
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1. IBD 基因座列表的生成...................................................................................... 3 1a. GWAS 数据和分析................................................................................................................................3队列和样本................................................................................................................................3 QC 和插补................................................................................................................................3主成分分析................................................................................................................4关联分析................................................................................................................4 1b．免疫芯片数据和分析................................................................................................................4 i．免疫芯片说明................................................................................................................4队列、样本和基因分型......................................................................................................5 iii．基因型检出和 QC ................................................................................................................5 iv.主成分分析 ................................................................................................................6 v. 关联分析 ................................................................................................................6 1c． GWAS/Immunochip 复制荟萃分析 ................................................................................7 i．主要信号分析................................................................................................................7将独立信号组合成基因座................................................................................7 1d．克罗恩病/溃疡性结肠炎可能性模型.................................................................8 1e.此基因座列表与之前的 CD 和 UC 列表的比较.......................................................9 1f. IBD、UC 和 CD 数据集中的上位分析.................................................................................10
1. Generation of IBD locus list ...................................................................... 3 1a. GWAS data and analysis .....................................................................................................3 i. Cohorts and samples ...........................................................................................................3 ii. QC and imputation.............................................................................................................3 iii. Principal component analysis...........................................................................................4 iv. Association analysis ..........................................................................................................4 1b. Immunochip data and analysis .............................................................................................4 i. Description of immunochip .................................................................................................4 ii. Cohorts, samples and genotyping ......................................................................................5 iii. Genotype calling and QC .................................................................................................5 iv. Principal component analysis ...........................................................................................6 v. Association analysis ...........................................................................................................6 1c. GWAS/Immunochip replication meta-analysis ....................................................................7 i. Analysis of primary signals.................................................................................................7 ii. Combination of independent signals into loci ...................................................................7 1d. Crohn’s disease/Ulcerative colitis likelihood modeling ..................................................8 1e. Comparison of this locus list to previous CD and UC lists..............................................9 1f. Epistasis analysis in IBD, UC and CD datasets .............................................................10