Additional file 2 of Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

Additional file 2: Table S1. Number of genes tested and Genomic inflation factor for each model and variant set. Table S2. Complete results of the genome-wide burden joint analysis, trans-pipeline meta-analysis and trans-ethnic meta-analysis on rare variants. Table S3. Best results of the genome-wide burden analysis on rare variants under a co-dominant and dominant model. Table S4. TLR7 homozygous and hemizygous variants (AF < 0.01). Table S5. Results of the genome-wide burden analysis on common and rare variants under a co-dominant model. Table S6. Results of the genome-wide burden analyses for the candidate genes identified by GWAS under co-dominant model. Table S7. Characteristics of patients and controls in the full sample and according to the inclusion in the Zhang Q. et al., Science 2020 paper. Table S8. Carriers of rare pLOF/bLOF variants in genes involved in type I IFN immunity to influenza virus. Table S9. Branchpoint variants identified by BPHunter and characteristics of the carriers. Table S10. Age and sex stratified analysis for the 15 type I IFN-related loci. Table S11. Enrichment analysis of rare variants, including missense and inframe variants, in genes involved in type I IFN immunity in the full cohort of 3269 cases and 1373 controls. Table S12. pLI and CoNeS distribution of the analyzed genes.

补充文件2：表S1。各模型及变异集的检测基因数量与基因组膨胀因子（genomic inflation factor）。表S2。罕见变异全基因组负担联合分析、跨流程元分析及跨种族元分析的完整结果。表S3。共显性与显性模型下罕见变异全基因组负担分析的最优结果。表S4。TLR7（Toll-like receptor 7）纯合与半合子变异（等位基因频率<0.01）。表S5。共显性模型下常见与罕见变异全基因组负担分析结果。表S6。全基因组关联研究（Genome-Wide Association Study, GWAS）筛选的候选基因在共显性模型下的全基因组负担分析结果。表S7。全样本中以及依据Zhang Q.等发表于《Science》2020年论文的纳入标准筛选的病例与对照受试者的基线特征。表S8。参与流感病毒I型干扰素（Type I Interferon, I型IFN）免疫通路的基因中罕见pLOF/bLOF变异的携带者情况。表S9。由BPHunter鉴定的剪接分支点变异及其携带者特征。表S10。针对15个I型干扰素相关基因座的年龄与性别分层分析结果。表S11。在包含3269名病例与1373名对照的全队列中，针对参与I型干扰素免疫通路的基因所开展的罕见变异（含错义变异与框内变异）富集分析结果。表S12。本次分析所涉及基因的pLI与CoNeS分布情况。