SAIGE-QTL: Single-nucleus Expression QTL Summary Statistics using Human Brain Cohort

https://github.com/RajLabMSSM/SingleBrain Full associations and top association summary statistics for cis-eQTLs mapped in the human brain single-nucleus RNA seq cohort(Fujita et al.[PMID: 38514782]) using SAIGE-QTL[PMID: 38798318], as part of the "SingleBrain" project. Sample size = 402 European ancestry donors. Each file has the following naming convention: {Cell type}_eqtl_{ASSOC}.tsv.gz References The following reference was used for mapping phenotypes: 1. GENCODE - GENCODE v38 comprehensive transcripts (https://www.gencodegenes.org/human/release_38.html) Cell type The following brain 7 major cell types were tested for genetic association: Ast: astrocytes End: endothelial cells Ext: excitatory neurons IN: inhibitory neurons MG: microglia OD: oligodendrocytes OPC: oligodendrocyte progenitor cell All phenotype matrices were scaled and centered and then quantile normalized. Associations Top associations (top_assoc.tsv.gz) list the SNP-feature pair with the lowest adjusted P-value (ACAT_P) for that feature. Full associations (full_assoc.tsv.gz) list all tested SNP-feature pairs. Data dictionary The columns of the two association files only differ by the presence of the ACAT_P column in the top associations. feature: the phenotype being tested CHR: chromosome POS: position (hg38) MarkerID: the genetic variant being tested Allele1: reference allele Allele2: alternate allele AC_Allele2: Alternate allele count AF_Allele2: Alternate allele frequency in the sample MissingRate: genotype missing rate BETA: Effect size estimate (per allele effect) SE: Standard error of beta Tstat: T-statistic for the effect size var: Variance of the score test statistic p.value: P-value p.value.NA: P-value computed using a normal approximation (Wald or score test), not SPA. Is.SPA: Whether the Saddlepoint Approximation (SPA) converged (TRUE/FALSE) N: Sample size used in the test p_bonf: P-value adjusted for the number of variants tested in that feature (Bonferroni) p_FDR: P-value adjusted for the number of variants tested in that feature (FDR) ACAT_P: Aggregated Cauchy Association Test (ACAT) p-value, which is a gene-level p-value combining multiple single-variant p-values for a given gene or region.https://github.com/RajLabMSSM/SingleBrain 本数据集为"SingleBrain"项目的组成部分，包含基于人类大脑单细胞核RNA测序队列（Fujita等[PMID: 38514782]）、采用SAIGE-QTL[PMID: 38798318]分析得到的顺式表达数量性状位点（cis-eQTL）关联结果，以及其顶级关联汇总统计量。 本数据集的样本量为402名欧洲血统捐赠者。 所有文件均遵循以下命名规则：{Cell type}_eqtl_{ASSOC}.tsv.gz ### 参考文献 用于表型定位的参考数据集如下： 1. GENCODE：GENCODE v38 综合转录本（https://www.gencodegenes.org/human/release_38.html） ### 检测细胞类型 本研究针对以下7种人类大脑主要细胞类型开展遗传关联分析： - Ast：星形胶质细胞（astrocytes） - End：内皮细胞（endothelial cells） - Ext：兴奋性神经元（excitatory neurons） - IN：抑制性神经元（inhibitory neurons） - MG：小胶质细胞（microglia） - OD：少突胶质细胞（oligodendrocytes） - OPC：少突胶质前体细胞（oligodendrocyte progenitor cell） ### 数据预处理 所有表型矩阵均经过标准化中心化处理，随后进行分位数归一化。 ### 关联结果文件说明 1. 顶级关联文件（top_assoc.tsv.gz）：列出每个特征对应的经校正P值（ACAT_P）最低的SNP-特征对。 2. 完整关联文件（full_assoc.tsv.gz）：列出所有经过测试的SNP-特征对。 ### 数据字典 两种关联文件的列仅存在一处差异：顶级关联文件包含ACAT_P列。各字段说明如下： - feature：待检测的表型 - CHR：染色体编号 - POS：基因组位置（hg38参考基因组） - MarkerID：待检测的遗传变异位点标识 - Allele1：参考等位基因 - Allele2：变异等位基因 - AC_Allele2：变异等位基因计数 - AF_Allele2：研究样本中变异等位基因的频率 - MissingRate：基因型缺失率 - BETA：效应大小估计值（每等位基因的效应） - SE：效应估计值的标准误 - Tstat：效应大小的T统计量 - var：得分检验统计量的方差 - p.value：原始P值 - p.value.NA：基于正态近似（Wald检验或得分检验，而非鞍点近似SPA）计算得到的P值 - Is.SPA：鞍点近似（Saddlepoint Approximation, SPA）是否收敛，取值为TRUE/FALSE - N：关联检验中使用的样本量 - p_bonf：针对该特征检测的变异数进行邦费罗尼校正（Bonferroni）后的P值 - p_FDR：针对该特征检测的变异数进行错误发现率（False Discovery Rate, FDR）校正后的P值 - ACAT_P：聚合柯西关联检验（Aggregated Cauchy Association Test, ACAT）P值，即整合单个基因/区域内多个单变异P值的基因水平P值。