Knockoff-based methods have become increasingly popular due to their enhanced power for locus discovery and their ability to prioritize putative causal variants in a genome-wide analysis. However, because of the substantial computational cost for generating knockoffs, existing knockoff approaches cannot analyze millions of rare genetic variants in biobank-scale whole-genome sequencing and whole-genome imputed datasets. We propose a scalable knockoff-based method for the analysis of common and rare variants across the genome, KnockoffScreen-AL, that is applicable to biobank-scale studies with hundreds of thousands of samples and millions of genetic variants. The application of KnockoffScreen-AL to the analysis of Alzheimer disease (AD) in 388,051 WG-imputed samples from the UK Biobank resulted in 31 significant loci, including 14 loci that are missed by conventional association tests on these data. We perform replication studies in an independent meta-analysis of clinically diagnosed AD with 94,437 samples, and additionally leverage single-cell RNA-sequencing data with 143,793 single-nucleus transcriptomes from 17 control subjects and AD-affected individuals, and proteomics data from 735 control subjects and affected indviduals with AD and related disorders to validate the genes at these significant loci. These multi-omics analyses show that 79.1% of the proximal genes at these loci and 76.2% of the genes at loci identified only by KnockoffScreen-AL exhibit at least suggestive signal (p < 0.05) in the scRNA-seq or proteomics analyses. We highlight a potentially causal gene in AD progression, EGFR, that shows significant differences in expression and protein levels between AD-affected individuals and healthy control subjects.

基于基因敲除的方法因其增强的基因座发现能力以及在全基因组分析中优先考虑推定的因果变异的能力而变得越来越流行。然而，由于生成仿制品的计算成本很高，现有的仿制品方法无法分析生物库规模的全基因组测序和全基因组估算数据集中的数百万稀有遗传变异。我们提出了一种可扩展的基于仿制的方法，用于分析整个基因组中的常见和罕见变异，KnockoffScreen-AL，适用于具有数十万个样本和数百万个遗传变异的生物样本库规模的研究。KnockoffScreen-AL的应用对来自英国生物库的 388,051 个 WG 估算样本中的阿尔茨海默病 (AD) 进行分析，得出 31 个重要位点，其中包括 14 个被这些数据的常规关联测试遗漏的位点。我们对临床诊断为 AD 的 94,437 个样本进行独立荟萃分析进行复制研究，另外还利用来自 17 名对照受试者和受 AD 影响的个体的 143,793 个单核转录组的单细胞 RNA 测序数据，以及来自 735 个对照的蛋白质组学数据研究对象和患有 AD 及相关疾病的受影响个体，以验证这些重要位点的基因。这些多组学分析表明，这些位点的 79.1% 的近端基因和仅由KnockoffScreen-AL识别的位点的 76.2% 的基因在 scRNA-seq 或蛋白质组学分析中至少表现出提示性信号 (p < 0.05)。我们强调了 AD 进展中的一个潜在致病基因EGFR，它显示受 AD 影响的个体和健康对照受试者之间的表达和蛋白质水平存在显着差异。