NG00126 – A fast and robust strategy to remove variant level artifacts in Alzheimer’s Disease Sequencing Project data (Belloy et al. 2022)

We performed Whole-exome and Whole-Genome association analyses with Alzheimer’s disease risk in ADSP data (NG00067.v5), focusing on non-Hispanic white individuals of European ancestry. Specifically, we designed novel variant filters that account for variant frequency differences across sequencing centers/platforms in the ADSP data. Here, we share the related summary statistics from the Alzheimer’s disease risk association analyses, together with those from the primary Fisher exact tests used to assess cross-center/platform variant frequency differences, as well as relevant information from other gnomAD filters and duplicate sample filters that were implemented. Technical and analytical details regarding the filters and association models are detailed in the manuscript. ADSP WES analyses included 11,573 individuals (5,418 controls and 6,155 cases). ADSP WGS analyses included 6,533 individuals (2,949 controls and 3,584 cases). The p-value data is generally available to all users using the public link. However, gaining access to the complete dataset requires a formal data request.