FunGen-AD Resources#

About FunGen-AD#

The Alzheimer’s Disease Sequencing Project Functional Genomics Consortium (FunGen-AD) is a collaborative initiative aimed at understanding the molecular mechanisms underlying Alzheimer’s disease through multi-omic and genetic screening approaches.

Available Resources#

FunGen-xQTL#

The FunGen-xQTL project provides comprehensive molecular quantitative trait loci (QTL) analyses across multiple molecular phenotypes, along with integrative analysis for neurodegenerative disorders particularly Alzheimer’s disease. All datasets are hosted on Synapse: variant & gene summaries (syn69865684), xQTL models (syn69670588), raw QTL data (syn69670632).

• xQTL Analysis and xQTL-GWAS Integration Results along with File Format Description
• Study Cohorts - Information about participating cohorts including ROSMAP, Knight ADRC, MSBB, MiGA, MAGENTA, STARNET, EFIGA, WHICAP, and MetaBrain
• GWAS Summary Statistics - Alzheimer’s disease GWAS data from major studies (Bellenguez 2022, Kunkle 2019, Wightman 2021, Jansen 2019) and integrated AD fine-mapping and colocalization analyses
• Molecular Phenotypes - Multi-omic data including:
  • Gene expression (bulk RNA-seq: ROSMAP DLPFC/PCC/AC/microglia/monocyte, MSBB, Knight ADRC, MetaBrain, MiGA, MAGENTA, STARNET)
  • Alternative splicing (bulk RNA-seq and single-nucleus with ISSAC method)
  • Proteomics including glycoproteomics (brain and CSF)
  • DNA methylation
  • Histone modification (H3K9ac ChIP-seq)
  • Chromatin accessibility (snATAC-seq)
  • Metabolomics (brain, CSF, and plasma)
  • Single-nucleus RNA-seq (ROSMAP DLPFC: CUIMC, MIT, and mega cohorts)
  • Genotype (WGS) and covariates
• xQTL Data - Molecular QTL associations organized by modality: eQTL, sQTL, pQTL, gpQTL, mQTL, haQTL, caQTL, metaQTL
• Reference Data - ADSP-based LD reference panels (16,905 European ancestry samples) and other analytical resources

Software resources implementing the xQTL analysis are also available:

• xQTL Analysis Protocol - Standardized computational protocols for QTL mapping, fine-mapping, colocalization, and integrative analyses
• xQTL Companion Statistical Methods Implementation - Fine-mapping, enrichment, colocalization, TWAS, and Mendelian randomization tools

Data Access#

All datasets are available through controlled access via:

• Synapse — variant & gene summaries (syn69865684)
• Synapse — xQTL models (syn69670588)
• Synapse — raw QTL data (syn69670632)
• Synapse — reference files (syn69670634)
• NIAGADS (genomics data)

This resource is actively maintained by the FunGen-AD Analysis Working Group and reflects data generated through March 2026