The Genome Center for Alzheimer’s Disease (GCAD) is funded under the NIA cooperative agreement (U54 AG052427) to identify genetic variants that cause, influence risk, or protect against this disorder, and to identify the underlying genes affected by these variants.

Information about ADSP study data could be found at the NIAGADS Data Sharing Service website: https://dss.niagads.org/datasets/ng00067/.

GCAD Mission

The role of the Genome Center for Alzheimer’s Disease (GCAD) is to coordinate the integration and meta-analysis of all available Alzheimer’s disease (AD) relevant genetic data with the goal of identifying AD risk/causative/protective genetic variants and eventual therapeutic targets.

To this end, GCAD will:

  • Assemble and harmonize whole-genome (WGS)/whole-exome (WES) sequencing data.
  • Build ADRD specific reference panels from GCAD WGS data for GWAS imputation.
  • Call structural variants from sequencing data (insertions, deletions, copy number variations) following best practices.
  • Support of Functional Genomics and Cognitive Systems Analysis of Alzheimer’s Disease Genetic and Phenotype data projects.
  • Facilitate analysis of GCAD genetic and functional data collection.
  • Identify candidate therapeutic targets by combining and reviewing analysis results by GCAD and other ADSP/non-ADSP projects.

As mandated by NIA, the GCAD will broadly disseminate all results and derivative data [e.g. imputed genotypes, variant call format (VCF) files recalled using ADSP protocols, etc.]. All GCAD results and derivative data will be distributed to ADSP and other AD investigators, particularly those working on functional analysis of AD-associated genetic variants.


GCAD External Advisory Board Core A Core B Core C Administrative Core Data Management, Harmonization, and Data Transfer Core Quality Control (QC)/Quality Assurance (QA) and Statistical Analysis Core

coordinates all aspects of GCAD activities.

Specific tasks of the Core A are:

  • Coordinate acquisition of ADRD genetics, functional genomics, and phenotype data with NIA officials, ADSP investigators, sequencing facilities, and other participating investigators and projects.
  • Coordinate data processing, harmonization and analyses by working with the other two cores, tracking and sharing progress.
  • Support/foster collaboration with key research projects and contributors to ADSP with teleconferences, face-to-face meetings, and GCAD website.
  • Disseminate data and findings to a diverse group of investigators by data production newsletters, gene verification committee, and research round table.
  • Provide administrative support to GCAD including governance, Institution Review Board (IRB) protocol review, and data sharing compliance.

harmonizes all genetic and phenotype data, and fully annotates all variants.

Specific tasks of Core B are:

  • Receive and manage all relevant data including whole genome/whole exome sequencing, phenotypes, and functional genomics data.
  • Calling SNVs, indels and structural variants (SVs) from sequencing data.
  • Develop a GCAD haplotype reference panel with Alzheimer’s disease and related dementia (ADRD)-specific variants from GCAD WGS data for GWAS imputation.
  • Facilitate harmonization of FG/omics data identified by Core A with best practices/workflows, and incorporate significant findings into the GCAD/ADSP genetic variant annotation workflow.
  • Support GCAD IT and information dissemination activities with cloud computing and website IT management, data management and transfer, and workflow optimization and maintenance.

reviews data production quality and designs analysis protocols.

Core C tasks include:

  • Evaluate quality of updated variant calling pipelines.
  • Develop and Extend Quality Control/Quality Assurance (QC/QA) Pipelines.
  • Evaluate QC/QA of Sequencing Joint Calling and Perform Association Analysis of ADSP and other large-scale sequencing projects in US and Europe.
  • Developing and Extending SV calling workflow.