Submitted by rcweibel on Thu, 06/09/2016 - 16:22
Core A (Administrative Core) coordinates all aspects of GCAD activities.
Specific tasks of the Administrative Core are:
- Support and foster collaboration between ADSP and AD genetics investigators, and RFA-AG-16002 investigators;
- Coordinate the collection of genetic and phenotype data from ADSP Discovery and Replication phase, and all relevant non-ADSP data, and transfer the data to Core B;
- Coordinate data harmonization of all AD-relevant genetic and phenotype data and analysis for AD risk and protective variants;
- Distribute analysis-ready files and analysis results to ADSP and all AD genetics investigators. Files will be fully annotated. Analysis files will be results from joint and meta- analysis results generated by GCAD, the ADSP, and RFA-AG-16002;
- Disseminate data/findings to a diverse group of investigators including ADSP investigators and Replication phase collaborators, AD genetics investigators including those funded by NIA through other mechanisms (e.g. RO1’s), and the broader scientific community through data sharing via National Institute on Aging Genetics of Alzheimer’s Disease storage site (NIAGADS) and database of Genotypes and Phenotypes (dbGaP);
- Lead Research Round table where genetic results are shared with AD investigators working on molecular mechanisms related to pathogenesis.
Core B (Data Management, Harmonization, and Data Transfer Core) harmonizes all genetic and phenotype data, and fully annotate all variants.
Specific tasks of Core B are:
- Capture and maintain all relevant data including sequence data, genotypes, phenotypes, analysis results, and other relevant data from ADSP Discovery Phase, Replication Phase, and non-ADSP sources;
- Harmonize genotype and phenotype data using protocols in collaboration with Core C;
- Impute single nucleotide variants (SNVs) for all genome-wide SNV array data using the Haplotype Reference Consortium (HRC) reference panels and AD-specific variants from ADSP WES/WGS data;
- Call structural variants (SVs) for ADSP Replication and non-ADSP data;
- Provide in silico annotation analysis-ready files using the Genome Wide Annotation Resource (GWAR) and current ADSP protocols;
- Transfer information to ADSP, RFA-AG-16002 U01, and the general research community via GCAD/ADSP website, relational databases, and NIA approved data repositories including dbGaP and NIAGADS;
- Provide infrastructure and support for GCAD computing and analyses.
Core C (Biostatistics and Data Analysis Core) designs all harmonization and annotation protocols.
Core C tasks include:
- Re-evaluate the Discovery Phase analyses for additional findings that may be considered in the Replication Phase;
- Design and conduct Replication Phase analyses;
- Design and conduct comprehensive analyses of the aggregate Discovery and Replication Phase data;
- Design and conduct analyses to incorporate genetic data generated outside the ADSP for subjects and families used in the ADSP discovery and Replication Phases;
- Design and conduct the Extended Replication Phase analyses to incorporate genetic data from subjects and cohorts not directly involved in the ADSP project;
- Design post analyses;
- Develop novel analyses approaches.