Core B (Data Management, Harmonization, and Information Transfer) is mandated by RFA-AG-16001 as part of the NIA Coordinating Center for Genetics and Genomics of Alzheimer's Disease (CGAD). Core B's primary goal is to facilitate the analysis of the Replication Phase and Extended Replication Phase of the Alzheimer's Disease Sequence Project (ADSP) by harmonizing all Alzheimer's disease (AD) relevant genotype and phenotype data. The Replication Phase will use ADSP data and the Extended Replication Phase will use non- ADSP data (Core A, Tables 3-5), and data for both phases will be harmonized by Core B. Harmonization will use protocols developed by the ADSP and re-evaluated by Core C. Core B will produce fully annotated analysis-ready files. These files/data will be distributed to Core C and all ADSP/RFA-AG16002 UO1 and AD genetics investigators. Core C will develop and implement analyses plans, in collaboration with other ADSP/RFA-AG16002 UO1 investigators (also see the Overall Component). Core B will provide the high- performance computing infrastructure for computationally intensive tasks. Core B will manage all CGAD phenotype, genotype, annotation, and analysis results, and distribute data/files to all ADSP/RFA-AG16002 investigators, to Genotypes and Phenotypes (dbGaP), and to NIA Genetics of Alzheimer's Data Storage Site (NIAGADS). Specific tasks of Core B are: 1) 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; 2) Harmonize genotype and phenotype data using protocols in collaboration with Core C; 3) 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; 4) Call structural variants (SVs) for ADSP Replication and non-ADSP data; 5) Provide in silico annotation analysis-ready files using the Genome Wide Annotation Resource (GWAR) and current ADSP protocols; 6) Transfer information to ADSP, RFA-AG-16002 U01, and the general research community via CGAD/ADSP website, relational databases, and NIA approved data repositories including dbGaP and NIAGADS; 7) Provide infrastructure and support for CGAD computing and analyses.
| Raghavan, Neha S; Brickman, Adam M; Andrews, Howard et al. (2018) Whole-exome sequencing in 20,197 persons for rare variants in Alzheimer's disease. Ann Clin Transl Neurol 5:832-842 |
| Zhou, Zilu; Wang, Weixin; Wang, Li-San et al. (2018) Integrative DNA copy number detection and genotyping from sequencing and array-based platforms. Bioinformatics 34:2349-2355 |
| Sivley, R Michael; Dou, Xiaoyi; Meiler, Jens et al. (2018) Comprehensive Analysis of Constraint on the Spatial Distribution of Missense Variants in Human Protein Structures. Am J Hum Genet 102:415-426 |
| Blue, Elizabeth E; Bis, Joshua C; Dorschner, Michael O et al. (2018) Genetic Variation in Genes Underlying Diverse Dementias May Explain a Small Proportion of Cases in the Alzheimer's Disease Sequencing Project. Dement Geriatr Cogn Disord 45:1-17 |
| Leung, Yuk Yee; Valladares, Otto; Chou, Yi-Fan et al. (2018) VCPA: genomic Variant Calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. Bioinformatics : |
