PgmNr 1215: The Alzheimer’s Disease Sequencing Project (ADSP) data update 2017.Authors:
Y. Zhao 1; A.B. Kuzma 1; K.M. Faber 3; W.J. Salerno 6; Y.Y. Leung 1; L.B. Cantwell 1; M. Feolo 4; A. Stine 4; N. Gupta 5; R. Fulton 7; O. Valladares 1; R. Cweibel 1; E. Applebaum 7; S.H. Choi 2; K.L. Hamilton-Nelson 11; H.-J. Lin 1; D. Muzny 6; L. Qu 1; D. Reyes 9; J. Waligorski 7; J. Farrell 12; A.C. Naj 1; J.C. Bis 8; A.L. DeStefano 2; S. Seshadri 10; E. Boerwinkle 6; G.D. Schellenberg 1; T.M. Foroud 3; L.-S. Wang 1; Alzheimer's Disease Sequencing Project Data Flow Work Group
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1) Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA; 2) School of Public Health, Boston University, Boston, MA; 3) Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana; 4) National Center for Biotechnology Information, National Institutes of health, Bethesda MD; 5) Broad Institute of Harvard and MIT, Cambridge, MA; 6) Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; 7) The Genome Institute, Washington Univ., St. Louis, MO; 8) Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA; 9) Taub Institute for Research on Alzheimer's Disease, Columbia University, New York; 10) Department of Neurology, Boston University School of Medicine, Boston, MA; 11) John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL; 12) School of Medicine, Boston University, Boston, MA
Statement of Purpose. The Alzheimer’s Disease Sequencing Project (ADSP) was established in 2012 as a key initiative to meet the goals of the National Alzheimer’s Project ACT (NAPA) to prevent and effectively treat Alzheimer’s disease (AD) by 2025. Developed jointly by National Institute on Aging (NIA) and the National Human Genome Research Institute (NHGRI), the aims of the ADSP are to: 1) identify protective genomic variants in older adults at risk for AD, 2) identify new risk variants among AD cases, and 3) examine these factors in multi-ethnic populations to identify therapeutic targets for disease prevention.
Methods. The ADSP Data Flow Work Group (DFWG) and the NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) support data production, sharing and management for the ADSP, and facilitation of data access to the community. Samples are contributed by the AD Genetics Consortium (ADGC) and Cohorts for Heart and Aging Research in Genomic Epidemiology consortium (CHARGE). Sample plating and shipping is coordinated by the National Cell Repository for AD (NCRAD). Whole-exome (WES) and whole-genome (WGS) sequencing data were generated by three NHGRI funded Sequencing Centers and quality controlled by the ADSP. The DFWG maintains the ADSP web site, providing study design, cohort information, news releases, and application instructions for ADSP access. The ADSP Data Portal is a collaboration with the Database of Genotypes and Phenotypes (dbGaP), Sequence Read Archive (SRA), and NIAGADS. The portal allows users to explore the ADSP project data archived at dbGaP with NIH iTrust user authentication. Approved investigators identify data and download files using a customizable filtering system and check-out cart function.
Results. The ADSP has completed whole-exome sequencing of 10,939 unrelated cases and controls, whole-genome sequencing of 892 members from 159 families, and whole-genome sequencing of 3,144 unrelated cases and controls. All newly sequenced genomes are being processed on GRCh38 by the Genome Center for AD (GCAD) and are expected to be available in late 2017. Accompanying each sample are phenotypes that were harmonized according to ADSP protocols.
Conclusion. The DFWG provides support to all ADSP Work Groups for data related issues, coordinates with dbGaP for data transfers, and reviews, posts, and notifies members of new results generated by other Work Groups. Find additional information at the ADSP website (www.niagads.org/adsp).