The Alzheimer’s Genomics Database is a user-friendly AD-centric interactive knowledgebase and genome browser, which provides unrestricted access to GWAS summary statistics from the NIAGADS repository, as well as to annotated variants called from ongoing the Alzheimer’s Disease Sequencing Project’s (ADSP) joint-genotype calling efforts. We sat down with Dr. Emily Greenfest-Allen,…
Category: ADSP
Updates to the Data Access Request Management (DARM) and Data Sharing Service (DSS) Portals
The NIAGADS team has been hard at work writing and testing code to improve user experience in the DARM and DSS portals. We are happy to share that the following features are now available to users: DARM Administrator Role Added – Investigators can now designate “Administrators” to complete data applications…
Creating the Largest Joint-Called Whole Exome Sequencing (WES) Dataset for Alzheimer’s Disease (AD)
Over the last 20 years, the technology for DNA sequencing has rapidly evolved, making it possible to sequence individual whole genomes on a large scale. But when trying to find the underlying genetic causes of disease, every sequence donated matters. How can the sequences generated using older technology be reused?…
15 Genotyping Array Datasets From the Alzheimer’s Disease Research Centers (ADRC) Now Available!
We are thrilled to announce the release of 15 much-anticipated genotyping array datasets from participants recruited from the Alzheimer’s Disease Research Centers (ADRC)! These datasets, ADC1 through ADC15, are now available on the NIAGADS Data Sharing Service (DSS). DNA was prepared by the National Centralized Repository for Alzheimer’s Disease and…
Introducing hipFG: A high-throughput harmonization and integration pipeline for genomic annotations, QTLs, and chromatin interactions
A major challenge facing researchers today is the cleanup and harmonization of data for use in their work. As datasets get larger and the types of outputs continue to grow, this problem will continue to grow exponentially. Manually cleaning this data can be time consuming and prone to human error. Addressing…
Alzheimer’s Disease Sequencing Project Update: Round 2 of the Harmonized Phenotypes and R4 36KAnnotations Released
A new version of ng00067, the ADSP Umbrella Dataset is available on NIAGADS DSS. The ng00067.v11release consists of: The round 2 harmonized phenotypes from the Phenotype Harmonization Consortium, which includes a subset of harmonized, ADSP-sequenced participant data from the following studies: o Anti-Amyloid Treatment in Asymptomatic Alzheimer’s study (A4 Study)o…
ADSP R4 Quality-controlled Data for WGS Bi-allelic Autosomes is Here!
The ADSP has recently unveiled an updated version of the dataset (ng00067.v10) that encompasses valuable genetic information. This release comprises two key components: Furthermore, the R4 quality-controlled pVCF offers compact and compact filtered versions, providing smaller files that are more convenient to handle. Additionally, a user-friendly script has been made…
ADSP Releases Additional 19K Whole Genomes via NIAGADS DSS
On October 6, 2022, the Alzheimer’s Disease Sequencing Project (ADSP) released a new dataset comprised of 19,456 newly sequenced genomes together with joint genotype calls totaling 36,361 genomes with previously released genomes. The data release includes sequencing reads in the CRAM file format, individual sample genotype calls in the genomic…
ADSP releases quality-controlled whole-genome data on nearly 17,000 samples
NIAGADS is pleased to announce the release of the Release 3 (R3) WGS ADSP quality-controlled joint genotype called pVCF containing 16,905 samples. Additionally, this release includes a quality-controlled X-chromosome pseudoautosomal region (PAR) pVCF containing 20,503 whole exomes from Release 2 (R2) as well as R3 individual-level VCF structural variant (SV)…
NIAGADS DSS Releases Additional 17K Whole Genomes
NIAGADS is pleased to announce the release of whole genome sequencing (WGS) data from 16,906 samples through the Data Sharing Service (DSS). The data release includes CRAMs, gVCFs, and project-level VCFs across all samples. The pVCF released here is provided as a preview to the formal ADSP quality control that will be released in a few months. Additionally, this release…