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News

Creating the Largest Joint-Called Whole Exome Sequencing (WES) Dataset for Alzheimer’s Disease (AD)

March 18, 2024
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? And can researchers analyze sequence data generated in different locations, on different platforms, using different technologies? These are becoming increasingly important issues for the research community to address. The Genome Center for Alzheimer’s Disease ( GCAD ) tackled these...

15 Genotyping Array Datasets From the Alzheimer's Disease Research Centers (ADRC) Now Available via DSS!

February 9, 2024
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 Related Dementias (NCRAD) and phenotypes were provided by the National Alzheimer’s Coordinating Center (NACC) . Collection and harmonization were facilitated by the Alzheimer's Disease Genetics Consortium (ADGC) , which included rigorous quality...

Introducing hipFG: A high-throughput harmonization and integration pipeline for genomic annotations, QTLs, and chromatin interactions

January 5, 2024
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 these needs for cleanup and harmonization of functional genomics data is how hipFG (Harmonization and Integration Pipeline for Functional Genomics ) , a high-throughput harmonization and integration pipeline, was born. We sat down with Jeffrey Cifello, lead code developer for the hipFG...

Alzheimer’s Disease Sequencing Project Update: Round 2 of the Harmonized Phenotypes and R4 36K Annotations Released

December 12, 2023
A new version of ng00067, the ADSP Umbrella Dataset is available on NIAGADS DSS . The ng00067.v11 release 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: Anti-Amyloid Treatment in Asymptomatic Alzheimer’s study (A4 Study) Adult Changes in Thought (ACT) Study Alzheimer’s Disease Neuroimaging Initiative (ADNI) Estudio Familiar de Influencia Genetica en Alzheimer (EFIGA) Memory & Aging Project at Knight Alzheimer’s Disease Research Center (MAP at...

ADSP R4 Quality-controlled Data for WGS Bi-allelic Autosomes is Here!

August 16, 2023
The ADSP has recently unveiled an updated version of the dataset (ng00067.v10) that encompasses valuable genetic information. This release comprises two key components: 1. A quality-controlled project-level Variant Call Format (pVCF) file for bi-allelic autosomes derived from the R4 whole genome sequencing (WGS) dataset, encompassing 36,361 samples. 2. Individual-level structural variant calls generated by two callers, Manta and Smoove, specifically for the new samples introduced in R4 (n=19,451). Furthermore, the R4 quality-controlled pVCF offers compact and compact filtered versions,...

See you at the Alzheimer’s Association International Conference (AAIC)!

July 15, 2023
Check out NIAGADS at the Alzheimer’s Association International Conference NIAGADS will be at the Alzheimer’s Association International Conference being held in Amsterdam, Netherlands and virtually. Hear About the Latest NIAGADS Developments! Our team will be presenting posters. Please stop by for a deep dive into recent advances for NIAGADS and ADSP. Posters are also viewable online on Twitter @NIAGADS. Date Title Poster Number 7/17 ADSP Whole Genome Sequencing (WGS) Release 4 Data Update from Genome Center for Alzheimer’s Disease P2-016 7/17 The Prediction of Alzheimer’s Disease through...
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