NIAGADS Alzheimer’s GenomicsDB: A resource for exploring Alzheimer’s Disease genetic and genomic knowledge

AbstractINTRODUCTIONThe NIAGADS Alzheimer’s Genomics Database is an interactive knowledgebase for AD genetics that provides access to GWAS summary statistics datasets deposited at NIAGADS, a national genetics data repository for AD and related dementia (ADRD).METHODSThe website makes available >70 genome-wide summary statistics datasets from GWAS and genome sequencing analysis for AD/ADRD. Variants identified from these datasets are mapped to up-to-date variant and gene annotations from a variety of resources and linked to functional genomics data.The database is powered by a big data optimized relational database and ontologies to consistently annotate study designs and phenotypes, facilitating data harmonization and efficient real-time data analysis and variant or gene report generation.RESULTSDetailed variant reports provide tabular and interactive graphical summaries of known ADRD associations, as well as highlight variants flagged by the Alzheimer’s Disease Sequencing Project (ADSP). Gene reports provide summaries of co-located ADRD risk-associated variants and have been expanded to include meta-analysis results from aggregate association tests performed by the ADSP allowing us to flag genes with genetic-evidence for AD.DISCUSSIONThe GenomicsDB makes available >100 million variant annotations, including ~30 million (5 million novel) variants identified as AD-relevant by ADSP, for browsing and real-time mining via the website or programmatically through a REST API. With a newly redesigned, efficient, search interface and comprehensive record pages linking summary statistics to variant and gene annotations, this resource makes these data both accessible and interpretable, establishing itself as valuable tool for AD research.

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DEF8 and Autophagy-Associated Genes are Altered in Mild Cognitive Impairment, Probable Alzheimer’s Disease Patients and a Transgenic Model of the Disease

Journal of Alzheimer s Disease ◽

10.3233/jad-201264 ◽

2021 ◽

pp. 1-16

Author(s):

Esteban Leyton ◽

Diego Matus ◽

Sandra Espinoza ◽

José Matías Benitez ◽

Bastián I. Cortes ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Cognitive Impairment ◽

Mild Cognitive Impairment ◽

Real Time ◽

Real Time Pcr ◽

Mononuclear Cells ◽

Differentially Expressed ◽

Protein Levels ◽

5Xfad Mice

Background: Disturbances in the autophagy/endolysosomal systems are proposed as early signatures of Alzheimer’s disease (AD). However, few studies are available concerning autophagy gene expression in AD patients. Objective: To explore the differential expression of classical genes involved in the autophagy pathway, among them a less characterized one, DEF8 (Differentially expressed in FDCP 8), initially considered a Rubicon family member, in peripheral blood mononuclear cells (PBMCs) from individuals with mild cognitive impairment (MCI) and probable AD (pAD) and correlate the results with the expression of DEF8 in the brain of 5xFAD mice. Method: By real-time PCR and flow cytometry, we evaluated autophagy genes levels in PBMCs from MCI and pAD patients. We evaluated DEF8 levels and its localization in brain samples of the 5xFAD mice by real-time PCR, western blot, and immunofluorescence. Results: Transcriptional levels of DEF8 were significantly reduced in PBMCs of MCI and pAD patients compared with healthy donors, correlating with the MoCA and MoCA-MIS cognitive tests scores. DEF8 protein levels were increased in lymphocytes from MCI but not pAD, compared to controls. In the case of brain samples from 5xFAD mice, we observed a reduced mRNA expression and augmented protein levels in 5xFAD compared to age-matched wild-type mice. DEF8 presented a neuronal localization. Conclusion: DEF8, a protein proposed to act at the final step of the autophagy/endolysosomal pathway, is differentially expressed in PBMCs of MCI and pAD and neurons of 5xFAD mice. These results suggest a potential role for DEF8 in the pathophysiology of AD.

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Real-Time Gesture Recognition Using Deep Learning Towards Alzheimer’s Disease Applications

Brain Function Assessment in Learning - Lecture Notes in Computer Science ◽

10.1007/978-3-030-60735-7_8 ◽

2020 ◽

pp. 75-86

Author(s):

Marulasidda Swamy Kibbanahalli Shivalingappa ◽

Hamdi Ben Abdessalem ◽

Claude Frasson

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Deep Learning ◽

Real Time ◽

Gesture Recognition

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Cassandra-based data repository design for food supply chain traceability

VINE Journal of Information and Knowledge Management Systems ◽

10.1108/vjikms-08-2019-0119 ◽

2020 ◽

Vol ahead-of-print (ahead-of-print) ◽

Author(s):

Sandeep Kumar Singh ◽

Mamata Jenamani

Keyword(s):

Supply Chain ◽

Real Time ◽

Radio Frequency Identification ◽

Query Language ◽

Data Repository ◽

Time Data ◽

Content Type ◽

The Real ◽

Traceability System ◽

Real Time Data

Purpose The purpose of this paper is to design a supply chain database schema for Cassandra to store real-time data generated by Radio Frequency IDentification technology in a traceability system. Design/methodology/approach The real-time data generated in such traceability systems are of high frequency and volume, making it difficult to handle by traditional relational database technologies. To overcome this difficulty, a NoSQL database repository based on Casandra is proposed. The efficacy of the proposed schema is compared with two such databases, document-based MongoDB and column family-based Cassandra, which are suitable for storing traceability data. Findings The proposed Cassandra-based data repository outperforms the traditional Structured Query Language-based and MongoDB system from the literature in terms of concurrent reading, and works at par with respect to writing and updating of tracing queries. Originality/value The proposed schema is able to store the real-time data generated in a supply chain with low latency. To test the performance of the Cassandra-based data repository, a test-bed is designed in the lab and supply chain operations of Indian Public Distribution System are simulated to generate data.

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Investigating the genetic relationship between Alzheimer’s disease and cancer using GWAS summary statistics

Human Genetics ◽

10.1007/s00439-017-1831-6 ◽

2017 ◽

Vol 136 (10) ◽

pp. 1341-1351 ◽

Cited By ~ 16

Author(s):

Yen-Chen Anne Feng ◽

◽

Kelly Cho ◽

Sara Lindstrom ◽

Peter Kraft ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Genetic Relationship ◽

Summary Statistics

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P1-018: Rare Deleterious And Loss-of-Function Variants in OPRL1 and GAS2L2 Contribute to the Risk of Late-Onset Alzheimer’s Disease: Alzheimer’s Disease Sequencing Project Case-Control Study

Alzheimer s & Dementia ◽

10.1016/j.jalz.2016.06.765 ◽

2016 ◽

Vol 12 ◽

pp. P406-P406

Author(s):

Xueqiu Jian ◽

Joshua C. Bis ◽

Brian W. Kunkle ◽

Kara L. Hamilton ◽

Gary W. Beecham ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Case Control Study ◽

Late Onset ◽

Case Control ◽

Loss Of Function ◽

Sequencing Project ◽

Control Study

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Noninvasive label-free nanoplasmonic optical imaging for real-time monitoring of in vitro amyloid fibrogenesis

Nanoscale ◽

10.1039/c3nr06269d ◽

2014 ◽

Vol 6 (7) ◽

pp. 3561-3565 ◽

Cited By ~ 6

Author(s):

Sung Sik Lee ◽

Luke P. Lee

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Optical Imaging ◽

Real Time ◽

Label Free ◽

Real Time Monitoring ◽

Pathological Mechanism

We utilize nanoplasmonic optical imaging as the noninvasive and label-free method in order to monitorin vitroamyloid fibrogenesis in real-time, which is considered as the primary pathological mechanism of Alzheimer's disease.

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