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Pavel P. Kuksa, Chia-Lun Liu, Wei Fu, Liming Qu, Yi Zhao, Zivadin Katanic, Kaylyn Clark, Amanda B. Kuzma, Pei-Chuan Ho, Kai-Teh Tzeng, Otto Valladares, Shin-Yi Chou, Adam C. Naj, Gerard D. Schellenberg, Li-San Wang, and Yuk Yee Leung. Alzheimer's Disease Variant Portal: A Catalog of Genetic Findings for Alzheimer's Disease. Journal of Alzheimer's Disease, Preprint(Preprint):1–17, IOS Press, 2022.
Background: Recent Alzheimer's disease (AD) genetics findings from genome-wide association studies (GWAS) span progressively larger and more diverse populations and outcomes. Currently, there is no up-to-date resource providing harmonized and searchable information on all AD genetic associations found by GWAS, nor linking the reported genetic variants and genes with functional and genomic annotations. Objective: Create an integrated/harmonized, and literature-derived collection of population-specific AD genetic associations. Methods: We developed the Alzheimer's Disease Variant Portal (ADVP), an extensive collection of associations curated from >200 GWAS publications from Alzheimer's Disease Genetics Consortium and other consortia. Genetic associations were systematically extracted, harmonized, and annotated from both the genome-wide significant and suggestive loci reported in these publications. To ensure consistent representation of AD genetic findings, all the extracted genetic association information was harmonized across specifically designed publication, variant, and association categories. Results: ADVP V1.0 (February 2021) catalogs 6,990 associations related to disease-risk, expression quantitative traits, endophenotypes, or neuropathology. This extensive harmonization effort led to a catalog containing >900 loci, >1,800 variants, >80 cohorts, and 8 populations. Besides, ADVP provides investigators with a seamless integration of genomic and publicly available functional annotations across multiple databases per harmonized variant and gene records, thus facilitating further understanding and analyses of these genetics findings. Conclusion: ADVP is a valuable resource for investigators to quickly and systematically explore high-confidence AD genetic findings and provides insights into population-specific AD genetic architecture. ADVP is continually maintained and enhanced by NIAGADS and is freely accessible at https://advp.niagads.org .
@article{jad2022advp,
abstract = {Background: Recent Alzheimer's disease (AD) genetics findings from genome-wide association studies (GWAS) span progressively larger and more diverse populations and outcomes. Currently, there is no up-to-date resource providing harmonized and searchable information on all AD genetic associations found by GWAS, nor linking the reported genetic variants and genes with functional and genomic annotations. Objective: Create an integrated/harmonized, and literature-derived collection of population-specific AD genetic associations. Methods: We developed the Alzheimer's Disease Variant Portal (ADVP), an extensive collection of associations curated from >200 GWAS publications from Alzheimer's Disease Genetics Consortium and other consortia. Genetic associations were systematically extracted, harmonized, and annotated from both the genome-wide significant and suggestive loci reported in these publications. To ensure consistent representation of AD genetic findings, all the extracted genetic association information was harmonized across specifically designed publication, variant, and association categories. Results: ADVP V1.0 (February 2021) catalogs 6,990 associations related to disease-risk, expression quantitative traits, endophenotypes, or neuropathology. This extensive harmonization effort led to a catalog containing >900 loci, >1,800 variants, >80 cohorts, and 8 populations. Besides, ADVP provides investigators with a seamless integration of genomic and publicly available functional annotations across multiple databases per harmonized variant and gene records, thus facilitating further understanding and analyses of these genetics findings. Conclusion: ADVP is a valuable resource for investigators to quickly and systematically explore high-confidence AD genetic findings and provides insights into population-specific AD genetic architecture. ADVP is continually maintained and enhanced by NIAGADS and is freely accessible at https://advp.niagads.org .},
author = {Kuksa, Pavel P. and Liu, Chia-Lun and Fu, Wei and Qu, Liming and Zhao, Yi and Katanic, Zivadin and Clark, Kaylyn and Kuzma, Amanda B. and Ho, Pei-Chuan and Tzeng, Kai-Teh and Valladares, Otto and Chou, Shin-Yi and Naj, Adam C. and Schellenberg, Gerard D. and Wang, Li-San and Leung, Yuk Yee},
bib2html_pubtype = {Journal},
date-added = {2022-01-26 12:35:25 -0500},
date-modified = {2022-01-26 12:36:32 -0500},
doi = {10.3233/JAD-215055},
isbn = {1875-8908},
journal = {Journal of Alzheimer's Disease},
keywords = {AD GWAS literature curation; Alzheimer's disease; data curation; database; genome-wide association studies; harmonization},
number = {Preprint},
pages = {1--17},
publisher = {IOS Press},
title = {Alzheimer's Disease Variant Portal: A Catalog of Genetic Findings for Alzheimer's Disease},
volume = {Preprint},
year = {2022},
bdsk-url-1 = {https://doi.org/10.3233/JAD-215055}}
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