ArticleBioinformatics (Oxford, England)2018
Functional annotation of genomic variants in studies of late-onset Alzheimer's disease.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed.
- Alzheimer's Disease Sequencing Project release 4 whole genome sequencing dataset.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Alzheimer's Disease Sequencing Project Release 4 Whole Genome Sequencing Dataset.medRxiv : the preprint server for health sciences · 2024Article
- NIAGADS Alzheimer's GenomicsDB: A resource for exploring Alzheimer's disease genetic and genomic knowledge.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024Article
- Human whole-exome genotype data for Alzheimer's disease.Nature communications · 2024Article
- Exploration of Tools for the Interpretation of Human Non-Coding Variants.International journal of molecular sciences · 2022Review
- Scalable approaches for functional analyses of whole-genome sequencing non-coding variants.Human molecular genetics · 2022Review
- Identification of risk genes for Alzheimer's disease by gene embedding.Cell genomics · 2022Article
- An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease-related patterns.Genome research · 2022Article
- Alzheimer's Disease Variant Portal: A Catalog of Genetic Findings for Alzheimer's Disease.Journal of Alzheimer's disease : JAD · 2022Article
- M-DATA: A statistical approach to jointly analyzing de novo mutations for multiple traits.PLoS genetics · 2021Article
- Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing.Medicinal research reviews · 2020Review
- Author Correction: Genome-wide human brain eQTLs: In-depth analysis and insights using the UKBEC dataset.Scientific reports · 2020Article
- PSCAN: Spatial scan tests guided by protein structures improve complex disease gene discovery and signal variant detection.Genome biology · 2020Article
- Hadoop and PySpark for reproducibility and scalability of genomic sequencing studies.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2020Article
- Bringing radiomics into a multi-omics framework for a comprehensive genotype-phenotype characterization of oncological diseases.Journal of translational medicine · 2019Review
- GWAS and Beyond: Using Omics Approaches to Interpret SNP Associations.Current genetic medicine reports · 2019Article
- Rare genetic variation implicated in non-Hispanic white families with Alzheimer disease.Neurology. Genetics · 2018Article
- Genetic Variation in Genes Underlying Diverse Dementias May Explain a Small Proportion of Cases in the Alzheimer's Disease Sequencing Project.Dementia and geriatric cognitive disorders · 2018Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Motivation: Annotation of genomic variants is an increasingly important and complex part of the analysis of sequence-based genomic analyses. Computational predictions of variant function are routinely incorporated into gene-based analyses of rare-variants, though to date most studies use limited information for assessing variant function that is often agnostic of the disease being studied. Results: In this work, we outline an annotation process motivated by the Alzheimer's Disease Sequencing Project, illustrate the impact of including tissue-specific transcript sets and sources of gene regulatory information and assess the potential impact of changing genomic builds on the annotation process. While these factors only impact a small proportion of total variant annotations (∼5%), they influence the potential analysis of a large fraction of genes (∼25%). Availability and implementation: Individual variant annotations are available via the NIAGADS GenomicsDB, at https://www.niagads.org/genomics/ tools-and-software/databases/genomics-database. Annotations are also available for bulk download at https://www.niagads.org/datasets. Annotation processing software is available at http://www.icompbio.net/resources/software-and-downloads/. Supplementary information: Supplementary data are available at Bioinformatics online.
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Registered trials
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