Functional annotation of genomic variants in studies of late-onset Alzheimer’s disease

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 tools-and-software/databases/genomics-database. Annotations are also available for bulk download at Annotation processing software is available at
Supplementary information: Supplementary data are available at Bioinformatics online.