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

TitleFunctional annotation of genomic variants in studies of late-onset Alzheimer's disease.
Publication TypeJournal Article
Year of Publication2018
AuthorsButkiewicz M, Blue EE, Leung YYee, Jian X, Marcora E, Renton AE, Kuzma A, San Wang L-, Koboldt DC, Haines JL, Bush WS
JournalBioinformatics
Volume34
Issue16
Pagination2724-2731
Date Published2018 Aug 15
ISSN1367-4811
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.

DOI10.1093/bioinformatics/bty177
Alternate JournalBioinformatics
PubMed ID29590295
PubMed Central IDPMC6084586
Grant ListU01 AG032984 / AG / NIA NIH HHS / United States