Bioinformatics (Oxford, England) · 2018
Functional annotation of genomic variants in studies of late-onset Alzheimer's disease.
СтатьяПоддержка NIH: внешняя программаНазвание и аннотация: Перевод пока не подготовлен
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Butkiewicz Mariusz, Blue Elizabeth E, Leung Yuk Yee, Jian Xueqiu, Marcora Edoardo, Renton Alan E, Kuzma Amanda, Wang Li-San, Koboldt Daniel C, Haines Jonathan L, Bush William S
Аннотация
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.
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.