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Nucleic Acids Res. 2017 Jan 4;45(D1):D804-D811. doi: 10.1093/nar/gkw865. Epub 2016 Oct 5.

denovo-db: a compendium of human de novo variants.

Author information

1
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA tychele@u.washington.edu.
2
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
3
Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
4
Medical Scientist Training Program, Department of Pathology, University ofWashington, Seattle, WA 98105, USA.
5
Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98105, USA.

Abstract

Whole-exome and whole-genome sequencing have facilitated the large-scale discovery of de novo variants in human disease. To date, most de novo discovery through next-generation sequencing focused on congenital heart disease and neurodevelopmental disorders (NDDs). Currently, de novo variants are one of the most significant risk factors for NDDs with a substantial overlap of genes involved in more than one NDD. To facilitate better usage of published data, provide standardization of annotation, and improve accessibility, we created denovo-db (http://denovo-db.gs.washington.edu), a database for human de novo variants. As of July 2016, denovo-db contained 40 different studies and 32,991 de novo variants from 23,098 trios. Database features include basic variant information (chromosome location, change, type); detailed annotation at the transcript and protein levels; severity scores; frequency; validation status; and, most importantly, the phenotype of the individual with the variant. We included a feature on our browsable website to download any query result, including a downloadable file of the full database with additional variant details. denovo-db provides necessary information for researchers to compare their data to other individuals with the same phenotype and also to controls allowing for a better understanding of the biology of de novo variants and their contribution to disease.

PMID:
27907889
PMCID:
PMC5210614
DOI:
10.1093/nar/gkw865
[Indexed for MEDLINE]
Free PMC Article

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