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

Titledenovo-db: a compendium of human de novo variants.
Publication TypeJournal Article
Year of Publication2017
AuthorsTurner, TN, Yi, Q, Krumm, N, Huddleston, J, Hoekzema, K, Stessman, HAF, Doebley, A-L, Bernier, RA, Nickerson, DA, Eichler, EE
JournalNucleic Acids Res
Date Published2017 01 04
KeywordsComputational Biology, Databases, Nucleic Acid, Genetic Association Studies, Genetic Variation, Germ-Line Mutation, Humans, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Web Browser

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 (, 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.

Alternate JournalNucleic Acids Res.
PubMed ID27907889
PubMed Central IDPMC5210614
Grant ListU54 HG006493 / HG / NHGRI NIH HHS / United States
U54 HD083091 / HD / NICHD NIH HHS / United States
T32 HG000035 / HG / NHGRI NIH HHS / United States
UM1 HG006493 / HG / NHGRI NIH HHS / United States
T32 GM007266 / GM / NIGMS NIH HHS / United States
R01 MH101221 / MH / NIMH NIH HHS / United States
/ HH / Howard Hughes Medical Institute / United States