Description
denovo-db (version 1.6.1) is a curated database of germline de novo variants in the human genome,
defined as variants present in children but absent in their parents. With advancements in
whole-exome and whole-genome sequencing, denovo-db consolidates data from extensive genetic
studies, including those on neurodevelopmental disorders, but is not restricted to specific
phenotypes. This database provides essential resources for researchers investigating variant
characteristics, mutability, and associated phenotypes.
Display Convention and Configuration
The denovo-db track's mouseover tooltip provides the following information about the data:
- Position: Specifies the chromosomal range where the variant is located
- Variant: Describes the specific genetic change at this location
- Primary Phenotype: Indicates the primary phenotype associated with the sample
- Validation: Specifies the validation status of the variant
- Transcript: Specifies the transcript ID
Methods
denovo-db was assembled by integrating published literature on de novo variants identified
through large-scale whole-exome and whole-genome studies. Variants in the database are annotated
with relevant genetic information, including functional scores like CADD and validation status,
ensuring utility for genetic research. As of version 1.6, the database includes data from the
Simons Simplex
Collection (SSC), with usage restrictions detailed on the denovo-db's
Usage page.
For more detailed information on the methods used for this track, please visit the following
webpage:
https://denovo-db.gs.washington.edu/denovo-db/index.jsp
Contact
If you have questions or comments about the denovo-db, please write to:
denovo-db,
denovo-db@uw.
edu
The use of Simons Simplex Collection (SSC) is limited to projects related to advancing the field of
autism and related developmental disorder research. Questions on SSC consents should be directed to
collections@sfari.
org
Data access
The underlying data for the denovo-db track can be explored interactively using the
REST API, the
Table Browser or the
Data Integrator.
The bigBed format files for hg19 are available from our
/gbdb directory on the
downloads server.
The raw data files used to generate this track can be found on the denovo-db
website.
References
Washington.edu, 2024. https://denovo-db.gs.washington.edu/denovo-db/Usage.jsp
(accessed Nov. 25, 2024).
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