denovo-db Track Settings
 
denovo-db v.1.6.1   (All Variation tracks)

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Display data as a density graph:
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 Configure 		 non-ssc samples  Non-Simons Simplex Collection samples from denovo-db   Data format 
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 Configure 		 ssc samples  Simons Simplex Collection samples from denovo-db   Data format 
Assembly: Human Feb. 2009 (GRCh37/hg19)

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
  • Transcipt: 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).