New changes implemented to SFARI Gene

Human Gene module. The 'scrubber' shows each gene in the SFARI Gene database by its chromosomal location. Different colors indicate different gene score categories. Image credit: SFARI Gene.

Current estimates suggest that variation in several hundred genes could affect susceptibility to autism spectrum disorder (ASD). The Simons Foundation Autism Research Initiative (SFARI) and other funding agencies are supporting efforts to identify as many ASD risk genes as possible, with an eye toward understanding how mutations may impact typical brain development and result in the complex spectrum of behaviors that we term autism.

One such effort led to the creation of SFARI Gene, a trusted, comprehensive and dynamic database that captures ASD risk genes from the published literature and tells autism researchers what it is known about them.

To help strengthen the aspects of SFARI Gene that are most useful to the autism research community, SFARI has recently made a number of changes to the database. These changes affect several SFARI Gene modules, as follows:

  • Gene-scoring module. In order to simplify SFARI Gene’s gene-scoring system, the number of ranking categories has been reduced from seven to four (S-syndromic, 1-high confidence, 2-strong candidate, 3-suggestive evidence). The new category 1 (high-confidence genes) will be taken from the SPARK gene list, which includes genes for which there is sufficient evidence in the literature that they are deemed ‘returnable’ results to families in a clinical setting. The new category 2 (strong candidate genes) will include genes listed in the previous category 3; the new category 3 (suggestive evidence) will list genes from the old category 4. Categories 5 and 6 of the previous version of SFARI Gene have been removed from the new gene-scoring module.

  • Copy number variant (CNV) module. The scope of annotation for the CNV module has been scaled back and focused on curation of recurrent CNVs associated with ASD. Rare single instances of CNVs will no longer be annotated. The CNV scrubber will be populated by CNVs called from analyses of the Simons Simplex Collection.

  • Animal models module. The scope of this module has been substantially scaled back by limiting curation to high-impact mouse models of ASD identified based on stringent selection criteria.

  • Protein interaction (PIN) module. The PIN module will no longer be hosted on the current SFARI Gene site.

Given the regular citation of the Human Gene module in the literature, curation of the autism risk gene list will continue as before, using the current annotation model.

“Our goal is for SFARI Gene to continue to be a sustainable and trusted resource for geneticists and non-geneticists working on autism,” says SFARI senior scientist Alan Packer.

A full description of the new changes can be found here. An archive of the previous version of the site will be maintained here. As always, we welcome user feedback here.

For all other inquiries, please email us at [email protected].

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