Resource

Id: gene_properties/gene_scores/SFARI_gene_score_2024_Q1
Type: gene_score
Version: 0
Summary:

SFARI gene score 2024 Q1 release

Description:

Introduction

SFARI Gene (https://gene.sfari.org/) is a comprehensive database that includes any gene associated with autism risk, regardless of the nature of the evidence supporting its link to ASD. Embracing this inclusive approach may result in a considerable number of false positives. Hence, there's a recognition of the necessity to establish a ranking system. This system provides users with an estimate of the evidence strength supporting each gene's link to autism. In collaboration with MindSpec curators and a team of expert autism geneticists, a set of criteria has been established. These criteria facilitate the categorization of genes into one of four tiers. This framework aids users in easily identifying genes with a more robust association with autism risk.

Score definitions

Category Description
1 (High Confidence) Each of these genes has been clearly implicated in ASD-typically by the presence of at least three de novo likely-gene-disrupting mutations being reported in the literature-and such mutations identified in the sequencing of the SPARK cohort are typically returned to the participants. Some of these gene meet the most rigorous threshold of genome-wide significance; all at least meet a threshold false discovery rate of < 0.1.
2 (Strong Candidate) Genes with two reported de novo likely-gene-disrupting mutations. A gene uniquely implicated by a genome-wide association study, either reaching genome-wide significance or, if not, consistently replicated and accompanied by evidence that the risk variant has a functional effect.
3 (Suggestive Evidence) Genes with a single reported de novo likely-gene-disrupting mutation. Evidence from a significant but unreplicated association study, or a series of rare inherited mutations for which there is not a rigorous statistical comparison with controls.

Processing Details

SFARI-Gene_genes_03-28-2024release_04-25-2024export.csv downloaded on 2024 April 25 from https://gene.sfari.org/tools/.

DataPrep.py reads the original file, renames column "gene-symbol" to "gene" and creates a .gz file with the same name.

Labels:

Scores

ID Type Description Histograms Range
gene-score
Evidence strength supporting a gene's association with autism
Small values desc: strong evidence for association with ASD
Large values desc: weak evidence for association with ASD
gene-score
[1.000, 3.000]

Files

Filename Size md5
DataPrep.py 299.0 B f9d96d79f5a38bfecc49a9252238d197
SFARI-Gene_genes_03-28-2024release_04-25-2024export.csv 126.05 KB c697256eff3c72acb4960d5c1c032575
SFARI-Gene_genes_03-28-2024release_04-25-2024export.csv.gz 28.11 KB 5853500566a79fbb4aadcd1c90f1ea9c
genomic_resource.yaml 2.76 KB 3335cd71d8e734f756e62f80674f7834
statistics/