type: gene_score
filename: SFARI-Gene_genes_01-13-2021release_05-04-2021export.csv.gz
scores:
  - id: SFARI gene score
    desc: "Evidence strength supporting a gene's association with autism"
    histogram:
      type: number
      number_of_bins: 3
      view_range:
        min: 1
        max: 4
      x_log_scale: false
      y_log_scale: false
      # type: categorical
      # value_order: [1, 2, 3]

    small_values_desc: "strong evidence for association with ASD"
    large_values_desc: "weak evidence for association with ASD"
meta:
  summary: |
    SFARI gene score release 01-13-2021
  description: |
    ### Introduction
    SFARI Gene [(https://gene.sfari.org/)](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\_01-13-2021release\_05-04-2021export.csv downloaded on 2021 May 4 from [https://gene.sfari.org/tools/](https://gene.sfari.org/tools/). 

    DataPrep.py reads the original file and creates a .gz file with the same name.