Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform

The statistics comprise the number of variants of various types in the available data sets. Gene profiles organize data as a virtual table with a row for each human gene and columns organized into sections. The table shows a small part of the complete gene profiles in GPF-SFARI, containing the statistics for 20 of the genes most strongly implicated in autism. In GPF-SFARI's gene profiles, the first section of columns shows if each of the genes has been listed as a top candidate in five high-profile autism genetic analysis papers. The first 12 of the shown genes have been listed in all five papers. The second, third, and fourth column sections contain variant counts from the SPARK, SSC, and sequencing de novo collections, respectively. The sections for SPARK and SSC show the counts of de novo LGDs, de novo missense, and transmitted LGDs separately for the children affected with autism and for their unaffected siblings (“controls”). The sequencing de novo section shows the counts for de novo LGD and missense variants in individuals with autism, epilepsy, schizophrenia, developmental disorder, intellectual disability, congenital heart disease, and controls. In each column, the number of variants of the particular type in each gene is shown, as well as the rate in terms of the number of variants per 1000 individuals. The fifth section shows if the gene belongs to five genes strongly implicated in the etiology of autism: syndromic autism genes, CHD8 target genes, genes encoding chromatin modifiers, essential genes, and genes encoding FMRP target RNAs. The last section shows two popular gene scores (RVIS and pLI) related to the gene's degree of intolerance to damaging mutations computed through analysis of damaging variants in large human populations. We note that the table is a stylized representation of the gene profiles page on GPF-SFARI, designed to reduce white space.