As with the other modules of SFARI Gene, the content of the CNV module originates entirely from published scientific literature. MindSpec researchers systematically search, collect, and extract information on CNVs from autism case cohorts and, when available, unaffected control cohorts. CNVs in the module are organized based on the locus (chromosomal region or band) in which they were observed in each annotated report.
CNV reports generally fall into three broad categories:
Case studies typically involve one or, at most, a few individuals with autism in which one or more potentially relevant CNVs have been identified. Case studies frequently have very detailed information on the clinical history and profile of the individual(s) in the report.
Studies focused on one particular CNV locus
Studies focused on one particular CNV locus?A number of reports deal with either identifying the frequency of CNVs at a particular locus across a given population with autism, or describing the range of phenotypes within a group of individuals with autism with CNVs at a specific locus.
Large-scale, genome-wide CNV screens
Large-scale, genome-wide CNV screens?In this type of report, large populations of individuals affected by autism are screened across their genomes for CNVs. While such reports typically do not have a great deal of detail with regard to the clinical histories of individuals in the case cohorts, they are critical for determining the frequencies and prevalence of potentially pathogenic CNVs across the genome.
For any given CNV locus, a published report can be characterized as either validated or unvalidated. In validated reports, an independent secondary methodology was used to confirm at least one copy number variant within the locus of interest following its initial discovery. If a report is unvalidated, no subsequent confirmation step was performed following the initial discovery of any CNV at the locus of interest.?
Additional information for every CNV locus can be found on the corresponding CNV summary page via external links to two genome browsers: the UCSC Genome Browser and the NCBI Genome Browser. Both genome browsers provide valuable information on the genetic composition of each CNV in the module. If a CNV locus in the module is associated with one or more genetic disorders or syndromes in the DECIPHER database, external links are provided to the corresponding syndrome(s) on the DECIPHER website. If there is no corresponding syndrome or genetic disorder in the DECIPHER database, no external link to DECIPHER is provided.