Autism Spectrum Disorders via the CHD8 Gene

Autism Spectrum Disorders (ASD) include several neurodevelopmental disorders characterized by varying degrees of social impairment, communication ability, and propensity for restricted interests and repetitive behavior(s) (Levy et al. 2009). ASD usually presents by age 3. Diagnosis is based on the degree and severity of symptoms and behaviors (Diagnostic and Statistical Manual of Mental Disorders (DSM-5); McPartland et al. 2016). Comorbidities occur in more than 70% of cases and include intellectual disability (ID), epilepsy, language deficits, and gastrointestinal problems (Sztainberg and Zoghbi 2016). Recent studies using whole exome trios have identified novel gene candidates, with familial and de novo variants from several hundred genes now implicated in the development of ASD (Bourgeron 2016).

CHD8 (chromodomain helicase DNA-binding protein 8) is a member of the chromodomain, helicase, DNA binding group of proteins that regulate chromatin structure. Specifically, CHD8 regulates the Wnt-β-catenin signaling pathway which impacts cell development, fate, and adult stem cell proliferation (Nishiyama et al. 2012; Bernier et al. 2014). CHD8 is widely expressed in the adult and developing brain (including the neocortex, hippocampus, amygdala, and striatum), and expression decreases during fetal and postnatal development (Bernier et al. 2014). Individuals with CHD8 variants present with ASD of a particular subtype, with clinical features including increased occipitofrontal circumference, macrocephaly (80%), pronounced supraorbital brow ridges (78%), wide-set eyes with down-slanted palpebral fissures (67%), broad nose with full nasal tip, pointed chin, slender, tall build (86%), large, flat feet, gastrointestinal problems (80%, particularly constipation), and sleep disturbances (67%, specifically falling asleep) (Bernier et al. 2014).

Genetic aberrations are reported to be responsible for 50%-90% and 15%-50% of ASD and ID cases, respectively, and inheritance overall is multifactorial (Larsen et al. 2016; Karam et al. 2015). Incidence of ASD is approximately 1 in 68 individuals with a male-to-female ratio of 4:1 (Center for Disease Control 2014). De novo missense and likely gene disrupting variants are 15% and 75% more frequent in ASD patients than unaffected controls, respectively (Iossifov et al. 2014).

The human CHD8 gene contains 37 protein-coding exons which are alternatively spliced into two protein isoforms: short (CHD8_S, also known as duplin) and long (CHD8_L). Both protein isoforms are able to inhibit Wnt-β-catenin activity, which only requires the chromodomain and histone H1 binding domain (present in both isoforms). The CHD8_L isoform also contains a Snf2 helicase domain that modulates chromatin structure in an ATP-dependent manner and a CTCF protein binding domain that impacts the insulator and transcriptional activity of CTCF gene targets (Nishiyama et al. 2012).

Nearly all CHD8 variants implicated in ASD development are de novo nonsense, frameshift, or canonical splice sites variants (92%), strongly supporting an autosomal dominant mode of inheritance. At least two missense variants near CHD8 splice sites and a 5 kb duplication of the C-terminal region of the CHD8 gene were found to be inherited. Inherited variants considered mild resulted in less severe clinical features and were inherited from unaffected parents. In contrast, severe variants were inherited from parents presenting with ASD features (Bernier et al. 2014). A balanced chromosomal translocation disrupting CHD8 has also been reported in an individual with ASD (Talkowski et al. 2012).

Homozygous loss-of-function variants have not been reported to date. Studies of CHD8 null mice reveal death occurs during early embryogenesis from widespread apoptosis, which is ameliorated by deletion of p53 in the same null background (Nishiyama et al. 2004; Nishiyama et al. 2009). Further studies have shown disruption of CHD8 results in increased proliferation of neoplastic cells, and may be an indicator of gastric cancer (Nishiyama et al. 2012; Sawada et al. 2013). In one study, two individuals over the age of 40 with truncating variants in CHD8 and ASD features both developed tumors. Therefore, it may be important for individuals with CHD8 truncating variants to undergo additional screening for colorectal and other cancers (Bernier et al. 2014).

Currently, the contribution of de novo and inherited factors to Autism Spectrum Disorders (ASD) risk is estimated to be approximately 50-60% (Krumm et al. 2015). CHD8 is categorized as a gene with ‘high confidence and syndromic features’ regarding its susceptibility for ASD in the Simons Foundation Autism Research Initiative (SFARI) Database (https://gene.sfari.org/GeneDetail/CHD8). However, more than 700 genes have been associated with ASD features (Bourgeron 2016). Based on a recent large CHD8-specific study of 6,176 ASD cases, causative variants in CHD8 were identified in approximately 20 individuals (0.33% of individuals) (Bernier et al. 2014; O’Roak et al. 2012).

Additional Sanger sequencing is performed for any regions not captured or with insufficient number of sequence reads.

This test provides full coverage of all coding exons of the CHD8 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).