Characterization of intellectual disability and autism comorbidity through gene panel sequencing

Abstract

Intellectual disability (ID) and autism spectrum disorder (ASD) are clinically and genetically heterogeneous diseases. Recent whole exome sequencing studies indicated that genes associated with different neurological diseases are shared across disorders and converge on common functional pathways. Using the Ion Torrent platform, we developed a low-cost next-generation sequencing gene panel that has been transferred into clinical practice, replacing single disease-gene analyses for the early diagnosis of individuals with ID/ASD. The gene panel was designed using an innovative in silico approach based on disease networks and mining data from public resources to score disease-gene associations. We analyzed 150 unrelated individuals with ID and/or ASD and a confident diagnosis has been reached in 26 cases (17%). Likely pathogenic mutations have been identified in another 15 patients, reaching a total diagnostic yield of 27%. Our data also support the pathogenic role of genes recently proposed to be involved in ASD. Although many of the identified variants need further investigation to be considered disease-causing, our results indicate the efficiency of the targeted gene panel on the identification of novel and rare variants in patients with ID and ASD.

Keywords: ASD; ID; NGS; comorbidity; gene panel; variant interpretation.

Figure 1.. Workflow describing the important steps in the classification of selected variants.

Abbreviations: genotype quality (GQ); Allele Frequency (AF); Autosomal Dominant (AD); Autosomal Recessive (AR); X-linked, dominant (XLD).

Figure 2.. DYRK1A missense mutation affect catalytic pocket of kinase domain

A) Domain architecture of DYRK1A. Protein sequence presents regions biased toward polar (serine and threonine) and aromatic (histidine residues). NLS = nuclear localization signal. B) DYRK1A p.Lys175 and neighboring residues are conserved among orthologous sequences. Amino acids are colored by conservation, according to ClustalX color code. C) DYRK1A p. Lys175Asn variant and wild type residues are mapped to kinase domain structure (4yu2.pdb, chain A). Residues involved in nucleotide binding are represented in orange sticks, wild-type lysine (K) in red and asparagine (N) in green.

Figure 3.. EHMT1 missense mutation affects SET domain.

Causative variants identified in our patient cohort are mapped to the EHMT1. Protein sequence presents regions biased toward polar (glutamine and arginine) and a poly-alanine motif. The ankyrin domain (orange) is involved with the histone H3K9me binding. The Pre-SET domain (green) contributes to SET domain stabilization B) EHMT1 p.Gly1193 and neighboring residues are conserved among orthologous sequences. Amino acids are colored by conservation, according ClustalX color code. C) EHMT1 p.Gly1193Arg variant (red) and wild type glycine (orange) are mapped to SET domain structure (2igq.pdb, chain A) Residues involved in H3K9 binding and the S-adenosyl-L-methionine molecule are represented in blue sticks.

Figure 4.. The novel likely hypomorphic mutation of CASK may alter L27 domain dimerization

A) Covariation network of L27 domain (PF02828). Nodes are the residues (L27 domain numbering) coloured by conservation from red to light blue (highest to lowest respectively). B) Nodes are coloured by cumulative Mutual information (cMI) from violet to yellow (highest to lowest respectively). Edges are the top 0.1% covariation scores (Mutual Information) calculated with Mistic2 (Colell et al., 2018). C) Ribbon representation of the L27- SAP97 complex. CASK domain L27 is coloured green (chain B 1RSO PDB) and SAP97 violet (chain A 1RSO PDB). In sticks are shown the residues that interact (their R) with Y387 in the complex. D) same coloring schema. Y387 was “in silico” mutated to H387. Mutation and figures were generated by UCSF Chimera (Pettersen et al., 2004).