Clinical Application of a Customized Gene Panel for Identifying Autism Spectrum Disorder-Associated Variants

Abstract

Background and Objectives: Autism spectrum disorder (ASD) is a neurodevelopmental disorder that belong to genetic and epigenetic mechanism. Despite the recent advantages in next-generation sequencing (NGS) technology, ASD etiology is still unclear. Materials and Methods: In this study, we tested a customized target genetic panel consisting of 74 genes in a cohort of 53 ASD individuals. The tested panel was designed from the SFARI database. Results: Among 53 patients analyzed using a targeted genetic panel, 102 rare variants were identified, with nine individuals carrying likely pathogenic or pathogenic variants considered genetically "positive." We identified six de novo variants across five genes (POGZ 2 variants, NCOR1, CHD2, ADNP, and GRIN2B), including two variants of uncertain significance in POGZ p.Thr451Met and NCOR1 p.Glu1137Lys, one likely pathogenic variant in GRIN2B p.Leu714Gln, and three pathogenic variants in POGZ p.Leu775Valfs32, CHD2 p.Thr1108Metfs8, and ADNP p.Pro5Argfs*2. Conclusions: This study presents a comprehensive characterization of the targeted gene panel used for genetic analysis, while critically evaluating its diagnostic limitations within the context of contemporary genomic approaches. A pivotal accomplishment of this study was the ClinVar submission of novel de novo variants which expands the documented mutational spectrum of ASD-associated genes and enhances future diagnostic interpretation.

Keywords: SFARI database; next-generation sequencing; novel variant identification; target genetic panel.

Figure 1

Pie charts illustrating variant classification across the examined cohort, and the differential inheritance. (a) Classification of the 102 genetic variants identified across the 53 examined ASD individuals. Dark green indicates benign variants; light green illustrates the likely benign variants; grey depicts the variant of uncertain significance (VUS); orange illustrates the likely pathogenic variants; red depicts the pathogenic variants. (b) Pie chart illustrating the inheritance of the 102 variants found in this study.

Figure 2

Distribution of the genetic variants identified in this study across the 45 genes of the target genetic panel in which they were found. Dark green was used for benign variants, light green for likely benign variants, orange for likely pathogenic variants, red for pathogenic variants, and gray for variants of uncertain significance (VUS).

Figure 3

Violin plots displaying FPKM (fragments per kilobase million) expression levels for the nine genes harboring pathogenic or likely pathogenic variants identified in this study. Expression profiles across neural cell types were obtained from the BrainRNAseq database (https://brainrnaseq.org/) (accessed on 10 June 2025), revealing cell-type-specific expression patterns for each ASD-associated gene.