Chromosomal microarray and whole-exome sequence analysis in Taiwanese patients with autism spectrum disorder

Abstract

Background: Autism spectrum disorder (ASD) is defined as a group of genetically and clinically heterogeneous neurodevelopmental disorders. Interplay between de novo and inherited rare variants has been suspected in the development of ASD.

Methods: Here, we applied 750K oligonucleotide microarray analysis and whole-exome sequencing (WES) to five trios from Taiwanese families with ASD.

Results: The chromosomal microarray analysis revealed three representative known diagnostic copy number variants that contributed to the clinical presentation: the chromosome locations 2q13, 1q21.1q21.2, and 9q33.1. WES detected 22 rare variants in all trios, including four that were newly discovered, one of which is a de novo variant. Sequencing variants of JMJD1C, TCF12, BIRC6, and NHS have not been previously reported. A novel de novo variant was identified in NHS (p.I7T). Additionally, seven pathogenic variants, including SMPD1, FUT2, BCHE, MYBPC3, DUOX2, EYS, and FLG, were detected in four probands. One of the involved genes, SMPD1, had previously been reported to be mutated in patients with Parkinson's disease.

Conclusions: These findings suggest that de novo or inherited rare variants and copy number variants may be double or multiple hits of the probands that lead to ASD. WES could be useful in identifying possible causative ASD variants.

Keywords: Autism spectrum disorder; Chromosomal microarray analysis; Copy number variant; Whole-exome sequencing.

Figure 1

Chromatograms of the heterozygous missense variants in JMJD1C (a), TCF12 (b), BIRC6 (c), and de novo variant in NHS (d)