Molecular diagnosis of 405 individuals with autism spectrum disorder

Abstract

Autism spectrum disorder (ASD) is caused by combined genetic and environmental factors. Genetic heritability in ASD is estimated as 60-90%, and genetic investigations have revealed many monogenic factors. We analyzed 405 patients with ASD using family-based exome sequencing to detect disease-causing single-nucleotide variants (SNVs), small insertions and deletions (indels), and copy number variations (CNVs) for molecular diagnoses. All candidate variants were validated by Sanger sequencing or quantitative polymerase chain reaction and were evaluated using the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines for molecular diagnosis. We identified 55 disease-causing SNVs/indels in 53 affected individuals and 13 disease-causing CNVs in 13 affected individuals, achieving a molecular diagnosis in 66 of 405 affected individuals (16.3%). Among the 55 disease-causing SNVs/indels, 51 occurred de novo, 2 were compound heterozygous (in one patient), and 2 were X-linked hemizygous variants inherited from unaffected mothers. The molecular diagnosis rate in females was significantly higher than that in males. We analyzed affected sibling cases of 24 quads and 2 quintets, but only one pair of siblings shared an identical pathogenic variant. Notably, there was a higher molecular diagnostic rate in simplex cases than in multiplex families. Our simulation indicated that the diagnostic yield is increasing by 0.63% (range 0-2.5%) per year. Based on our simple simulation, diagnostic yield is improving over time. Thus, periodical reevaluation of ES data should be strongly encouraged in undiagnosed ASD patients.

Fig. 1. Genetic architecture in our autism spectrum disorder (ASD) cohort.

A Identified monogenic single-nucleotide variants (SNVs) including small insertions and deletions and copy number variations (CNVs) in our ASD cohort. B The number of individuals with pathogenic SNVs and CNVs leading to a molecular diagnosis under the respective genetic inheritance modes. C Size distribution of 25 candidate CNVs. D The diagnostic yields in male and female individuals with either SNVs or CNVs.

Fig. 2. Gene ontology (GO) enrichment analysis for our autism spectrum disorder (ASD) cohort.

GO analysis was performed for 52 genes with pathogenic variants. A Visualization of GO enrichment analyzed with DAVID 6.8. Top 9 categories with a false discovery rate of <0.01 are shown. B Top 25 enriched GO terms analyzed with enrichGO are shown. Count: the number of hit genes within each category. Hits (%): proportion of the 52 input genes included in each GO term.