Next-generation Sequencing And Molecular Analysis Of 3 Unexplained Intellectual Disability Patients

Background: Intellectual disability（ID） is a disability characterized by significant limitations in both intellectual functioning and in adaptive behavior with onset before the age of 18. However, developmental delay（DD） is applied to the child aged 5 years or less with intellectual disability who often have motor, cognitive, and speech delays. ID/DD has an estimated prevalence of approximately 2% to 3% and the etiology is complex. It can be caused by genetic and non-genetic factors, for example, abnormity during pregnancy, anoxia of delivery, or postnatal infection or dystrophy. The genetic causes are estimated to be responsible for approximately a quarter to one-half of identified cases, including chromosomal imbalances, copy number variants as well as point mutations. A genetic underpinning of this disorder has long been recognized since an extra copy of chromosome 21 was discovered as the cause of Down’s syndrome in 1959. Down’s syndrome remains the most important chromosomal cause of intellectual disability. Single-gene causes have also been identified for a number of intellectual disability syndromes and include both autosomal and X-linked genes. Intellectual disability is characterized by impaired cognitive, linguistic, and social abilities. It often co-occurs with other neurological disorders such as autism spectrum disorders（ASD）, epilepsy and sensory impairments. Intellectual disability affects severely population quality and brings significant spiritual and economic burden for the family and society. Genetic research have enabled genomewide discovery of single nucleotide variants and chromosomal copy number changes in individuals with intellectual disability.Objective: To explore the genetic etiology in unexplained ID/DD patients and improve the diagnosis and management of ID/DD patients, and provide the theoretical basis for genetic counseling, risk assessment and prenatal diagnosis.Methods: In this study targeted sequencing and whole genome low-coverage sequencing with the aid of next generation sequencing platforms were performed. We developed a custom panel to capture the exons of 670 genes associated with ID/DD to detect single nucleotide variants（SNVs） and analyze copy number variants（CNVs） by whole genome low-coverage sequencing. Then pathogenic or likely pathogenic mutations and CNVs were validated by sanger sequencing and QPCR, respectively.Results: Two probands were identified likely pathogenic variants by targeted sequencing: c.754C>T and c.1015₁016delAT in HEXA, c.2999A>T and ex20-21 del in CC2D2 A. The proband ID003 was found to carry a pathogenic copy number variant by whole genome low-coverage sequencing. All variants were confirmed by Sanger sequencing or QPCR.Conclusions: Analysis molecular genetics in 3 unexplained ID/DD patients through next-generation sequencing and provide the theoretical basis for the etiological diagnosis.