De novo copy number variations in candidate genomic regions in patients of severe autism spectrum disorder in Vietnam

Bui, Hoa Thi Phuong; Huy Do, Duong; Ly, Ha Thi Thanh; Tran, Kien Trung; Le, Huong Thi Thanh; Nguyen, Kien Trung; Pham, Linh Thi Dieu; Le, Hau Duc; Le, Vinh Sy; Mukhopadhyay, Arijit; Nguyen, Liem Thanh

Abstract

Autism spectrum disorder (ASD) is a developmental disorder with a prevalence of around 1% children worldwide and characterized by patient behaviour (communication, social interaction, and personal development). Data on the efficacy of diagnostic tests using copy number variations (CNVs) in candidate genes in ASD is currently around 10% but it is overrepresented by patients of Caucasian background. We report here that the diagnostic success of de novo candidate CNVs in Vietnamese ASD patients is around 6%. We recruited one hundred trios (both parents and a child) where the child was clinically diagnosed with ASD while the parents were not affected. We performed genetic screening to exclude RETT syndrome and Fragile X syndrome and performed genome-wide DNA microarray (aCGH) on all probands and their parents to analyse for de novo CNVs. We detected 1708 non-redundant CNVs in 100 patients and 118 (7%) of them were de novo. Using the filter for known CNVs from the Simons Foundation Autism Research Initiative (SFARI) database, we identified six CNVs (one gain and five loss CNVs) in six patients (3 males and 3 females). Notably, 3 of our patients had a deletion involving the SHANK3 gene–which is the highest compared to previous reports. This is the first report of candidate CNVs in ASD patients from Vietnam and provides the framework for building a CNV based test as the first tier screening for clinical management.

Citation

Bui, H. T. P., Huy Do, D., Ly, H. T. T., Tran, K. T., Le, H. T. T., Nguyen, K. T., …Nguyen, L. T. (in press). De novo copy number variations in candidate genomic regions in patients of severe autism spectrum disorder in Vietnam. PloS one, 19(3), e0290936. https://doi.org/10.1371/journal.pone.0290936

• Journal Article Type: Article
• Acceptance Date: Dec 9, 2023
• Online Publication Date: Mar 7, 2024
• Deposit Date: Mar 11, 2024
• Publicly Available Date: Mar 11, 2024
• Journal: PLOS ONE
• Print ISSN: 1932-6203
• Publisher: Public Library of Science
• Peer Reviewed: Peer Reviewed
• Volume: 19
• Issue: 3
• Pages: e0290936
• DOI: https://doi.org/10.1371/journal.pone.0290936