Comparative yield of molecular diagnostic algorithms for autism spectrum disorder diagnosis in India: Evidence supporting whole exome sequencing as first tier test

Abstract Background: Autism spectrum disorder (ASD) affects 1 in 100 children globally with a rapidly increasing prevalence. To the best of our knowledge, no data exists on the genetic architecture of ASD in India. This study aimed to identify the genetic architecture of ASD in India and to assess the use of whole exome sequencing (WES) as a first-tier test instead of chromosomal microarray (CMA) for genetic diagnosis. Methods: Between 2020 to 2022, 101 patient-parent trios of Indian origin diagnosed with ASD according to the Diagnostic and Statistical Manual, 5th edition, were recruited. All probands underwent a sequential genetic testing pathway consisting of karyotyping, Fragile-X testing (in male probands only), CMA and WES. Candidate variant validation and parental segregation analysis was performed using orthogonal methods. Results: Of 101 trios, 3 (2.9%) and 30 (29.7%) trios received a confirmed genetic diagnosis from CMA and WES, respectively. Amongst diagnosis from WES, SNVs were detected in 27 cases (90%) and CNVs in 3 cases (10%), including the 3 CNVs detected from CMA. Segregation analysis showed 66.6% (n=3 for CNVs and n=17 for SNVs) and 16.6% (n=5) of the cases had de novo and recessive variants respectively, which is in concordance with the distribution of variant types and mode of inheritance observed in ASD patients of non-Hispanic white/ European ethnicity. MECP2 gene was the most recurrently mutated gene (n=6; 20%) in the present cohort. Majority of the detected genes are involved in synaptic formation, transcription and its regulation, ubiquitination and chromatin remodeling. Limitations: There is a possibility of ascertainment bias related to probands primarily having non-syndromic form of ASD. Furthermore, it needs to be considered that CMA and WES was carried out in the proband only, therefore, detailed assessment of all potential de novo variants couldn’t be carried out. Conclusions: Our study suggests de novo variants as a major cause of ASD in the Indian population. Furthermore, we provide evidence of a significant difference in the diagnostic yield between CMA (3%) and WES (30%) which supports the implementation of WES as a first-tier test for genetic diagnosis of ASD in India.