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Towards a Change in the Diagnostic Algorithm of Autism Spectrum Disorders: Evidence Supporting Whole Exome Sequencing as a First-Tier Test.

ABSTRACT: Autism spectrum disorder (ASD) is a prevalent and extremely heterogeneous neurodevelopmental disorder (NDD) with a strong genetic component. In recent years, the clinical relevance of de novo mutations to the aetiology of ASD has been demonstrated. Current guidelines recommend chromosomal microarray (CMA) and a FMR1 testing as first-tier tests, but there is increasing evidence that support the use of NGS for the diagnosis of NDDs. Specifically in ASD, it has not been extensively evaluated and, thus, we performed and compared the clinical utility of CMA, FMR1 testing, and/or whole exome sequencing (WES) in a cohort of 343 ASD patients. We achieved a global diagnostic rate of 12.8% (44/343), the majority of them being characterised by WES (33/44; 75%) compared to CMA (9/44; 20.4%) or FMR1 testing (2/44; 4.5%). Taking into account the age at which genetic testing was carried out, we identified a causal genetic alteration in 22.5% (37/164) of patients over 5 years old, but only in 3.9% (7/179) of patients under this age. Our data evidence the higher diagnostic power of WES compared to CMA in the study of ASD and support the implementation of WES as a first-tier test for the genetic diagnosis of this disorder, when there is no suspicion of fragile X syndrome.

SUBMITTER: Arteche-Lopez A

PROVIDER: S-EPMC8068856 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundAutism 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.MethodsBetween 2020 and 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.ResultsOf 101 trios, no probands were identified with a gross chromosomal anomaly or Fragile-X. Three (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 affected genes identified in the study cohort are involved in synaptic formation, transcription and its regulation, ubiquitination and chromatin remodeling.ConclusionsOur study suggests de novo variants as a major cause of ASD in the Indian population, with Rett syndrome as the most commonly detected disorder. 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.

Project description:The Rapid Interactive screening Test for Autism in Toddlers (RITA-T) is a fast and inexpensive early screening measure for autism spectrum disorder (ASD) that was tested previously in children 18-36 months-old; the current validation study compared the RITA-T with the Autism Diagnostic Observation Schedule™ Second Edition (ADOS-2). The hypothesis is to validate the RITA-T with comparison to the ADOS-2. Thirty-five individuals (18-84 months-old) identified as at risk for ASD received the RITA-T and the ADOS-2 during a single visit. Participants were split into two age groups and both whole-group and sub-group data analysis were conducted. With all participants, RITA-T scores correlated significantly with ADOS-2 total scores (P < 0.001), social affect (SA) sub-scores (P < 0.001), and restrictive and repetitive behavior (RRB) sub-scores (P < 0.05). Similarly, ADOS-2 total and SA scores were significantly correlated in both age groups, while the RRB sub-score was only significant in females (P < 0.05). Lastly, correlations using subgroups based on ethnicity were only significant in the minority ("Other") group for ADOS-2 total scores and in the Asian group for SA sub-scores (P < 0.05). Our receiver operating characteristic analysis showed that the optimal cut-off score of the RITA-T was consistently at 14, with a sensitivity of 81% and a specificity of 89% in the combined age group with the ADOS-2 and with a sensitivity 74% and specificity 50% with the DSM-5; The area under the curve was 0.84 (95%CI: 0.69-0.99) for ASD classified by ADOS-2 and 0.89 (95%CI: 0.79-0.99) for ASD diagnosed by DSM-5. The RITA-T performed similarly to the ADOS-2 when both were administered in a single visit. Significant correlations between the measures help validate the potential usefulness of the RITA-T as a rapid early screening measure of ASD. This study helps to show that the RITA-T may be used in a larger age range than originally reported and in different ethnic groups. The study involves human participants and was reviewed and approved by the Institutional Review Board (IRB) of Massachusetts General Hospital (MGH, 2017P0000857).

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Towards a Change in the Diagnostic Algorithm of Autism Spectrum Disorders: Evidence Supporting Whole Exome Sequencing as a First-Tier Test.

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