InDels and small CNVs in patients whit Autism Spectrum Disorder

Author(s)

Isabela Mayá Wayhs Silva

• Document type: Master's Dissertation
• Press: São Paulo.
• Institution: Universidade de São Paulo (USP). Instituto de Biociências (IBIOC/SB)
• Defense date: 2017-04-05

Examining board members

Maria Rita dos Santos e Passos Bueno; Ana Cristina Victorino Krepischi; Leslie Domenici Kulikowski

• Advisor: Maria Rita dos Santos e Passos Bueno

Abstract

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder. It is characterized by significant and persistent deficits in communication and social interaction, and by restricted and repetitive patterns of behavior, interests or activities. ASD is considered a common disease, affecting 1 in 68 children and a proportion of 4.2 boys affected for each girl.The etiology of autism has a strong genetic component. In this context, genomic methodologies of high-throughput (new generation sequencing, microarray) contributed to the knowledge about the genetics of ASD. However, in approximately 70% of patients with ASD, the disorder remains with unidentified etiology. Therefore, foi this work, it was hypothesized that small CNVs (between 1 and 50 Kb), which are below the resolution of most commercial microarrays and and whose detection still has limitations for its detection detection through NGS, could contribute to the phenotype in a proportion of cases. As a first step to address this hypothesis, it was performed the methodology of custom aCGH 60K, covering a total of 269 ASD candidate genes, in order to select potentially pathogenic CNVs among 98 Brazilian patients with idiopathic ASD. With this initial screening, the prevalence of potentially pathogenic CNVs obtained was 9%, with 20% of them characterized as small. The subsequent analysis was performed using the 180K custom aCGH methodology, which covered a total of 1527 TEA candidate genes. A total of 63 patients with autism were analyzed with this new array. From these hybridizations, the prevalence of potentially pathogenic CNVs obtained was 12.7%, with 62.5% of them classified as small. This detection rate is quite significant, particularly considering that the sample of patients used was pre-screened, in order to exclude patients with the most prevalent CNVs in ASD in the regions 15q11-q13, 16p11.2 and 22q13.3. The last approach used in this work was to compare the detection of CNVs by the methodology of aCGH, gold standard reference for CNVs detection, with the next generation sequencing (NGS).Data from 9 patients obtained by NGS were analyzed using NextGene and XHMM software. The softwares, however, presented discrepant results among themselves and little overlap with the data of aCGH 180K, of 38.9% and 50%, considering NextGene and XHMM respectively. These results suggest that the customized aCGH represents a promising approach for the detection of small CNVs and that these, in turn, can contribute to the risk of ASD in at least 6,3 % of cases (AU)

• FAPESP's process: 14/13056-7 - Characterization of INDELs and small CNVs in patients with autism spectrum disorder
• Grantee: Isabela Mayá Wayhs Silva
• Support Opportunities: Scholarships in Brazil - Master