Publication details
Exómové sekvenovanie ako účinný nástroj pre detekciu intragénových variantov v počte kópií u detských pacientov s neurovývojovými ochoreniami
| Title in English | Exome sequencing as an effective tool for the detection of intragenic copy-number variations in paediatric patients with neurodevelopmental disorders |
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| Authors | |
| Year of publication | 2022 |
| Type | Appeared in Conference without Proceedings |
| MU Faculty or unit | |
| Citation | |
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| Description | Copy-number variations (CNVs) represent a fundamental source of genetic variability and play an imporant role in the pathogenesis of neurodevelopmental disorders (NDDs). A large portion of causative CNVs remain unidentified. Array-CGH is still a first-line test for their detection but its resolution routinely does not allow to detect intragenic CNVs which may be responsible for the manifestation of pathological phenotype. Novel sequencing techniques open new options for complex genome analysis. Exome sequencing (ES) overcomes technical limitations of array-CGH and significantly improves diagnostic yield of causative CNVs in paediatric patients with NDDs. Our aim is to review the technical parameters of ES for the detection of intragenic CNVs in the molecular diagnostics of NDDs. We present our experience with ES data analysis in the diagnostics of paediatric NDDs using commercial kit Human Core Exome (Twist Bioscience) and Illumina NovaSeq 600 sequencing platform. The data were processed using two different bioinformatics pipelines and CNVs were then filtered using in-house-developed approach. CNVs were classified using ACMG standards, relevant scientific literature and clinical data. They were visualized using the Integrative Genomics Viewer (IGV). Trio-based analysis (patients and their parents) was selected for higher effectivity and reliability. Our study included 59 patients with NDDs, which were previously examined by array-CGH without the findings of clinically relevant CNVs. Using ES, causative CNVs were detected in three patients (5.1%). Single-exon deletion of the GRIN2A gene was revealed in two affected siblings with epileptic aphasia as it was inherited from slightly affected father. Secondly, we identified de novo deletion of three exons in the ZC4H2 gene in a girl with a rare C-linked Wieacker-Wolff syndrome. In two unrelated individuals we identified non-pathogenic homozygous deletion of exon 2 in the KLK15 gene. Its origin is dated before the migration from Africa 70 000 years ago. CNVs were verified using qPCR and interpreted using the information from genomic databases, relevant scientific literature and individual's anamnesis. Our results suggest the ES as an effective tool for the detection of intragenic CNVs. Its implementation to the routine molecular diagnostics would improve the diagnostic yield and simplified the diagnostics algorithm due to the simultaneous detection of sequence variants and CNVs. Supported by Ministry of Health of the Czech Republic, grant nr. NU20-07-00145 and by projects of Faculty of Science of Masaryk University MUNI/A/1522/2020, MUNI/A/1325/2021. |
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