Characterization of genomic structural variations in Slovenian children with unexplained intellectual disabilities or developmental delay, congenital anomalies, and autistic spectrum disorders

• Main Author: Krgovic, Danijela
• Format: Dissertation
• Language: Slovenian
• Subjects: genetics
• ISBN: 9781321691696; 1321691696

In spite of intensive genetic diagnostics, in about half of the children with neurodevelopmental disorders the cause of the disorder still remains unexplained. During the last two decades, use of molecular karyotyping dramatically changed the understanding the role of the genomic abnormalities in these disorders. The method has enabled the examination of the entire human genome at a higher resolution. This lead to the identification of submicroscopic genomic rearrangements called copy--number variations (CNV). These are deletions or duplications of several kilo (kb) to few maga (Mb) base pairs in size. The CNVs are part of a normal diversity of the human genome (benign CNVs) or they can be cause of various diseases and disorders (pathogenic CNVs). Use of molecular karyotyping in diagnostics of neurodevelopmental disorders significantly increased the number of patients for whom a clinically relevant aberration can be detected. Therefore, this method became a first--tier test in diagnostics of children with intellectual disabilities (ID), developmental delay (DD), congenital anomalies and autistic spectrum disorders (ASD).
Systematic assessment of the application of the method in the Slovenian population has not been evaluated so far. Therefore, we performed a study of CNVs in 159 children with ASD and 126 children with ID/DD. In the first group of patients, pathogenic CNV was identified in 12.6%. In ID/DD group the CNV with clinical significance, was detected in 15% of children. Variants with unknown significance were determined in 7% of children with ASD and 10% of children with ID/DD. Further evaluation of these CNVs in literature and genotype--phenotype correlation with new patients published in databases of CNVs determined in persons with neurodevelopmental disorders will hopefully lead to better understanding of their role in pathogenesis of these disorders.
Pathogenic CNVs were usually identified in known microdeletion or microduplication syndromes regions or there were encompassing the gene known to cause a certain neurodevelopment disorder. An example of these are a duplication of the chromosomeregion 16p11.2 associated with autism. During our study, we were also able to detect some previously unpublished of rarely published cases in literature. In the ASD group, we identified a deletion of the last exon of SHANK3 gene in a boy with autism, and severe regression in DD and verbal communication. SHANK3 gene is a key gene of Phelan--McDermid syndrome (PMS). Usually large deletions of the 22q13.3 regions are reported in these patients. The analyzed deletion was crucial for proper diagnosis in our proband, since he presented the full clinical picture of PMS, even though he is a carrier of one of the smallest reported deletions of the SHANK3 gene. We were also fist to describe a smallest submicroscopic deletion of 11q22.3 in a girl with mild ID and profound dysplastic features. We also described a complex rearrangement on chromosome 5p in a newborn girl with DD, with left ear anomalies and a specific high-pitch cry. The proband was a carrier of the de novo terminal deletion in the region of the Cri--du--Chat syndrome (CDCS), followed by a much larger duplication with an inversion in the region of Trisomy 5p. This is the seventh such complex rearrangement described in the literature thus far. The genotype-phenotype correlation and data from the literature have shown that the clinical picture of our proband cantains the phenotypic features of both syndromes. In comparison with other patients described in the literature, we also tryed to more precisely define the critical regions of these two syndromes, such as: critical region for "cat--like" cry for CDCS and critical region for Trisomy 5p.
During our study we also performed the statistical analysis of all CNVs detected in patients and the in--house control group. With statistical analysis we tryed to evaluate whether there was a statistically significant difference between the presence of CNV in the specific chromosomal locus in subjects with ASD or ID/DD, compared to CNVs in the general Slovenian and other populations. The difference would indicate a potential role of the analyzed CNV in the development of specific disorders. At the same time, we tryed to determine whether there was a CNV specific for the Slovenian population. The results of the statistical analysis showed that deletions within the variable region 2q37.3 are more frequent in the Slovenian population than reported in the database of benign CNVs for other populations. They are also more frequent in the ASD and ID/DD groups. The frequency of deletions in the ID/DD group was comparable to the one determined for an in--house control group. Deletions in region 2q37.3 are two times more frequent in ASD group compared to the in--house control group. In some sections of the 2q37.3 region, the frequency of deletion is five to eight times greater in ASD group comparing to the deletions described in other populations. The significant departure in frequency of deletion in region 2q37.3 in the ASD group could be a potential cause of increased susceptibility for ASD with a variable clinical picture. A confirmation of this assumption requires further extensive research, with a larger number of subjects with more detailed clinical descriptions.
Statistical evaluation of the analyzed CNV gave us an insight into the difference in the presence of CNVs in ASD and ID/DD groups compared to the general population of Slovenian and published data for other populations. More importantly, the study of CNVs in Slovenian children showed us the important role of these aberrations in aetiology of neurodevelopmental disorders and the importance of molecular karyotyping in their diagnosis.