Wellington, New Zealand – Researchers at the University of Otago’s Department of Paediatrics and Child Health think that the analysis of intronic regions through various methods could uncover novel variants responsible for causing Dravet syndrome (DS), according to a study recently published in Epilepsia Open.
“We demonstrate that targeted interrogation of deep intronic regions using multiple genomics technologies, coupled with functional analysis, can reveal hidden causes of unsolved monogenic developmental and epileptic encephalopathies syndromes,” the authors wrote.
This retrospective study included a cohort of children with DEEs from New Zealand, who remained undiagnosed despite extensive genetic testing, including single nucleotide polymorphism arrays, exome sequencing, and genome sequencing. Among 89 unsolved cases, 3 children with a high likelihood of monogenic DEE were identified: 2 with DS and 1 with lissencephaly, associated with variants in SCN1A and PAFAH1B1, respectively.
The breakthrough came when researchers conducted a secondary analysis, delving into the deep intronic regions of the implicated genes using multiple sequencing and bioinformatics strategies. This approach unearthed a novel de novo deep intronic 12 kb deletion in PAFAH1B1 in a child with lissencephaly.
On the other hand, DS is caused by SCN1A variants in over 80% of cases, showcasing the significance of targeted genetic investigations. Notably, this syndrome has been a focal point for intronic discoveries, particularly within highly conserved regions of SCN1A introns.
Researchers delved into these conserved areas, identifying pathogenic splicing variants in what is referred to as “poison exons.” Subsequent advancements include developing splicing reporter assays designed to characterize deep intronic variants within SCN1A functionally. Notably, the study distinguishes the deep intronic deletion found in PAFAH1B1 from those in SCN1A’s “poison exons,” as it does not occur in a highly conserved region.
Experimental validation demonstrated that the deep intronic deletion disrupted mRNA splicing, resulting in partial intron retention and disruption of the LisH motif—a crucial element for neuronal growth regulation. The study emphasizes the importance of employing advanced genomics technologies and functional analysis to uncover hidden causes of unsolved monogenic DEE syndromes.
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