Whole Exome Sequencing in a Series of Patients with a Clinical Diagnosis of Tuberous Sclerosis Not Confirmed by Targeted TSC1/TSC2 Sequencing

Abstract

Background: Approximately fifteen percent of patients with tuberous sclerosis complex (TSC) phenotype do not have any genetic disease-causing mutations which could be responsible for the development of TSC. The lack of a proper diagnosis significantly affects the quality of life for these patients and their families. Methods: The aim of our study was to use Whole Exome Sequencing (WES) in order to identify the genes responsible for the phenotype of nine patients with clinical signs of TSC, but without confirmed tuberous sclerosis complex 1/ tuberous sclerosis complex 2 (TSC1/TSC2) mutations using routine molecular genetic diagnostic tools. Results: We found previously overlooked heterozygous nonsense mutations in TSC1, and a heterozygous intronic variant in TSC2. In one patient, two heterozygous missense variants were found in polycystic kidney and hepatic disease 1 (PKHD1), confirming polycystic kidney disease type 4. A heterozygous missense mutation in solute carrier family 12 member 5 (SLC12A5) was found in one patient, which is linked to cause susceptibility to idiopathic generalized epilepsy type 14. Heterozygous nonsense variant ring finger protein 213 (RNF213) was identified in one patient, which is associated with susceptibility to Moyamoya disease type 2. In the remaining three patients WES could not reveal any variants clinically relevant to the described phenotypes. Conclusion: Patients without appropriate diagnosis due to the lack of sensitivity of the currently used routine diagnostic methods can significantly profit from the wider application of next generation sequencing technologies in order to identify genes and variants responsible for their symptoms.

Neuronal K+-Cl- cotransporter KCC2 as a promising drug target for epilepsy treatment

“…This suggests that reduced KCC2 activity may be involved in the mechanisms underlying increased excitability in the brains of epileptic patients. The identification of various KCC2 mutations (encoded by SLC12A5 ) has further highlighted the association between KCC2 dysfunction and the development of epilepsy [ 41 – 46 ]. A summary of the KCC2 mutations discovered in human epilepsy can be found in Table 1 [ 47 ], with their localization shown in Fig.…”

“…Consequently, it has been concluded that R952H is a susceptibility variant for IGE [ 44 , 45 ]. Additionally, a novel KCC2 variant, V4731, has recently been discovered in Hungarian patients with IGE [ 41 , 46 ]. The existing literature on epileptic patients with KCC2 mutations has emphasized the role of accumulated high intracellular Cl - concentration resulting from reduced KCC2-dependent Cl - extrusion, which may underlie the hyperexcitability observed in epilepsy.…”

Genome sequencing using machine learning with a special focus on tuberculosis

“…WES provides high-throughput outcomes at a low cost. Here, Bartha and his colleagues looked at analysis methods that would allow WES data to be used in clinical and research settings [6]. WES can detect SNVs (single nucleotide variants) and copy number variations (CNVs) are two types of genetic variations (CNVs) in the beginning, and the information gathered from both approaches can be merged and used further.…”

“…One patient had a heterozygous missense mutation in solute carrier family 12 member 5 (SLC12A5), which has been associated to idiopathic generalized epilepsy type 14. One patient had a heterozygous nonsense variation of ring finger protein 213 (RNF213), which is linked to Moyamoya disease type susceptibility [6].…”

“…The P1-macro average (P1-macro) is a variant of the P1-score, composed of the average of the P1-score of the positive class and the P1-score of the negative class Equation (6). The more the model hits the prediction in both classes (positive and negative), the P1-macro tends to indicate, in general, a degree of a model correctness without bias by balanced or imbalanced the data set.…”