The Utility of Next-Generation Sequencing in Gene Discovery for Mutation-Negative Patients with Rett Syndrome

Abstract

Rett syndrome (RTT) is a rare, severe disorder of neuronal plasticity that predominantly affects girls. Girls with RTT usually appear asymptomatic in the first 6–18 months of life, but gradually develop severe motor, cognitive, and behavioral abnormalities that persist for life. A predominance of neuronal and synaptic dysfunction, with altered excitatory–inhibitory neuronal synaptic transmission and synaptic plasticity, are overarching features of RTT in children and in mouse models. Over 90% of patients with classical RTT have mutations in the X-linked methyl-CpG-binding (MECP2) gene, while other genes, including cyclin-dependent kinase-like 5 (CDKL5), Forkhead box protein G1 (FOXG1), myocyte-specific enhancer factor 2C (MEF2C), and transcription factor 4 (TCF4), have been associated with phenotypes overlapping with RTT. However, there remain a proportion of patients who carry a clinical diagnosis of RTT, but who are mutation negative. In recent years, next-generation sequencing technologies have revolutionized approaches to genetic studies, making whole-exome and even whole-genome sequencing possible strategies for the detection of rare and de novo mutations, aiding the discovery of novel disease genes. Here, we review the recent progress that is emerging in identifying pathogenic variations, specifically from exome sequencing in RTT patients, and emphasize the need for the use of this technology to identify known and new disease genes in RTT patients.

The utility of Next Generation Sequencing for molecular diagnostics in Rett syndrome

“…It is also remarkable that, in addition to STXBP1 (EEIE4), we found mutations in genes related to EEIE: KCNQ2 (EEIE7), SCN1A (EEIE6) , SCN2A (EEIE11), GRIN2B (EEIE27) and HCN1 (EEIE24) genes. Furthermore, we also found members of the solute carrier families related to epilepsy: SLC6A1 (myoclonic-atonic epilepsy) and SLC2A1 (idiopathic generalized epilepsy) genes 33 , 35 .…”

Monogenic disorders that mimic the phenotype of Rett syndrome

“…MECP2 encodes a transcription factor implicated in a number of regulatory processes in the brain important for neuronal development and growth [5]. Over time, researchers have identified other causes of RTT besides MECP2 mutations, including defects in CDKL5 (cyclin-dependent kinase-like 5), FOXG1 (forkhead box protein G1), and MEF2C (myocyte-specific enhancer factor 2C) [6]. …”

“…The advent of next-generation sequencing has ushered in the discovery of other causes of Rett-like presentations in patients without MECP2 defects [6]. In one study that evaluated 21 females with features of RTT, two-thirds of the patients had pathogenic variants in genes other than MECP2 , CDKL5 , and FOXG1 [7].…”

Defining the Clinical Value of a Genomic Diagnosis in the Era of Next-Generation Sequencing

“…As a result, the trend in clinical genetics has been toward the use of multigene testing to achieve a molecular diagnosis in individuals with a genetic condition (132). These same technological advances have also facilitated the discovery of a large number of disease genes (7,48,116). We are now at a juncture where genomic technologies are advancing more quickly than we can resolve questions regarding which testing methods are most cost effective, efficient, and accurate.…”

“…Sequencing the coding region of the genome, otherwise known as exome sequencing (7), has become a more prominent technique within the last several years, particularly as a gene discovery tool in the research setting (7,44,45,48,116). The Centers for Mendelian Genomics, funded by the National Institutes of Health to elucidate the genetic etiology of Mendelian phenotypes, have generated exome data for 16,226 individuals, discovered an association with disease for 647 genes using conservative disease causality criteria, and identified another 309 genes that are likely to be disease causing (28).…”