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

Silvia M Vidal ,Jean-Rémi Trotta,Núria Brandi,Paola Pacheco,Merçè Pineda ,Àngels García‐Cazorla ,Edgar Gerotina,Sophia Derdak,Laura Campello Blasco ,María Del Mar O’callaghan ,Judith Armstrong

doi:10.1038/s41598-017-11620-3

Abstract

Rett syndrome (RTT) is an early-onset neurodevelopmental disorder that almost exclusively affects girls and is totally disabling. Three genes have been identified that cause RTT: MECP2, CDKL5 and FOXG1. However, the etiology of some of RTT patients still remains unknown. Recently, next generation sequencing (NGS) has promoted genetic diagnoses because of the quickness and affordability of the method. To evaluate the usefulness of NGS in genetic diagnosis, we present the genetic study of RTT-like patients using different techniques based on this technology. We studied 1577 patients with RTT-like clinical diagnoses and reviewed patients who were previously studied and thought to have RTT genes by Sanger sequencing. Genetically, 477 of 1577 patients with a RTT-like suspicion have been diagnosed. Positive results were found in 30% by Sanger sequencing, 23% with a custom panel, 24% with a commercial panel and 32% with whole exome sequencing. A genetic study using NGS allows the study of a larger number of genes associated with RTT-like symptoms simultaneously, providing genetic study of a wider group of patients as well as significantly reducing the response time and cost of the study.

Highlights

Rett syndrome (RTT) is an early-onset neurodevelopmental disorder that almost exclusively affects girls and is totally disabling
In this variant RTT group of patients, some have mutations in other genes that are associated with RTT: cyclin-dependent kinase-like[5] (CDKL5; MIM *300203), which is described in individuals with an early seizure onset variant of RTT13, and Forkhead box protein G1 (FOXG1; MIM *164874), which is responsible for the congenital variant of RTT14
242 patients were studied using the Haloplex Custom Panel (HCP, Agilent Technologies) (Santa Clara, California), including 46 that came from a negative study of Sanger sequencing (SS)

Summary

Introduction

Rett syndrome (RTT) is an early-onset neurodevelopmental disorder that almost exclusively affects girls and is totally disabling. A large number of reports support the evidence that mutations in the Methyl CpG binding protein 2 gene (MECP2; MIM *300005) are the major causes of classical RTT7,8. The majority of RTT patients have mutations in the MECP2 gene[10], approximately 5% of classical RTT and 25% of variant RTT patients are negative for MECP2 mutation[6,12] In this variant RTT group of patients, some have mutations in other genes that are associated with RTT: cyclin-dependent kinase-like[5] (CDKL5; MIM *300203), which is described in individuals with an early seizure onset variant of RTT13, and Forkhead box protein G1 (FOXG1; MIM *164874), which is responsible for the congenital variant of RTT14. The etiology of a subset of patients with a clinical diagnosis of RTT or RTT-like symptoms remains unknown

Methods

Results

Conclusion