Efficient strategy for the molecular diagnosis of intractable early-onset epilepsy using targeted gene sequencing

John Hoon Rim,Soon Sung Kwon,Min Jung Cho,Heung Dong Kim,Song Ee Youn,Jong Rak Choi,Joon Soo Lee,Ara Ko,Se Hee Kim,Hyun Woo Kim,Hoon-Chul Kang,Jieun Kim,Seung-Tae Lee,Hee Jung Chung,Jihun Kim,In Sik Hwang,Young Mock Lee

doi:10.1186/s12920-018-0320-7

Abstract

BackgroundWe intended to evaluate diagnostic utility of a targeted gene sequencing by using next generation sequencing (NGS) panel in patients with intractable early-onset epilepsy (EOE) and find the efficient analytical step for increasing the diagnosis rate.MethodsWe assessed 74 patients with EOE whose seizures started before 3 years of age using a customized NGS panel that included 172 genes. Single nucleotide variants (SNVs) and exonic and chromosomal copy number variations (CNVs) were intensively examined with our customized pipeline and crosschecked with commercial or pre-built software. Variants were filtered and prioritized by in-depth clinical review, and finally classified according to the American College of Medical Genetics and Genomics guidelines. Each case was further discussed in a monthly consensus meeting that included the participation of all laboratory personnel, bioinformaticians, geneticists, and clinicians.ResultsThe NGS panel identified 28 patients (37.8%) with genetic abnormalities; 25 patients had pathogenic or likely pathogenic SNVs in 17 genes including SXTBP1 (n = 3), CDKL5 (n = 2), KCNQ2 (n = 2), SCN1A (n = 2), SYNGAP1 (n = 2), GNAO1 (n = 2), KCNT1 (n = 2), BRAT1, WWOX, ZEB2, CHD2, PRICKLE2, COL4A1, DNM1, SCN8A, MECP2, SLC9A6 (n = 1). The other 3 patients had pathogenic CNVs (2 duplications and 1 deletion) with varying sizes (from 2.5 Mb to 12 Mb). The overall diagnostic yield was 37.8% after following our step-by-step approach for clinical consensus.ConclusionsNGS is a useful diagnostic tool with great utility for patients with EOE. Diagnostic yields can be maximized with a standardized and team-based approach.

Highlights

We intended to evaluate diagnostic utility of a targeted gene sequencing by using generation sequencing (NGS) panel in patients with intractable early-onset epilepsy (EOE) and find the efficient analytical step for increasing the diagnosis rate
Clinical factors associated with genetic abnormalities When all patients with EOE were assessed together, we did not find statistically significant differences in gender, age of seizure onset, and history of neonatal seizures between the patients with sufficient genetic cause group identified by next generation sequencing (NGS) and the patients with negative results group, except for history of febrile seizures (28.6% vs. 6.5%)
Single-gene mutations accounted for 89.2% of all abnormalities detected; these included 16 mutations (57.1%) in major affected genes in our study (STXBP1, CDKL5, KCNQ2, SCN1A, KCNT1, SYNGAP1, MECP2, and GNAO1) and 9 mutations (32.1%) in various genes (BRAT1, WWOX, ZEB2, CHD2, PRICKLE2, COL4A1, DNM1, SCN8A, and SLC9A6)

Summary

Introduction

We intended to evaluate diagnostic utility of a targeted gene sequencing by using generation sequencing (NGS) panel in patients with intractable early-onset epilepsy (EOE) and find the efficient analytical step for increasing the diagnosis rate. Clinical questions regarding the identification of patients who are most likely to show positive genetic results, and strategies to increase the diagnostic yields of NGS panel still remain to be explored. We used a customized NGS panel to clinically and genetically investigate a highly selected group of patients who developed EOE in infancy or early childhood (≤3 years of age). Our goal was to optimize the clinical use of NGS panel for EOE by finding the most important analytical step that determines the diagnosis rate and identifying patients who are most likely to show genetic abnormalities

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