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

 John Hoon Rim  ;  Se Hee Kim  ;  In Sik Hwang  ;  Soon Sung Kwon  ;  Jieun Kim  ;  Hyun Woo Kim  ;  Min Jung Cho  ;  Ara Ko  ;  Song Ee Youn  ;  Jihun Kim  ;  Young Mock Lee  ;  Hee Jung Chung  ;  Joon Soo Lee  ;  Heung Dong Kim  ;  Jong Rak Choi  ;  Seung-Tae Lee  ;  Hoon-Chul Kang 
 BMC Medical Genomics, Vol.11(1) : 6, 2018 
Journal Title
 BMC Medical Genomics 
Issue Date
Diagnostic yield ; Early-onset epilepsy ; Next-generation sequencing
BACKGROUND: We 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. METHODS: We 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. RESULTS: The 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. CONCLUSIONS: NGS is a useful diagnostic tool with great utility for patients with EOE. Diagnostic yields can be maximized with a standardized and team-based approach.
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1. College of Medicine (의과대학) > Dept. of Pediatrics (소아청소년과학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Laboratory Medicine (진단검사의학교실) > 1. Journal Papers
Yonsei Authors
강훈철(Kang, Hoon Chul) ORCID logo https://orcid.org/0000-0002-3659-8847
김세희(Kim, Se Hee) ORCID logo https://orcid.org/0000-0001-7773-1942
김흥동(Kim, Heung Dong) ORCID logo https://orcid.org/0000-0002-8031-7336
이승태(Lee, Seung-Tae) ORCID logo https://orcid.org/0000-0003-1047-1415
이영목(Lee, Young Mock) ORCID logo https://orcid.org/0000-0002-5838-249X
이준수(Lee, Joon Soo) ORCID logo https://orcid.org/0000-0001-9036-9343
최종락(Choi, Jong Rak) ORCID logo https://orcid.org/0000-0002-0608-2989
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