• Journal of Genetic Medicine
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• 제15권2호
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• pp.87-91
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• 2018

X-linked dominant mutations in lysosome-associated membrane protein 2 (LAMP2) gene have been shown to be the cause of Danon disease, which is a rare disease associated with clinical triad of cardiomyopathy, skeletal myopathy, and mental retardation. Cardiac involvement is a common manifestation and is the leading cause of death in Danon disease. We report a case of a 24-month-old boy with hemizygous LAMP2 mutation who presented with failure to thrive and early-onset hypertrophic cardiomyopathy. We applied targeted exome sequencing and found a novel hemizygous c.692del variant in exon 5 of the LAMP2 gene, resulting a frameshift mutation p.Thr231Ilefs*11. Our study indicates that target next-generation sequencing can be used as a fast and highly sensitive screening method for inherited cardiomyopathy.

• Journal of Genetic Medicine
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• 제7권2호
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• pp.119-124
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• 2010

약 7,000 여개의 단일유전자질환이 보고되어 있지만 보고된 질환의 절반도 아직 원인 유전자가 밝혀지지 못한 상황이다. 그리고 기존에 밝혀진 원인 유전자의 돌연변이형들은 대부분 단백질을 코딩하는 부위의 돌연변이에 의하여 발생하고 있어서 인간 유전체에서 단백질을 코딩하는 엑손 부위만을 선별적으로 분리하여 염기서열을 분석하는 엑솜 염기서열 분석 방법은 희귀한 유전질환의 신규 원인 유전자 발굴을 위한 매우 효과적인 유전 분석법이 될 것이다. 엑솜은 전체 유전체의 약 1.5% 정도를 차지하고 있어서 매우 경제적으로 분석이 가능하다. 그리고 엑솜 염기서열 분석 방법은 엑솜 부위를 선별하는 기술과 대용량 염기서열 분석기술로 수행된다. Freeman-Sheldon 증후군의 원인 유전자를 엑솜 염기서열 분석 방법으로 발굴한 이후로 단일유전자질환의 원인 유전자 발굴을 위한 표준 분석법으로 엑솜 염기서열 분석방법이 사용되고 있다. 향후에는 엑솜 염기서열 분석 방법이 다양한 복합질병의 유전분석에도 활용되어 개인 맞춤의학의 실현을 앞당기는데 크게 기여할 것으로 기대된다.

• BMB Reports
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• 제54권7호
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• pp.386-391
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• 2021

Owing to rapid advancements in NGS (next generation sequencing), genomic alteration is now considered an essential predictive biomarkers that impact the treatment decision in many cases of cancer. Among the various predictive biomarkers, tumor mutation burden (TMB) was identified by NGS and was considered to be useful in predicting a clinical response in cancer cases treated by immunotherapy. In this study, we directly compared the lab-developed-test (LDT) results by target sequencing panel, K-MASTER panel v3.0 and whole-exome sequencing (WES) to evaluate the concordance of TMB. As an initial step, the reference materials (n = 3) with known TMB status were used as an exploratory test. To validate and evaluate TMB, we used one hundred samples that were acquired from surgically resected tissues of non-small cell lung cancer (NSCLC) patients. The TMB of each sample was tested by using both LDT and WES methods, which extracted the DNA from samples at the same time. In addition, we evaluated the impact of capture region, which might lead to different values of TMB; the evaluation of capture region was based on the size of NGS and target sequencing panels. In this pilot study, TMB was evaluated by LDT and WES by using duplicated reference samples; the results of TMB showed high concordance rate (R² = 0.887). This was also reflected in clinical samples (n = 100), which showed R² of 0.71. The difference between the coding sequence ratio (3.49%) and the ratio of mutations (4.8%) indicated that the LDT panel identified a relatively higher number of mutations. It was feasible to calculate TMB with LDT panel, which can be useful in clinical practice. Furthermore, a customized approach must be developed for calculating TMB, which differs according to cancer types and specific clinical settings.

• Journal of Interdisciplinary Genomics
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• 제4권1호
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• pp.7-10
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• 2022

Purpose:Maturity onset diabetes of the young (MODY) is the most common hereditary form of diabetes mellitus (DM), with similar clinical manifestations to type 1 or type 2 DM, leading to diagnostic ambiguity. Despite increased genetic research on monogenic DM, studies with Asian populations are limited. Therefore, we investigated mutation in possible monogenic DM and MODY in Korean children and aldolescents. Methods: Targeted panel exome sequencing including 32 targets genes was performed for 41 patients with suspected monogenic DM at Kyungpook National University Children's Hospital. Results: Variants were detected in 19 patients, including those in known MODY-associated genes (HNF4A, GCK, HNF1A, CEL, PAX4, INS, and BLK) and monogenic DM-associated genes (WFS1, FRX6, and GLIS3). Conclusion: MODY variants were detected more than expected. Targeted exon sequencing is helpful in diagnosing MODY or possible monogenic DM patients.

• 대한유전성대사질환학회지
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• 제17권3호
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• pp.96-102
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• 2017

당원병 IX형은 phosphorylase kinase 효소 결핍으로 분해되지 않은 당원이 간 또는 근육에 축적되는 유전성대사이상질환이다. 당원병 IXa형은 당원병 IX형 중 가장 흔한 형태로 PHKA2 유전자 변이로 발생한다. 당원병 IXa형의 임상증상은 간 비대, 간 효소 수치 상승, 성장 지연, 저혈당 등이 있다. 그러나, 이러한 임상 증상은 다른 타입의 당원병의 증상과 비슷하거나 겹쳐서 임상적으로는 구분하기가 어렵다. 저자들은 표적 엑솜 시퀀싱으로 진단된 가족성 당원병 IXa형 증례를 보고하고자 한다. 4세 남아가 간 비대와 간 효소 수치 상승을 주소로 내원하였다. 간 조직검사결과 간세포에 당원이 축적되어 있어 당원병을 의심하였으나 G6PC 유전자 검사는 음성이었다. 이에 당원병 타입을 감별진단 하기 위해 표적 엑솜시퀀싱을 시행하였으며, PHKA2 유전자에서 질환과의 연관성이 이미 보고된 바 있는 c.3632C>T (p.Thr121Met) 변이가 반접합체(hemizygote)로 발견되어 당원병 IXa로 진단하였다. 가족 유전자 검사를 통해 어머니가 이형접합체 보인자임을 확인하였으며, 남동생이 같은 변이를 가진 반접합체임을 확인하였다. 28개월 된 환자의 남동생 역시 신체 검진 상 간 비대가 있었으며, 혈액검사상 간 효소 수치가 상승되어 있어 같은 질환으로 확진하였다. 이환된 형제 모두 생 옥수수 전분 섭취와 복합 탄수화물을 섭취하도록 식이 조절을 하였으며 2년 추적관찰 동안 정상 성장 발달을 보이고 있다. 당원병과 같이 임상적으로 구분이 어려우며 유전학적으로 다양한 유전자 변이를 보이는 당원병과 같은 질환의 분자 유전학적 감별진단에 표적 엑솜 시퀀싱이 유용한 진단법이 될 수 있다. 신속하고 정확한 분자 유전학적 감별진단을 통해 환자와 보호자에게 질병의 적절한 치료법, 질병의 예후에 관한 정확한 정보를 제공할 수 있을 뿐 아니라, 적절한 유전상담을 제공할 수 있다.

• Clinical and Experimental Pediatrics
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• 제63권6호
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• pp.195-202
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• 2020

Developments in next-generation sequencing (NGS) techogies have assisted in clarifying the diagnosis and treatment of developmental delay/intellectual disability (DD/ID) via molecular genetic testing. Advances in DNA sequencing technology have not only allowed the evolution of targeted panels but also, and more currently enabled genome-wide analyses to progress from research era to clinical practice. Broad acceptance of accuracy-guided targeted gene panel, whole-exome sequencing (WES), and whole-genome sequencing (WGS) for DD/ID need prospective analyses of the increasing cost-effectiveness versus conventional genetic testing. Choosing the appropriate sequencing method requires individual planning. Data are required to guide best-practice recommendations for genomic testing, regarding various clinical phenotypes in an etiologic approach. Targeted panel testing may be recommended as a firsttier testing approach for children with DD/ID. Family-based trio testing by WES/WGS can be used as a second test for DD/ID in undiagnosed children who previously tested negative on a targeted panel. The role of NGS in molecular diagnostics, treatment, prediction of prognosis will continue to increase further in the coming years. Given the rapid pace of changes in the past 10 years, all medical providers should be aware of the changes in the transformative genetics field.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제22권6호
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• pp.581-587
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• 2019

Arthrogryposis-renal dysfunction-cholestasis (ARC) syndrome is a rare autosomal recessive multisystemic disease that is associated with the liver, kidney, skin, and central nervous and musculoskeletal systems. ARC occurs as a result of mutations in the VPS33B (Vacuolar protein sorting 33 homolog B) or VIPAR (VPS33B interacting protein, apical-basolateral polarity regulator) genes. A female infant presented with neonatal cholestasis with a severe clinical outcome. She was diagnosed with ARC syndrome using targeted exome sequencing (TES). Exome sequencing revealed compound heterozygous mutations, c.707A>T and c.239+5G>A, in VPS33B, where c.707A>T was a novel variant; the resultant functional protein defects were predicted via in silico analysis. c.239+5G>A, a pathogenic mutation that affects splicing, is found in less than 0.1% of the general population. Invasive techniques, such as liver biopsies, did not contribute to a differential diagnosis of ARC syndrome; thus, early TES together with clinical presentations constituted an apparently accurate diagnostic procedure.

• Clinical and Experimental Pediatrics
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• 제61권12호
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• pp.403-406
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• 2018

Floating-Harbor syndrome is a rare autosomal dominant genetic disorder associated with SRCAP mutation. To date, approximately 50 cases of Floating-Harbor syndrome have been reported, but none have been reported in Korea yet. Floating-Harbor syndrome is characterized by delayed bony maturation, unique facial features, and language impairment. Here, we present a 6-year-old boy with a triangular face, deep-set protruding eyes, low-set ears, wide nose with narrow nasal bridge, short philtrum, long thin lips, clinodactyly, and developmental delay that was transferred to our pediatric clinic for genetic evaluation. He showed progressive delay in the area of language and cognition-adaption as he grew. He had previously undergone chromosomal analysis at another hospital due to his language delay, but his karyotype was normal. We performed targeted exome sequencing, considering several syndromes with similar phenotypes. Library preparation was performed with the TruSight One sequencing panel, which enriches the sample for about 4,800 genes of clinical relevance. Massively parallel sequencing was conducted with NextSeq. An identified variant was confirmed by Sanger sequencing of the patient and his parents. Finally, the patient was confirmed as the first Korean case of Floating-Harbor syndrome with a novel SRCAP (Snf2 related CREBBP activator protein) mutation (c.7732dupT, p.Ser2578Phefs*6), resulting in early termination of the protein; it was not found in either of his healthy parents or a control population. To our knowledge, this is the first study to describe a boy with Floating-Harbor syndrome with a novel SRCAP mutation diagnosed by targeted exome sequencing in Korea.

• 대한유전성대사질환학회지
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• 제23권2호
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• pp.1-7
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• 2023

유전성 대사질환은 생화학적 대사 이상에 의해 발생하는 질환 군으로, 매우 다양할 뿐만 아니라 임상 양상이 서로 겹칠 수 있어 진단에 어려움을 겪을 수 있다. 과거에는 유전성 대사질환의 원인이 될 수 있는 유전자를 선정한 후 한 개씩 분석하는 방식으로 유전자 검사를 시행했다. 하지만, 최근에는 차세대 염기서열분석 기술이 발전함에 따라 유전성 대사질환과 관련된 수백-수천개의 유전자를 한꺼번에 분석하거나, 인간의 모든 유전자를 포함하는 엑솜/게놈 분석을 시행한 후 원인 유전자를 찾는 방식으로 유전 진단의 패러다임이 바뀌고 있다. 본 종설에서는 차세대 염기서열분석을 이용한 유전성 대사질환의 유전 진단 방법과 진단율 및 주의점 등을 살펴보고자 한다.

• Journal of mucopolysaccharidosis and rare diseases
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• 제3권1호
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• pp.28-32
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• 2017

Lipoid congenital adrenal hyperplasia (LCAH) is the severe form of congenital adrenal hyperplasia and is characterized by adrenal insufficiency with hyperpigmentation and female external genitalia irrespective of genetic sex. The steroidogenic acute regulatory protein (StAR) is required for the transport of cholesterol into the mitochondria for steroidogenesis, and defects in the StAR gene account for the majority of LCAH cases. In this report, we present a two-day-old hyperpigmented infant with phenotypical female genitalia. With consideration of the clinical and laboratory findings, the infant was suspected of having adrenal insufficiency due to LCAH and treated with glucocorticoid, mineralocorticoid, and sodium chloride. Karyotyping revealed 46, XY. Upon pelvis ultrasonography, adrenal hyperplasia with abdominal masses (thought to be the testicles) was reported. Molecular analysis with targeted exome sequencing revealed the homozygote mutation of c.772C>T ($p.Q258^*$) in exon 7 of the StAR gene. The early detection and treatment of adrenal insufficiency in infants with hyperpigmentation can prevent clinically apparent adrenal crises. During follow-up, the patient had a good clinical condition and maintained normal electrolyte and adrenocorticotropic hormone levels with medication.