• Genes and Genomics
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• 제40권12호
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• pp.1269-1277
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• 2018

Bcl2-associated athanogene 3 (BAG3) mutations have been reported to cause the myofibrillar myopathy (MFM) which shows progressive limb muscle weakness, respiratory failure, and cardiomyopathy. Myopathy patients with BAG3 mutation are very rare. We described a patient showing atypical phenotypes. We aimed to find the genetic cause of Korean patients with sensory motor polyneuropathy, myopathy and rigid spine. We performed whole exome sequencing (WES) with 423 patients with sensory motor polyneuropathy. We found BAG3 mutation in one patient with neuropathy, myopathy and rigid spine syndrome, and performed electrophysiological study, whole body MRI and muscle biopsy on the patient. A de novo heterozygous p.Pro209Leu (c.626C>T) mutation in BAG3 was identified in a female myopathy. She first noticed a gait disturbance and spinal rigidity at the age of 11, and serum creatine kinase levels were elevated ninefolds than normal. She showed an axonal sensory-motor polyneuropathy like Charcot-Marie-Tooth disease (CMT), myopathy, rigid spine and respiratory dysfunction; however, she did not show any cardiomyopathy, which is a common symptom in BAG3 mutation. Lower limb MRI and whole spine MRI showed bilateral symmetric fatty atrophy of muscles at the lower limb and paraspinal muscles. When we track traceable MRI 1 year later, the muscle damage progressed slowly. As far as our knowledge, this is the first Korean patient with BAG3 mutation. We described a BAG3 mutation patient with atypical phenotype of CMT and myopathy, and those are expected to broaden the clinical spectrum of the disease and help to diagnose it.

• Journal of Genetic Medicine
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• 제18권2호
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• pp.127-131
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• 2021

Autosomal recessive spinocerebellar ataxia 20 (SCAR20; OMIM #616354) is a recently described disorder that is characterized by ataxia, intellectual disability, cerebellar atrophy, macrocephaly, coarse face, and absent speech. It is caused by loss-of-function mutations in SNX14. To date, all cases with homozygous pathogenic variants have been identified in consanguineous families. This report describes the first Korean cases of SCAR20 family caused by homozygous variants in SNX14. Two siblings were referred to our clinic because of severe global developmental delay. They presented similar facial features, including a high forehead, long philtrum, thick lips, telecanthus, depressed nasal bridge, and broad base of the nose. Because the older sibling was unable to walk and newly developed ataxia, repeated brain magnetic resonance imaging (MRI) was performed at the age of 4 years, revealing progressive cerebellar atrophy compared with MRI performed at the age of 2 years. The younger sibling's MRI revealed a normal cerebellum at the age of 2 years. Whole-exome sequencing was performed, and homozygous variants, such as c.2746-2A>G, were identified in SNX14 from the older sibling. Sanger sequencing confirmed homozygous SNX14 variants in the two siblings as well as a heterozygous variant in both parents. This report extends our knowledge of the phenotypic and mutational spectrum of SCAR20. We also highlight the importance of deep phenotyping for the diagnosis of SCAR20 in individuals with developmental delay, ataxia, cerebellar atrophy, and distinct facial features.

• Journal of Genetic Medicine
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• 제21권1호
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• pp.31-35
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• 2024

Allan-Herndon-Dudley syndrome (AHDS) is a rare X-linked neurodevelopmental disorder with abnormal thyroid function caused by mutation in the solute carrier family 16 member 2 (SLC16A2) gene. Clinical manifestations of AHDS are global or axial hypotonia, a variety of movement disorders, severe intellectual disability, quadriplegia or spastic diplegia, growth failure, and seizures. A 10-year-old boy visited our hospital with the chief complaint of newly onset generalized tonic seizures with vocalization of weekly to daily frequency. He showed early infantile hypotonia, severe intellectual disability, and frequent respiratory infections. He could not walk independently and was non-verbal. Electroencephalogram revealed generalized slow spike and waves with multifocal spikes and slow background rhythms. His tonic seizures were controlled with more than two anti-seizure medications (ASMs). At 11 years of age, he was evaluated for thyroid function as part of regular screening for ASM maintenance and was found to have abnormal thyroid function. We performed whole exome sequencing for severe global developmental delay, drug-resistant epilepsy, and abnormal thyroid function. The hemizygous c.940C>T (p.Arg314Ter) variant in the SLC16A2 gene (NM_006517.5) was identified and confirmed based on Sanger sequencing. Herein, we describe a case of an AHDS patient with late-onset drug-resistant epilepsy combined with congenital hypotonia, global developmental delay, and abnormal thyroid function results. To the best of our knowledge, this is the oldest adolescent among AHDS cases reported in Korea. In this report, clinical characteristics of a mid-adolescence patient with AHDS were presented.

• Journal of Platform Technology
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• 제6권4호
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• pp.87-95
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• 2018

개인 전장 유전체 분석 가격의 하락으로 많은 국가들이 10만명에서 100만명까지의 대량 전장 유전체 분석과 엑솜 시퀀싱을 진행하고 있다. 하지만 많은 대형 프로젝트에서 대량의 데이터를 처리할 수 있는 프로그램이나 시스템의 부족으로 많은 비용이 클러스터 구축 및 시스템 구매 비용으로 소비되고 있다. 본 연구에서는 자체 서버나 클러스터 환경을 구축하지 않고도 동시에 수백 개 이상의 전장 유전체 및 엑솜에 대한 단일 염기 다형성(Single Nucleotide Polymorphism; SNP) 분석을 수행할 수 있고, 생물학자들도 쉽게 설치하여 운영할 수 있는 클라이언트 프로그램인 NGSOne을 개발하였다. 대표적인 SNP 분석 도구인 DRAGEN, BWA/GATK 및 Isaac/Strelka2를 선택하여 분석할 수 있고, 3개 툴에서 실행 시간 및 에러의 개수 면에서는 DRAGEN이 가장 좋은 성능을 보였다. 또한 NGSOne은 SNP 분석뿐만 아니라 다양한 분석 도구의 자동적인 실행을 위한 확장이 가능하다.

• 대한유전성대사질환학회지
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• 제23권1호
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• pp.25-30
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• 2023

아미노아실-tRNA 합성효소는 단백질을 만드는 번역(translation)단계에서 아미노산을 활성화시키고 적절한 아미노산을 해당 tRNA에 결합을 시키는 중요한 효소이며, IARS2 유전자는 미토콘드리아에서 작용하는 isoleucylt-RNA 합성효소를 코딩하는 핵의 유전자이다. IARS2 유전자의 돌연변이는 백내장, 성장 호르몬 결핍, 감각 신경병증, 감각신경성 난청, 골격 형성 이상 증후군의 특징을 보이는 CAGSSS (MIM#616007)라는 희귀 질환의 원인으로 상염색체 열성으로 유전된다. 현재까지 이 증례 보고를 포함하여 29명의 환자만이 보고가 되었음에도 단지 백내장의 증상만 나타냈던 환자, 그리고 신경학적 증상이 두드러지는 Leigh 증후군을 유발하면서 여러 장기에 영향을 주는 환자 등 다양한 임상 증상의 환자가 보고되었다. Leigh 증후군은 드문 진행성 신경 퇴행성 미토콘드리아 질환이다. 이 연구는 IARS2 연관된 Leigh 증후군의 환자에서 방광 기능의 이상의 표현형을 보고하는 첫 증례 보고로 의미가 있다. 5세의 한국인 여아는 복부 팽만을 동반한 복통으로 응급실에 내원하였으며, 복부CT에서 명백한 폐쇄 증상, 급성 신장염, 요로감염의 징후가 보이지 않으면서 현저하게 팽창된 방광이 확인 되었다. 여아의 발달 상태는 발달 저하를 보이면서, 6개월에 뒤집기가 가능하였지만 이후는 신경학적 퇴행으로 내원당시에는 목 가누기도 되지 않고, 의미 있는 단어를 말하지도 못하는 전반적인 발달 지연 상태였다. 2세에는 양쪽 눈의 백내장이 발생하여 수술한 과거력이 있었다. 뇌 MRI T2 강조영상에서는 양쪽에 대칭적으로 기저핵(basal ganglia)에 고신호를 보였고, 이는 Leigh 증후군에 전형적인 영상의 특징이다. Whole mitochondrial genome의 유전자검사를 시행했지만 의미 있는 돌연변이가 확인되지 않았으므로, Whole exome sequencing 검사를 시행했으며, IARS2 유전자의 이중대립유전자 돌연변이(biallelic mutation), c.2446C>T (p. Arg816Ter)와 c.2450G>A (p. Arg817His)가 확인이 되었고 부모님은 보인자였다. 현재까지 IARS2 유전자의 돌연변이를 가지는 환자 중에서 신경학적 발달 저하, 인지장애 등의 증상이 동반된 환자는 신체의 다중장기질환의 증상으로 심비대, 부정맥, 빈혈, 측만증, 청력 저하, 뇌전증, 부갑상선저하증이 알려졌으나, 이 연구에서 IARS2 유전자 돌연변이를 가진 환자에서 배뇨근의 이상을 동반한 과민성방광증상을 확인하여 방광이상증상을 처음 보고를 한다. IARS2 유전자의 이상이 확인된 환자에서는 하부요로이상증상이 동반 가능성에 대해서 인지하는 것이 필요하고, 증상이 보이면 배뇨 일지나 요역동학검사를 통해서 조기에 진단 및 치료가 환자의 관리에 필요할 수 있다. 이 증례 보고는 IARS2 유전자의 임상 양상의 확대 및 유전자의 이해를 넓히는데 기여할 것으로 기대된다.

• BMB Reports
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• 제51권11호
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• pp.584-589
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• 2018

Secondary prevention via earlier detection would afford the greatest chance for a cure in premalignant lesions. We investigated the exomic profiles of non-malignant and malignant changes in head and neck squamous cell carcinoma (HNSCC) and the genomic blueprint of human papillomavirus (HPV)-driven carcinogenesis in oropharyngeal squamous cell carcinoma (OPSCC). Whole-exome (WES) and whole-genome (WGS) sequencing were performed on peripheral blood and adjacent non-tumor and tumor specimens obtained from eight Korean HNSCC patients from 2013 to 2015. Next-generation sequencing yielded an average coverage of $94.3{\times}$ for WES and $35.3{\times}$ for WGS. In comparative genomic analysis of non-tumor and tumor tissue pairs, we were unable to identify common cancer-associated early mutations and copy number alterations (CNA) except in one pair. Interestingly, in this case, we observed that non-tumor tonsillar crypts adjacent to HPV-positive OPSCC appeared normal under a microscope; however, this tissue also showed weak p16 expression. WGS revealed the infection and integration of high-risk type HPV16 in this tissue as well as in the matched tumor. Furthermore, WES identified shared and tumor-specific genomic alterations for this pair. Clonal analysis enabled us to infer the process by which this transitional crypt epithelium (TrCE) evolved into a tumor; this evolution was accompanied by the subsequent accumulation of genomic alterations, including an ERBB3 mutation and large-scale CNAs, such as 3q27-qter amplification and 9p deletion. We suggest that HPV16-driven OPSCC carcinogenesis is a stepwise evolutionary process that is consistent with a multistep carcinogenesis model. Our results highlight the carcinogenic changes driven by HPV16 infection and provide a basis for the secondary prevention of OPSCC.

• 대한유전성대사질환학회지
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• 제15권1호
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• pp.49-54
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• 2015

다발성 골단이형성증은 비교적 흔한 골이형성증으로 소아기에 관절통과 관절 강직, 뒤뚱거리면 걸어가는 보행 및 일부에서 경한 저신장을 특징으로 하며 영상의학적 검사에서는 여러 관절에서 골단의 불규칙한 소견과 골화 지연을 보인다. 본 증례 환자는 임상적, 영상의학적으로 다발성 골단이형성증을 진단 할 수 있었으며 환자의 넓적다리 관절 영상 검사는 MATN3 유전자 변이를, 무릎 관절 영상 검사는 COMP 유전자 변이를 시사하였기에 MATN3과 COMP 유전자 변이에 대해 시퀀싱(sequencing)을 하였으나, 변이는 발견되지 않았다. 이후 엑솜시퀀싱(exomesequencing)을 시행하였으나, 기존에 다발성 골단이형성증과 관련이 있는 것으로 알려진 유전자에 대한 변이가 발견되지 않았다. 본 증례와 같이 임상적, 영상의학적으로 다발성 골단이형성증으로 진단가능 하였으나 분자유전학적으로 기존에 알려진 변이 유전자가 발견되지 않은 환자들을 위해 추가적인 연구가 필요할 것으로 보인다.

• Journal of Genetic Medicine
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• 제18권2호
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• pp.142-146
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• 2021

Alagille syndrome (AGS) is a rare autosomal dominant inherited disorder, with major clinical manifestations of bile duct paucity, cholestasis, cardiovascular anomaly, ophthalmic abnormalities, butterfly vertebrae, and dysmorphic facial appearance. It is caused by heterozygous mutations in JAG1 or NOTCH of the Notch signaling pathway presenting with variable phenotypic penetrance and involving multiple organ systems. The following case report describes a unique case of a 16-year-old female with AGS who presented with the primary complaint of renovascular hypertension. She had a medical history of ventricular septal defect and polycystic ovary syndrome. The patient had a dysmorphic facial appearance including frontal bossing, bulbous tip of the nose, a pointed chin with prognathism, and deeply set eyes with mild hypertelorism. Stenoocclusive changes of both renal arteries, celiac artery, lower part of the abdominal aorta, and left intracranial artery, along with absence of the left internal carotid artery were found on examination. Whole exome sequencing was performed and revealed a pathologic mutation of JAG1, leading to the diagnosis of AGS. Reverse phenotyping detected butterfly vertebrae and normal structure and function of the liver and gallbladder. While the representative symptom of AGS in most scenarios is a hepatic problem, in this case, the presenting clinical features were the vascular anomalies. Clinical manifestations of AGS are diverse, and this case demonstrates that renovascular hypertension might be in some cases a presenting symptom of AGS.

• Journal of Genetic Medicine
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• 제19권2호
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• pp.85-93
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• 2022

Purpose: Cornelia de Lange syndrome (CdLS) is a rare genetically heterogeneous disorder caused by genetic variants of the cohesin complex. However, the diverse genetic etiologies and their phenotypic correlations in Korean patients with CdLS are still largely unknown. Hence, this study aimed to clarify the clinical characteristics and genetic background of Korean patients with CdLS. Materials and Methods: The medical records of 15 unrelated patients (3 males and 12 females) genetically confirmed to have CdLS were retrospectively reviewed. All individuals were diagnosed with CdLS using target gene analysis, whole-exome sequencing, and/or chromosomal microarray analysis. The clinical score (CS) was calculated to assess disease severity. Results: The median age at diagnosis was 1.7 (range, 0.0-11.8) years, and median follow-up duration was 3.8 (range, 0.4-11.7) years. Eight (53.3%) patients showed classic phenotypes of CdLS, two (13.3%) showed non-classic phenotypes, and five (33.3%) had other phenotypes sharing limited signs of CdLS. Fifteen causative variants were identified: NIPBL in five (33.3%, including 3 males), SMC1A in three (20.0%), SMC3 in three (20.0%), and HDAC8 in four (26.7%) patients. The CS was significantly higher in the NIPBL group than in the non-NIPBL group (14.2±1.3 vs. 8.7±2.9, P<0.001). Conclusion: We identified the clinical and genetic heterogeneity of CdLS in Korean patients. Patients with variants of NIPBL had a more distinctive phenotype than those carrying variants of other cohesin complex genes (SMC1A, SMC3, and HDAC8). However, further studies are warranted to understand the pathogenesis of CdLS as a cohesinopathy and its genotype-phenotype correlations.

• Journal of Genetic Medicine
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• 제19권2호
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• pp.94-99
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• 2022

Lesch-Nyhan disease (LND) is a rare X-linked recessive inherited purine metabolic disorder that accompanies neurodevelopmental problems. Neurofibromatosis type 1 (NF1) is a relatively common autosomal dominant inherited genetic disorder characterized by tumors in various systems. Some children with NF1 also accompanies neurodevelopmental problems. Here, we describe a 5-year-old boy with a maternally inherited pathogenic variant in NF1 and hypoxanthine-guanine phosphoribosyltransferase (HPRT). He was referred for severe neurodevelopmental impairment and hyperuricemia. His mother was diagnosed with NF1 and the patient was also suspected of having NF1 because of cafe au lait macules. He had dystonia, rigidity, cognitive deficit, and speech/language impairment. Serum and urine uric acid concentrations were elevated. He had more severe neurodevelopmental delay than patients with only NF1, so his clinical symptoms could not be fully understood by the disease alone. To find the cause of his neurologic symptoms and hyperuricemia, the patient and his mother underwent a whole-exome sequencing test. As a result, the pathogenic variant c.151C>T (p.Arg51Ter) in HPRT1 was identified as hemizygote in the patient and heterozygote in his mother. The pathogenic variant c.7682C>G (p.Ser2561Ter) in NF-1 was identified as heterozygotes in both of them. Although the clinical symptoms of both diseases were overlapping and complicated, genetic testing was helpful for accurate diagnosis and treatment. Therefore, we suggest to consider preemptive genetic evaluation if there are symptoms not sufficiently explained by known existing diseases. And it is considered valuable to review this rare case to understand the clinical course and possible synergic effects of these diseases.