• 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.

• 한국동물위생학회지
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• 제46권1호
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• pp.93-106
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• 2023

Emerging and re-emerging zoonotic viruses become critical public health, economic, societal, and cultural burdens. The Coronavirus disease-19 (COVID-19) pandemic reveals needs for effective preparedness and responsiveness against the emergence of variants and the next virus outbreak. The targeted next-generation sequencing (NGS) significantly contributes to the acquisition of viral genome sequences directly from clinical specimens. Using this advanced NGS technology, the genomic epidemiology and surveillance play a critical role in identifying of infectious source and origin, tracking of transmission chains and virus evolution, and characterizing the virulence and developing of vaccines during the outbreak. In this review, we highlight the platforms and preparation of targeted NGS for the viral genomics. We also demonstrate the application of this strategy to take advantage of the responsiveness and prevention of emerging zoonotic viruses. This article provides broad and deep insights into the preparedness and responsiveness for the next zoonotic virus outbreak.

• 대한유전성대사질환학회지
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• 제17권1호
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• pp.18-23
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• 2017

${\beta}$-ureidopropionase 결핍증(${\beta}$-UPD)은 UPB1 유전자 변이에 의한 피리미딘 대사 이상에 의해 생기는 매우 드문 상염색체 열성 유전 질환으로 현재까지 전 세계에서 30여명 정도만 보고되었다. ${\beta}$-UPD는 무증상인 경우부터 심한 발달 지연, 소두증, 발작, 인지 저하의 증상을 보이는 경우까지 다양하다. 국내에서 진단된 유일한 ${\beta}$-UPD 여자 환자는 8세 10개월에 targeted next-generation sequencing 검사로 UPB1 유전자 변이를 확인 한 후, Sanger sequencing을 통해 확진하였다. 환자는 성장 장애, 발단 지연, 소두증, 반복되는 감염 및 난치성 뇌전증 증상을 보였으며, 11세 5개월에 원인 미상으로 갑자기 사망하였다. 이에 저자들은 ${\beta}$-UPD 환자의 장기간의 임상경과에 대해 보고하는 바이다.

• Genomics & Informatics
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• 제12권2호
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• pp.50-57
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• 2014

We present a new next-generation sequencing-based method to identify somatic mutations of lung cancer. It is a comprehensive mutation profiling protocol to detect somatic mutations in 30 genes found frequently in lung adenocarcinoma. The total length of the target regions is 107 kb, and a capture assay was designed to cover 99% of it. This method exhibited about 97% mean coverage at $30{\times}$ sequencing depth and 42% average specificity when sequencing of more than 3.25 Gb was carried out for the normal sample. We discovered 513 variations from targeted exome sequencing of lung cancer cells, which is 3.9-fold higher than in the normal sample. The variations in cancer cells included previously reported somatic mutations in the COSMIC database, such as variations in TP53, KRAS, and STK11 of sample H-23 and in EGFR of sample H-1650, especially with more than $1,000{\times}$ coverage. Among the somatic mutations, up to 91% of single nucleotide polymorphisms from the two cancer samples were validated by DNA microarray-based genotyping. Our results demonstrated the feasibility of high-throughput mutation profiling with lung adenocarcinoma samples, and the profiling method can be used as a robust and effective protocol for somatic variant screening.

• 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.

• Genomics & Informatics
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• 제14권2호
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• pp.42-45
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• 2016

Since next-generation sequencing (NGS) technique was adopted into clinical practices, revolutionary advances in diagnosing rare genetic diseases have been achieved through translating genomic medicine into precision or personalized management. Indeed, several successful cases of molecular diagnosis and treatment with personalized or targeted therapies of rare genetic diseases have been reported. Still, there are several obstacles to be overcome for wider application of NGS-based precision medicine, including high sequencing cost, incomplete variant sensitivity and accuracy, practical complexities, and a shortage of available treatment options.

• Clinical and Experimental Pediatrics
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• 제58권11호
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• pp.407-414
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• 2015

Early-onset epileptic encephalopathies are one of the most severe early onset epilepsies that can lead to progressive psychomotor impairment. These syndromes result from identifiable primary causes, such as structural, neurodegenerative, metabolic, or genetic defects, and an increasing number of novel genetic causes continue to be uncovered. A typical diagnostic approach includes documentation of anamnesis, determination of seizure semiology, electroencephalography, and neuroimaging. If primary biochemical investigations exclude precipitating conditions, a trial with the administration of a vitaminic compound (pyridoxine, pyridoxal-5-phosphate, or folinic acid) can then be initiated regardless of presumptive seizure causes. Patients with unclear etiologies should be considered for a further workup, which should include an evaluation for inherited metabolic defects and genetic analyses. Targeted next-generation sequencing panels showed a high diagnostic yield in patients with epileptic encephalopathy. Mutations associated with the emergence of epileptic encephalopathies can be identified in a targeted fashion by sequencing the most likely candidate genes. Next-generation sequencing technologies offer hope to a large number of patients with cryptogenic encephalopathies and will eventually lead to new therapeutic strategies and more favorable long-term outcomes.

• 대한임상검사과학회지
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• 제55권1호
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• pp.16-28
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• 2023

폐암은 크게 소세포성 폐암과 비소세포성 폐암으로 구분되며 비소세포성폐암이 차지하는 비율은 약 70%~80%이다. 비소세포성폐암 중 폐선암은 전체 폐암의 약 40%를 차지한다. 최근 유전자 프로파일링 기술이 발전하면서 종양의 발생 및 성장에 중요한 종양 유전자와 종양 억제 유전자의 변이에 대한 연구가 활발히 진행되어 폐암을 유발하는 특정 유전자들이 발견되면서 생존율에 큰 영향을 미치게 되었으며 특히 폐선암은 차세대 염기서열 분석법(next generation sequencing, NGS)을 이용한 동반진단을 통해 표적 치료로 생존을 높이는 데 도움을 얻을 수 있다. 본 연구는 한국인에서 폐선암을 유발하는 유전자 변이 검출을 위해 비소세포성폐암 환자의 파라핀 포매조직(formalin-fixed paraffin-embedded)으로 hematoxylin and eosin 염색을 시행하여 폐선암을 구분하였으며 정확한 폐선암 조직을 분류하기 위해 면역조직화학(immunohistochemistry, IHC)염색을 시행하였다. 그 결과를 바탕으로 NGS를 이용하여 유전자 변이의 종류와 패턴을 분석하였고 폐암을 유발하는 가장 대표적인 원인인 흡연과의 관계를 확인하였다. NGS 결과 단일염기서열변이(single nucleotide variation, SNV), 복제수변이 (copy number variation, CNV), 유전자 재배열을 확인하였으며 폐선암에서 SNV는 TP53 (44.6%), EGFR (35.7%), KRAS (10.7%), PIK3CA (6.2%), CDKN2A (4.4%) 순으로 발생하였고 CNV의 경우 EGFR (14%)이 가장 빈번하게 발생하였다. 또한 ALK, ROS1, RET 과 같은 유전자 재배열을 확인하였다. NGS의 신뢰도를 확인을 위하여 기존에 사용되고 있는 유전자 검사방법인 PCR-EGFR, IHC-ALK (D5F3), FISH-ROS1 검사를 추가적으로 시행하여 NGS 결과와 일치도를 확인하였다. 이 연구는 폐선암 환자에 대한 NGS가 여러 유전자의 돌연변이를 동시에 확인하여 치료 전략에 더욱 긍정적인 이익을 줄 수 있음을 보여준다.

• Journal of Korean Neurosurgical Society
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• 제61권3호
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• pp.376-385
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• 2018

Recent discoveries of brain tumor-related genes and fast advances in genomic testing technologies have led to the era of molecular diagnosis of brain tumor. Molecular profiling of brain tumor became the significant step in the diagnosis, the prediction of prognosis and the treatment of brain tumor. Because traditional molecular testing methods have limitations in time and cost for multiple gene tests, next-generation sequencing technologies are rapidly introduced into clinical practice. Targeted sequencing panels using these technologies have been developed for brain tumors. In this article, focused on pediatric brain tumor, key discoveries of brain tumor-related genes are reviewed and cancer panels used in the molecular profiling of brain tumor are discussed.

• 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.