• Genomics & Informatics
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• 제19권4호
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• pp.41.1-41.10
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• 2021

In addition to mutations and copy number alterations, gene fusions are commonly identified in cancers. In thyroid cancer, fusions of important cancer-related genes have been commonly reported; however, extant panels do not cover all clinically important gene fusions. In this study, we aimed to develop a custom RNA-based sequencing panel to identify the key fusions in thyroid cancer. Our ThyChase panel was designed to detect 87 types of gene fusion. As quality control of RNA sequencing, five housekeeping genes were included in this panel. When we applied this panel for the analysis of fusions containing reference RNA (HD796), three expected fusions (EML4-ALK, CCDC6-RET, and TPM3-NTRK1) were successfully identified. We confirmed the fusion breakpoint sequences of the three fusions from HD796 by Sanger sequencing. Regarding the limit of detection, this panel could detect the target fusions from a tumor sample containing a 1% fusion-positive tumor cellular fraction. Taken together, our ThyChase panel would be useful to identify gene fusions in the clinical field.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제24권1호
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• pp.1-6
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• 2021

Next-generation sequencing (NGS) technologies have changed the process of genetic diagnosis from a gene-by-gene approach to syndrome-based diagnostic gene panel sequencing (DPS), diagnostic exome sequencing (DES), and diagnostic genome sequencing (DGS). A priori information on the causative genes that might underlie a genetic condition is a prerequisite for genetic diagnosis before conducting clinical NGS tests. Theoretically, DPS, DES, and DGS do not require any information on specific candidate genes. Therefore, clinical NGS tests sometimes detect disease-related pathogenic variants in genes underlying different conditions from the initial diagnosis. These clinical NGS tests are expensive, but they can be a cost-effective approach for the rapid diagnosis of rare disorders with genetic heterogeneity, such as the glycogen storage disease, familial intrahepatic cholestasis, lysosomal storage disease, and primary immunodeficiency. In addition, DES or DGS may find novel genes that that were previously not linked to human diseases.

• Genomics & Informatics
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• 제15권4호
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• pp.136-141
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• 2017

Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) <1% can be identified, and any mutation with >3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation.

• 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.

• Molecules and Cells
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• 제39권5호
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• pp.382-388
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• 2016

Inherited peripheral neuropathies (IPN), which are a group of clinically and genetically heterogeneous peripheral nerve disorders including Charcot-Marie-Tooth disease (CMT), exhibit progressive degeneration of muscles in the extremities and loss of sensory function. Over 70 genes have been reported as genetic causatives and the number is still growing. We prepared a targeted gene panel for IPN diagnosis based on next generation sequencing (NGS). The gene panel was designed to detect mutations in 73 genes reported to be genetic causes of IPN or related peripheral neuropathies, and to detect duplication of the chromosome 17p12 region, the major genetic cause of CMT1A. We applied the gene panel to 115 samples from 63 non-CMT1A families, and isolated 15 pathogenic or likelypathogenic mutations in eight genes from 25 patients (17 families). Of them, eight mutations were unreported variants. Of particular interest, this study revealed several very rare mutations in the SPTLC2, DCTN1, and MARS genes. In addition, the effectiveness of the detection of CMT1A was confirmed by comparing five 17p12-nonduplicated controls and 15 CMT1A cases. In conclusion, we developed a gene panel for one step genetic diagnosis of IPN. It seems that its time- and cost-effectiveness are superior to previous tiered-genetic diagnosis algorithms, and it could be applied as a genetic diagnostic system for inherited peripheral neuropathies.

• 대한유전성대사질환학회지
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• 제20권1호
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• pp.24-28
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• 2020

당원병 III형은 GDE 결핍으로 분해되지 않은 당원이 간 또는 근육에 축적되는 유전대사이상질환이다. AGL 유전자 변이에 의해 발생하고 높은 유전적 이질성을 가지고 있다. 당원병 III형의 임상증상은 간 비대, 성장 지연, 저혈당 등이 있다. 이러한 임상 증상은 다른 타입의 당원병의 증상과 비슷하여 임상적으로는 구분하기가 어렵다. 저자들은 간 비대 주소로 내원한 11개월 환아에서 유전자 패널 검사로 진단된 당원병 III형 증례를 보고하고자 한다. 간 조직검사결과 간세포에 글리코겐이 축적되어 있어 당원병을 의심하였으며, 당원병 아형의 감별 진단을 위해 유전자 패널 검사를 시행하였다. 그 결과, AGL 유전자에서 이전에 보고된 바 없는 c.311_312del와 c.3314+1G>A 변이가 이형접합체로 발견되어 당원병 III형으로 진단하였다. 진단 후 생옥수수 전분가루를 복용하는 식이요법 시작하였고, 생후 35개월인 현재까지 급·만성 합병증 없는 상태이다. 또한, 가족 검사를 통해 부모가 각각 보인자임을 확인하였고, 임신된 동생의 융모막 검사에서도 동일한 변이가 확인되어 출산 후 재검 및 조기 식이요법을 시행할 예정이다. 유전자 패널 검사법은 당원병과 같이 임상적으로 구분이 어려우며 높은 유전적 이질성을 가진 질환의 감별 진단 시 시간과 비용을 아낄 수 있어 유용하다. 또한 정확한 분자 유전학적 진단은 환아와 가족에게 질환에 대한 정확한 정보 및 치료 예방, 산전 유전상담을 제공하는 데 도움이 된다.

• Genomics & Informatics
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• 제14권3호
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• pp.78-84
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• 2016

Extranodal natural killer (NK)/T-cell lymphoma, nasal type (NKTCL), is a malignant disorder of cytotoxic lymphocytes of NK or T cells. It is an aggressive neoplasm with a very poor prognosis. Although extranodal NKTCL reportedly has a strong association with Epstein-Barr virus, the molecular pathogenesis of NKTCL has been unexplored. The recent technological advancements in next-generation sequencing (NGS) have made DNA sequencing cost- and time-effective, with more reliable results. Using the Ion Proton Comprehensive Cancer Panel, we sequenced 409 cancer-related genes to identify somatic mutations in five NKTCL tissue samples. The sequencing analysis detected 25 mutations in 21 genes. Among them, KMT2D, a histone modification-related gene, was the most frequently mutated gene (four of the five cases). This result was consistent with recent NGS studies that have suggested KMT2D as a novel driver gene in NKTCL. Mutations were also found in ARID1A, a chromatin remodeling gene, and TP53, which also recurred in recent NGS studies. We also found mutations in 18 novel candidate genes, with molecular functions that were potentially implicated in cancer development. We suggest that these genes may result in multiple oncogenic events and may be used as potential bio-markers of NKTCL in the future.

• 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.

• Neonatal Medicine
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• 제28권2호
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• pp.89-93
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• 2021

Nemaline myopathy is a genetically heterogeneous neuromuscular disorder and one of the most common congenital myopathies. The clinical manifestations usually vary depending on the age of onset. Neonatal nemaline myopathy has the worst prognosis, primarily due to respiratory failure. Several genes associated with nemaline myopathy have been identified, including NEB, ACTA1, TPM3, TPM2, TNNT1, CFL2, KBTBD13, KLHL40, KLHL41, LMOD3, and KBTBD13. Here, we report a neonatal Korean female patient with nemaline myopathy carrying compound heterozygous mutations in the gene KLHL40 as revealed using next generation sequencing (NGS). The patient presented with postnatal cyanosis, respiratory failure, dysphagia, and hypotonia just after birth. To identify the genetic cause underlying the neonatal myopathy, NGS-based gene panel sequencing was performed. Compound heterozygous pathogenic variants were detected in KLHL40: c.[1405G>T];[1582G>A] (p. [Gly469cys];[Glu528Lys]). NGS allows quick and accurate diagnosis at a lower cost compared to traditional serial single gene sequencing, which is greatly advantageous in genetically heterogeneous disorders such as myopathies. Rapid diagnosis will facilitate efficient and timely genetic counseling, prediction of disease prognosis, and establishment of treatments.

• Journal of Genetic Medicine
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• 제15권1호
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• pp.24-27
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• 2018

Cornelia de Lange syndrome (CdLS) is a rare, clinically and genetically heterogeneous, multi-system developmental disorder caused by mutations in genes that encode components of the cohesin complex. X-linked CdLS caused by an SMC1A mutation is an extremely rare disease characterized by phenotypes milder than those of classic CdLS. In the Republic of Korea, based on a literature review, one family with SMC1A-related CdLS with mild phenotypes has been genetically confirmed to date. In this study, we describe the clinical features of a Korean boy with a hemizygous novel missense mutation and his mother with a heterozygous mutation, i.e., c.2447G>A (p.Arg816His) in SMC1A, identified by multi-gene panel sequencing. The proband had a mild phenotype with typical facial features and his mother exhibited a mild, subclinical phenotype. This study expands the clinical spectrum of patients with X-linked CdLS caused by SMC1A variants. Moreover, these findings reinforce the notion that a dominant negative effect in a carrier female with a heterozygous mutation in SMC1A results in a phenotype milder than that in a male patient with the same mutation.