• 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.

• BMB Reports
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• 제50권4호
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• pp.201-207
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• 2017

Alternations in usage of polyadenylation sites during transcription termination yield transcript isoforms from a gene. Recent findings of transcriptome-wide alternative polyadenylation (APA) as a molecular response to changes in biology position APA not only as a molecular event of early transcriptional termination but also as a cellular regulatory step affecting various biological pathways. With the development of high-throughput profiling technologies at a single nucleotide level and their applications targeted to the 3'-end of mRNAs, dynamics in the landscape of mRNA 3'-end is measureable at a global scale. In this review, methods and technologies that have been adopted to study APA events are discussed. In addition, various bioinformatics algorithms for APA isoform analysis using publicly available RNA-seq datasets are introduced.

• Journal of Genetic Medicine
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• 제12권2호
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• pp.66-71
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• 2015

Down syndrome screening with cell-free DNA (cfDNA) in the maternal plasma has recently received much attention in the prenatal diagnostic field. Indeed, a large amount of evidence has already accumulated to show that screening tests with cfDNA are more sensitive and specific than conventional maternal serum and/or ultrasound screening. Globally, more than 1,000,000 of these noninvasive prenatal tests (NIPTs) have been performed to date. There are several different methods for NIPTs that are currently commercially available, including shotgun massively parallel sequencing, targeted massively parallel sequencing, and single nucleotide polymorphism (SNP)-based methods. All of these methods have their own advantages and disadvantages. In this review, I will focus specifically on the SNP-based NIPT.

• Annals of Clinical Neurophysiology
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• 제22권1호
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• pp.29-32
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• 2020

Sarcoglycanopathies are a rare group of autosomal recessive limb-girdle muscular dystrophies (LGMDs) caused by genetic variants in α-, β-, γ-, or δ-sarcoglycan that maintain membrane integrity and contribute to molecular signal processing. High-throughput nucleotide sequencing was performed in patients with slowly progressive proximal muscle weakness from early childhood with respiratory involvement, which detected a novel homozygous nonsense variant (c.601C>T;p.Gln201Ter) in SGCB. This report informs about the clinical characteristics of LGMD2E (type-2E LGMD) in Korea and provides genetic confirmation of the disease.

• Journal of Genetic Medicine
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• 제12권1호
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• pp.6-11
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• 2015

Intellectual disability (ID) is the most common disability among people under the age of 20 years. In the absence of obvious non-genetic causes of ID, the majority of cases of severe ID are thought to have a genetic cause. The advent of technologies such as array comparative genomic hybridization, single nucleotide polymorphism genotyping arrays, and massively parallel sequencing has shown that de novo copy number variations and single nucleotide variations affecting coding regions are major causes of severe ID. This article reviews the genetic causes of ID along with diagnostic approaches for this disability.

• 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.

• 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.

• The Korean Journal of Legal Medicine
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• 제41권2호
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• pp.41-45
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• 2017

Fetal DNA (fDNA) detection in maternal serum is a challenge due to low copy number and the smaller size of fDNA fragments compared to DNA fragments derived from the mother. Massively parallel sequencing (MPS) is a useful technique for fetal genetic analysis that is able to detect and quantify small amounts of DNA. In this study, seven clinical samples of maternal serum potentially containing fDNA were analyzed with a commercial single nucleotide polymorphism (SNP) panel, the HID-Ion $AmpliSeq^{TM}$ Identity Panel, and the results were compared to those from previous studies. Reference profiles for mothers and fetuses were not available, but multiple Y chromosomal SNPs were detected in two samples, indicating that fDNA was present in the serum and thereby validating observations of autosomal SNPs. This suggests that SNP-based MPS can be valuable for fDNA detection, thereby offering an insight into fetal genetic status. This technology could also be used to detect small amounts of DNA in mixed DNA samples for forensic applications.

• International Journal of Oral Biology
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• 제45권3호
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• pp.77-83
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• 2020

In the oral cavity, complex microbial community is shaped by various host and environmental factors. Extensive literature describing the oral microbiome in the context of oral health and disease is available. Advances in DNA sequencing technologies and data analysis have drastically improved the analysis of the oral microbiome. For microbiome study, bacterial 16S ribosomal RNA gene amplification and sequencing is often employed owing to the cost-effective and fast nature of the method. In this review, practical considerations for performing a microbiome study, including experimental design, molecular analysis technology, and general data analysis, will be discussed.

• Journal of Genetic Medicine
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• 제20권2호
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• pp.46-51
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• 2023

Exonic copy number variation (CNV), involving deletions and duplications at the gene's exon level, presents challenges in detection due to their variable impact on gene function. The study delves into the complexities of identifying large CNVs and investigates less familiar but recurrent exonic CNVs, notably enriched in East Asian populations. Examining specific cases like DRC1, STX16, LAMA2, and CFTR highlights the clinical implications and prevalence of exonic CNVs in diverse populations. The review addresses diagnostic challenges, particularly for single exon alterations, advocating for a strategic, multi-method approach. Diagnostic methods, including multiplex ligation-dependent probe amplification, droplet digital PCR, and CNV screening using next-generation sequencing data, are discussed, with whole genome sequencing emerging as a powerful tool. The study underscores the crucial role of ethnic considerations in understanding specific CNV prevalence and ongoing efforts to unravel subtle variations. The ultimate goal is to advance rare disease diagnosis and treatment through ethnically-specific therapeutic interventions.