• 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.

• 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.

• Genomics & Informatics
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• 제18권1호
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• pp.10.1-10.9
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• 2020

Advancements in next generation sequencing (NGS) technologies have significantly increased the translational use of genomics data in the medical field as well as the demand for computational infrastructure capable processing that data. To enhance the current understanding of software and hardware used to compute large scale human genomic datasets (NGS), the performance and accuracy of optimized versions of GATK algorithms, including Parabricks and Sentieon, were compared to the results of the original application (GATK V4.1.0, Intel x86 CPUs). Parabricks was able to process a 50× whole-genome sequencing library in under 3 h and Sentieon finished in under 8 h, whereas GATK v4.1.0 needed nearly 24 h. These results were achieved while maintaining greater than 99% accuracy and precision compared to stock GATK. Sentieon's somatic pipeline achieved similar results greater than 99%. Additionally, the IBM POWER9 CPU performed well on bioinformatic workloads when tested with 10 different tools for alignment/mapping.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2011년도 한국컴퓨터종합학술대회논문집 Vol.38 No.1(B)
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• pp.466-469
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• 2011

최근에 등장한 Next Generation Sequencing(NGS)은 전통적인 방법에 비해 빠르고 저비용으로 대용량의 시퀀스 데이터를 이용한 차세대 시퀀싱 기술을 말한다. 이렇게 얻은 NGS 데이터를 분석하는 단계 중에서 alignment 단계는 시퀀서에서 얻은 대량의 read를 참조 염기서열에 맵핑하는 단계로 NGS 데이터 분석의 가장 기본이면서 핵심인 단계이다. alignment 도구는 긴 참조 염기서열을 색인화해서 짧은 read를 빠르게 맵핑하는 용도로 사용된다. 현재 많이 사용되고 있는 일반적인 alignment 도구들은 입력데이터에 대한 별도의 전처리 과정이 없으며 나열된 read를 순차적으로 맵핑하는 단순한 구조를 가지고 있다. 본 논문은 NGS 데이터의 특징 중에 특히 read간의 중복성이 존재하고 이를 이용한 read의 효율적 공통부분 서열을 찾는다. 중복이 가능한 read의 공통부분서열과 read의 관계를 그래프 이론의 Hitting Set 문제로 모델링하고 여러 read가 포함하는 공통 부분서열을 사용해서 alignment 단계의 효율을 높일 수 방법을 제안한다.

• 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.

• 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.

• Genomics & Informatics
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• 제11권4호
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• pp.191-199
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• 2013

High-throughput next-generation sequencing (NGS) technology produces a tremendous amount of raw sequence data. The challenges for researchers are to process the raw data, to map the sequences to genome, to discover variants that are different from the reference genome, and to prioritize/rank the variants for the question of interest. The recent development of many computational algorithms and programs has vastly improved the ability to translate sequence data into valuable information for disease gene identification. However, the NGS data analysis is complex and could be overwhelming for researchers who are not familiar with the process. Here, we outline the analysis pipeline and describe some of the most commonly used principles and tools for analyzing NGS data for disease gene identification.

• Animal Systematics, Evolution and Diversity
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• 제36권4호
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• pp.336-346
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• 2020

Mitochondrial genome is an important molecule for systematic and evolutionary studies in metazoans. The development of next-generation sequencing (NGS) technique has rapidly increased the number of mitogenome sequences. The process of generating mitochondrial genome based on NGS includes different steps, from DNA preparation, sequencing, assembly, and annotation. Despite the effort to improve sequencing, assembly, and annotation methods of mitogenome, the low quality and/or quantity sequence in the final map can still be generated through the work. Therefore, it is necessary to check and curate mitochondrial genome sequence after annotation for proofreading and feedback. In this study, we introduce the pipeline for sequencing and curation for mitogenome based on NGS. For this purpose, two mitogenome sequences of Dermatobranchus otome were sequenced by Illumina Miseq system with different amount of raw read data. Generated reads were targeted for assembly and annotation with commonly used programs. As abnormal repeat regions present in the mitogenomes after annotation, primers covering these regions were designed and conventional PCR followed by Sanger sequencing were performed to curate the mitogenome sequences. The obtained sequences were used to replace the abnormal region. Following the replacement, each mitochondrial genome was compared with the other as well as the sequences of close species available on the Genbank for confirmation. After curation, two mitogenomes of D. otome showed a typically circular molecule with 14,559 bp in size and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes. The phylogenetic tree revealed a close relationship between D. otome and Tritonia diomea. The finding of this study indicated the importance of caution and curation for the generation of mitogenome from NGS.

• 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.

• Genomics & Informatics
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• 제13권3호
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• pp.81-85
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• 2015

Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS) methodology is suggested as an effective means in genome characterization and detection of transgenic insertion locations. In the present study, we applied NGS to insert transgenic loci, specifically the epidermal growth factor (EGF) in genetically modified rice cells. A total of 29.3 Gb (${\sim}72{\times}coverage$) was sequenced with a $2{\times}150bp$ paired end method by Illumina HiSeq2500, which was consecutively mapped to the rice genome and T-vector sequence. The compatible pairs of reads were successfully mapped to 10 loci on the rice chromosome and vector sequences were validated to the insertion location by polymerase chain reaction (PCR) amplification. The EGF transgenic site was confirmed only on chromosome 4 by PCR. Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites.