• Journal of the Korean Association of Oral and Maxillofacial Surgeons
• /
• 제48권1호
• /
• pp.3-12
• /
• 2022

Selection of potential disease-specific biomarkers from saliva or epithelial tissues through next generation sequencing (NGS)-based protein studies has recently become possible. The early diagnosis of oral squamous cell carcinoma (OSCC) has been difficult, if not impossible, until now due to the lack of an effective OSCC biomarker and efficient molecular validation method. The aim of this study was to summarize the advances in the application of NGS in cancer research and to propose potential proteomic and genomic saliva biomarkers for NGS-based study in OSCC screening and diagnosis programs. We have reviewed four categories including definitions and use of NGS, salivary biomarkers and OSCC, current biomarkers using the NGS-based technique, and potential salivary biomarker candidates in OSCC using NGS.

• Genomics & Informatics
• /
• 제15권4호
• /
• pp.128-135
• /
• 2017

As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. However, it is still difficult to assemble the whole genome precisely, due to inherent limitations of short-read sequencing technologies. In particular, the complexities of plants are incomparable to those of microorganisms or animals because of whole-genome duplications, repeat insertions, and Numt insertions, etc. In this study, we describe a new method for detecting misassembly sequence regions of Brassica rapa with genotyping-by-sequencing, followed by MadMapper clustering. The misassembly candidate regions were cross-checked with BAC clone paired-ends library sequences that have been mapped to the reference genome. The results were further verified with gene synteny relations between Brassica rapa and Arabidopsis thaliana. We conclude that this method will help detect misassembly regions and be applicable to incompletely assembled reference genomes from a variety of species.

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

• 생태와환경
• /
• 제56권1호
• /
• pp.104-125
• /
• 2023

The predator-prey interaction in freshwater ecosystems is a crucial area in the ecological study field and one of example to find such interaction is to investigate stomach contents. However, traditional method through visual inspection often induce misidentification, as it depends critically on intactness of physically visible data. In this study, we utilized Next-Generations Sequencing (NGS) technology to test the applicability stomach content analysis and overcome such limitation. NGS was applied to analyze the stomach contents of the Hemibarbus labeo, Tachysurus fulvidraco, and Plecoglossus altivelis collected in the lower part of Nakdong River. As a result, T. fulvidraco had a higher number of Animalia operational taxonomic units (OTUs) intake rate than H. labeo. At the same time, P. altivelis had higher number of Plantae OTUs intake rate than T. fulvidraco and higher Protozoa OTUs intake rate than H. labeo respectively. Therefore, NGS technology application enable to overcome traditional method's limitation and discover hidden interspecific interaction which can further be used in appropriate habitat assessment.

• Archives of Plastic Surgery
• /
• 제47권3호
• /
• pp.203-208
• /
• 2020

Vascular anomalies are congenital localized abnormalities that result from improper development and maintenance of the vasculature. The lesions of vascular anomalies vary in location, type, and clinical severity of the phenotype, and the current treatment options are often unsatisfactory. Most vascular anomalies are sporadic, but patterns of inheritance have been noted in some cases, making genetic analysis relevant. Developments in the field of genomics, including next-generation sequencing, have provided novel insights into the genetic and molecular pathophysiological mechanisms underlying vascular anomalies. These insights may pave the way for new approaches to molecular diagnosis and potential disease-specific therapies. This article provides an introduction to genetic testing for vascular anomalies and presents a brief summary of the etiology and genetics of vascular anomalies.

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

• Journal of Mycology and Infection
• /
• 제24권2호
• /
• pp.37-44
• /
• 2019

To date, hundreds of fungal genomes have been sequenced, and many more are underway. Recently developed cutting-edge techniques generate very large amounts of data, and the field of fungal genomics in dermatology has consequently evolved substantially. Methodological improvements have broadened the scope of large-scale ecological studies in dermatology, including biodiversity assessments and genomic identification of fungi. Here, we aimed to provide a brief introduction to bioinformatic approaches to fungal genomics in the field of dermatology. We described the history and basic concepts of fungal genomics and presented sequencing-based techniques for fungal identification, including a list of the revised taxa of dermatophytes, as determined by current phylogenetic analysis. Finally, we discussed the emerging trends in fungal genomics in dermatology, such as next-generation sequencing.

• 한국미생물·생명공학회지
• /
• 제51권3호
• /
• pp.325-327
• /
• 2023

This paper presents the complete genome sequence of a novel marine actinomycete, Streptomyces sp. MMBL 11-1. The genome of Streptomyces sp. MMBL 11-1 was obtained through next-generation sequencing using the PacBio Sequel system and Illumina platform provided by Macrogen, Korea. The assembled genome consists of five contigs, with a total length of 8,496,900 bp and a G+C content of 71.6%. The genome harbors multiple biosynthetic gene clusters (BGCs) associated with producing microbial natural products (MNPs). The comprehensive genomic information of this type of strain will serve as a valuable resource for identifying other marine actinomycetes strains.

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

• 한국축산식품학회지
• /
• 제37권4호
• /
• pp.535-541
• /
• 2017

This study investigated the psychrotrophic bacteria isolated from chicken meat to characterize their microbial composition during refrigerated storage. The bacterial community was identified by the Illumina MiSeq method based on bacterial DNA extracted from spoiled chicken meat. Molecular identification of the isolated psychrotrophic bacteria was carried out using 16S rDNA sequencing and their putrefactive potential was investigated by the growth at low temperature as well as their proteolytic activities in chicken meat. From the Illumina sequencing, a total of 187,671 reads were obtained from 12 chicken samples. Regardless of the type of chicken meat (i.e., whole meat and chicken breast) and storage temperatures ($4^{\circ}C$ and $10^{\circ}C$), Pseudomonas weihenstephanensis and Pseudomonas congelans were the most prominent bacterial species. Serratia spp. and Acinetobacter spp. were prominent in chicken breast and whole chicken meat, respectively. The 118 isolated strains of psychrotrophic bacteria comprised Pseudomonas spp. (58.48%), Serratia spp. (10.17%), and Morganella spp. (6.78%). All isolates grew well at $10^{\circ}C$ and they induced different proteolytic activities depending on the species and strains. Parallel analysis of the next generation sequencing and culture dependent approach provides in-depth information on the biodiversity of the spoilage microbiota in chicken meat. Further study is needed to develop better preservation methods against these spoilage bacteria.