• Genomics & Informatics
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• v.20 no.1
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• pp.3.1-3.10
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• 2022

The recent development of whole-genome sequencing technologies paved the way for understanding the genomes of microorganisms. Every whole-genome sequencing (WGS) project requires a considerable cost and a massive effort to address the questions at hand. The final step of WGS is data analysis. The analysis of whole-genome sequence is dependent on highly sophisticated bioinformatics tools that the research personal have to buy. However, many laboratories and research institutions do not have the bioinformatics capabilities to analyze the genomic data and therefore, are unable to take maximum advantage of whole-genome sequencing. In this aspect, this study provides a guide for research personals on a set of bioinformatics tools available online that can be used to analyze whole-genome sequence data of bacterial genomes. The web interfaces described here have many advantages and, in most cases exempting the need for costly analysis tools and intensive computing resources.

• Journal of Genetic Medicine
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• v.20 no.1
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• pp.1-5
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• 2023

Until now, rare disease studies have mainly been carried out by detecting simple variants such as single nucleotide substitutions and short insertions and deletions in protein-coding regions of disease-associated gene panels using diagnostic next-generation sequencing in association with patient phenotypes. However, several recent studies reported that the detection rate hardly exceeds 50% even when whole-exome sequencing is applied. Therefore, the necessity of introducing whole-genome sequencing is emerging to discover more diverse genomic variants and examine their association with rare diseases. When no diagnosis is provided by whole-genome sequencing, additional omics techniques such as RNA-seq also can be considered to further interrogate causal variants. This paper will introduce a description of these multi-omics techniques and their applications in rare disease studies.

• Korean Journal of Veterinary Service
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• v.42 no.4
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• pp.297-300
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• 2019

In countries with FMD vaccination, as in Korea, typical clinical signs do not appear, and even in FMD positive cases, it is difficult to isolate the FMDV or obtain whole genome sequence. To overcome this problem, more rapid and simple NGS system is required to control FMD in Korea. FMDV (O/Boeun/ SKR/2017) RNA was extracted and sequenced using Ion Torrent's bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. The whole genome sequencing of raw data generated data of 1,839,864 (mean read length 283 bp) reads comprising a total of 521,641,058 (≥Q20 475,327,721). Compared with FMDV (GenBank accession No. MG983730), the FMDV sequences in this study showed 99.83% nucleotide identity. Further study is needed to identify these differences. In this study, fast and robust methods for benchtop next generation sequencing (NGS) system was developed for analysis of Foot-and-mouth disease virus (FMDV) whole genome sequences.

• Genomics & Informatics
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• v.15 no.4
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• pp.128-135
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• 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
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• v.16 no.3
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• pp.71-74
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• 2018

Because castration-resistant prostate cancer (CRPC) does not respond to androgen deprivation therapy and has a very poor prognosis, it is critical to identify a prognostic indicator for predicting high-risk patients who will develop CRPC. Here, we report a dataset of whole genomes from four pairs of primary prostate cancer (PC) and CRPC samples. The analysis of the paired PC and CRPC samples in the whole-genome data showed that the average number of somatic mutations per patients was 7,927 in CRPC tissues compared with primary PC tissues (range, 1,691 to 21,705). Our whole-genome sequencing data of primary PC and CRPC may be useful for understanding the genomic changes and molecular mechanisms that occur during the progression from PC to CRPC.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.2
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• pp.360-372
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• 2020

Objective: Specific genomic sites can be recognized and permanently modified by genome editing. The discovery of endonucleases has advanced genome editing in pigs, attenuating xenograft rejection and cross-species disease transmission. However, off-target mutagenesis caused by these nucleases is a major barrier to putative clinical applications. Furthermore, off-target mutagenesis by genome editing has not yet been addressed in pigs. Methods: Here, we generated genetically inheritable α-1,3-galactosyltransferase (GGTA1) knockout Yucatan miniature pigs by combining transcription activator-like effector nuclease (TALEN) and nuclear transfer. For precise estimation of genomic mutations induced by TALEN in GGTA1 knockout pigs, we obtained the whole-genome sequence of the donor cells for use as an internal control genome. Results: In-depth whole-genome sequencing analysis demonstrated that TALEN-mediated GGTA1 knockout pigs had a comparable mutation rate to homologous recombination-treated pigs and wild-type strain controls. RNA sequencing analysis associated with genomic mutations revealed that TALEN-induced off-target mutations had no discernable effect on RNA transcript abundance. Conclusion: Therefore, TALEN appears to be a precise and safe tool for generating genomeedited pigs, and the TALEN-mediated GGTA1 knockout Yucatan miniature pigs produced in this study can serve as a safe and effective organ and tissue resource for clinical applications.

• Genomics & Informatics
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• v.21 no.1
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• pp.11.1-11.5
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• 2023

Breast cancer is the most common cancer worldwide, and advanced breast cancer with metastases is incurable mainly with currently available therapies. Therefore, it is essential to understand molecular characteristics during the progression of breast carcinogenesis. Here, we report a dataset of whole genomes from the human mammary epithelial cell system derived from a reduction mammoplasty specimen. This system comprises pre-stasis 184D cells, considered normal, and seven cell lines along cancer progression series that are immortalized or additionally acquired anchorage-independent growth. Our analysis of the whole-genome sequencing (WGS) data indicates that those seven cancer progression series cells have somatic mutations whose number ranges from 8,393 to 39,564 (with an average of 30,591) compared to 184D cells. These WGS data and our mutation analysis will provide helpful information to identify driver mutations and elucidate molecular mechanisms for breast carcinogenesis.

• Journal of Genetic Medicine
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• v.12 no.2
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• pp.61-65
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• 2015

Whole genome sequencing (WGS)-based noninvasive prenatal test (NIPT) is the first method applied in the clinical setting out of various NIPT techniques. Several companies, such as Sequenom, BGI, and Illumina offer WGS-based NIPT, each with different technical and bioinformatic approaches. Sequenom, BGI, and Illumina utilize z-, t-, and L-scores, as well as normalized chromosome values, respectively, for trisomy detection. Their outstanding performance has been demonstrated in clinical studies of more than 100,000 pregnancies. The sensitivity and specificity for detection of trisomies 13, 18, and 21 were above 98%, as reported by all three companies. Unlike other techniques, WGS-based NIPT can detect other trisomies as well as clinically significant segmental duplications/deletions within a chromosome, which could expand the scope of NIPT. Incorrect results could be due to low fetal fraction, fetoplacental mosaicism, confined placental mosaicism or maternal copy number variation (CNV). Among those, maternal CNV is a significant contributor of false positive results and therefore genome wide scanning plays an important role in preventing the occurrence of false positives. In this article, the bioinformatic techniques and clinical performance of three major companies are comprehensively reviewed.

• Korean Journal of Plant Taxonomy
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• v.53 no.3
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• pp.181-200
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• 2023

Owing to the rapid development of sequencing technologies, more than 1,000 plant genomes have been sequenced and released. Among them, 69 Korean plant taxa (85 genome sequences) contain at least one whole-genome sequence despite the fact that some samples were not collected in Korea. The sequencing-by-synthesis method (next-generation sequencing) and the PacBio (third-generation sequencing) method were the most commonly used in studies appearing in 65 publications. Several scaffolding methods, such as the Hi-C and 10x types, have also been used for pseudo-chromosomal assembly. The most abundant families among the 69 taxa are Rosaceae (10 taxa), Brassicaceae (7 taxa), Fabaceae (7 taxa), and Poaceae (7 taxa). Due to the rapid release of plant genomes, it is necessary to assemble the current understanding of Korean plant species not only to understand their whole genomes as our own plant resources but also to establish new tools for utilizing plant resources efficiently with various analysis pipelines, including AI-based engines.

• Genomics & Informatics
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• v.10 no.1
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• pp.1-8
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• 2012

Recently, the technologies of DNA sequence variation and gene expression profiling have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the nextgeneration DNA sequencer (NGS) Roche/454 and Illumina/ Solexa systems, along with bioinformation analysis technologies of whole-genome $de$ $novo$ assembly, expression profiling, DNA variation discovery, and genotyping. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing $de$ $novo$ assembly of novel genome sequencing data. It is necessary to have DNA sequence information from a multiplatform NGS with at least $2{\times}$ and $30{\times}$ depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly. Massive shortlength reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a wholegenome transcriptome, depending on the tissue samples. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through $de$ $novo$ assembly in any whole-genome sequenced species. The $20{\times}$ and $50{\times}$ coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average $30{\times}$ coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence.