A5042831733- Genetic and phenotypic traits in livestock
- Agricultural Systems and Practices
- Cancer Genomics and Diagnostics
- Genomics and Rare Diseases
- Genetic Mapping and Diversity in Plants and Animals
- Immune cells in cancer
- Epigenetics and DNA Methylation
- Livestock Farming and Management
- Molecular Biology Techniques and Applications
- Acute Myeloid Leukemia Research
- Genomic variations and chromosomal abnormalities
- Genetic factors in colorectal cancer
- Animal Genetics and Reproduction
- Cancer Immunotherapy and Biomarkers
- Genetic Associations and Epidemiology
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Genetics, Bioinformatics, and Biomedical Research
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Cancer Cells and Metastasis
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- Livestock and Poultry Management
- Evolution and Genetic Dynamics
National Cancer Center
2024-2025
Catholic University of Korea
2024
Konkuk University
2018-2024
Abstract The cost-effectiveness of whole exome sequencing (WES) remains debated, primarily due to variability in variant calls. Evaluating the sensitivity and specificity WES results may clarify this issue. was performed by three companies (AA, BB, CC) using reference standards composed DNA from Hydatidiform mole individual blood at various ratios. Sensitivity assessed detection rate null-homozygote (N-H) alleles expected allelic fractions, while false positive (FP) errors were counted for...
Abstract Background: Next-generation sequencing (NGS) has emerged as a vital diagnostic tool for various diseases; however, errors associated with NGS present significant challenges to its clinical implementation. Specifically, in cancer diagnostics, the analysis of low-level mutations is complicated by contamination from normal cells and tumor heterogeneity. Results: In targeted (T-NGS) analyses involving reference-standard samples consisting mixtures homozygous Hydatidiform mole DNA blood...
Abstract Background Many studies have been performed to identify various genomic loci and genes associated with the meat quality in pigs. However, full genetic architecture of trait still remains unclear part because lack accurate identification related structural variations (SVs) which resulted from shortage target breeds, limitations sequencing data, incompleteness genome assemblies. The recent generation a new pig breed superior quality, called Nanchukmacdon, its chromosome-level assembly...
Background A spatially resolved, niche-level analysis of tumour microenvironments (TME) can provide insights into cellular interactions and their functional impacts in gastric cancers (GC). Objective Our goal was to translate the spatial organisation GC ecosystems a landscape involving malignant, stromal immune cells. Design We performed transcriptomics on nine primary samples using Visium platform delineate transcriptional dynamics cells within tissue architecture, highlighting crosstalks...
Abstract As plentiful high-quality genome assemblies have been accumulated, reference-guided assembly can be a good approach to reconstruct assembly. Here, we present chromosome-level of the Korean crossbred pig called Nanchukmacdon (the NCMD assembly) using with short and long reads. The contains 20 scaffolds total size 2.38 Gbp (N50: 138.77 Mbp). Its BUSCO score is 93.1%, which comparable reference assembly, 20,588 protein-coding genes, 8,651 non-coding 996.14 Mbp repetitive elements are...
Background: Previous studies have reported that genes highly expressed in leukemic stem cells (LSC) may dictate the survival probability of patients and expression-based cellular deconvolution be informative forecasting prognosis. However, whether prognosis acute myeloid leukemia (AML) can predicted using gene expression deconvoluted abundances is debatable. Methods: Nine different cell-type a training set composed AML samples 422 patients, were used to build model for predicting by least...
Deficiencies in DNA mismatch repair (MMRd) leave characteristic footprints of microsatellite instability (MSI) cancer genomes. We used data from the Cancer Genome Atlas and International Consortium to conduct a comprehensive analysis MSI-associated cancers, focusing on indel mutational signatures. classified MSI-high genomes into two subtypes based their profiles: deletion-dominant (MMRd-del) insertion-dominant (MMRd-ins). Compared with MMRd-del genomes, MMRd-ins exhibit distinct...
Abstract Background Although next generation sequencing (NGS) has been adopted as an essential diagnostic tool in various diseases, NGS errors have the most serious problem clinical implementation. Especially cancers, low level mutations not easy to analyze, due contaminating normal cells and tumor heterozygosity. Results In targeted (T-NGS) analyses for reference-standard samples containing mixtures of homozygote H. mole DNA with blood genomic at ratios from four certified service...
Abstract Background Advances in next-generation sequencing technologies have provided an opportunity to perform population-level comparative genomic analysis discover unique characteristics of domesticated animals. Duck is one the most popular waterfowls, which economically important as a source meat, eggs, and feathers. The objective this study population functional analyses Korean native duck, has distinct meat flavor texture phenotype, using whole-genome data. To features we conducted 20...
Determining the impact of somatic mutations requires understanding functional relationship genes acquiring mutations; however, it is largely unknown how in functionally related influence each other.
The cost-effectiveness of whole exome sequencing (WES) remains controversial due to variant call variability, necessitating sensitivity and specificity evaluation. WES was performed by three companies (AA, BB, CC) using reference standards composed DNA from hydatidiform mole individual blood at various ratios. Sensitivity assessed the detection rate null–homozygote (N–H) alleles expected allelic fractions, while false positive (FP) errors were counted for unexpected alleles. approximately...
Genetic disorders play an important role in cancer development. Especially, somatic variants, such as single nucleotide variations, insertions, deletions, and copy number specific genes, can promote tumorigenesis. Recently, NetSig has been developed that integrates existing protein interaction networks to predict driver genes. However, is limited use only directly interacting proteins. To address this issue, we a new statistic, called RWNetSig, be used genes by considering indirect well...