A5012207088- Cancer Genomics and Diagnostics
- Colorectal Cancer Treatments and Studies
- Cancer Immunotherapy and Biomarkers
- RNA modifications and cancer
- Genetic factors in colorectal cancer
- Ferroptosis and cancer prognosis
- Gene expression and cancer classification
- Cancer-related molecular mechanisms research
- Genetic Associations and Epidemiology
- MicroRNA in disease regulation
- Lymphoma Diagnosis and Treatment
- Lung Cancer Treatments and Mutations
- Evolution and Genetic Dynamics
- Epigenetics and DNA Methylation
- Genomics and Rare Diseases
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Circular RNAs in diseases
- Vestibular and auditory disorders
- Monoclonal and Polyclonal Antibodies Research
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Chromatin Dynamics
- Hearing, Cochlea, Tinnitus, Genetics
- Statistical Methods and Inference
Soongsil University
2019-2025
Institute of Electrical and Electronics Engineers
2018
Gorgias Press (United States)
2018
Catholic University of Korea
2015-2018
University of Ulsan
2015
Asan Medical Center
2014-2015
Ulsan College
2015
Seoul National University
2006-2013
Indiana University Bloomington
2011
Abstract Background MicroRNAs (miRNAs) are small noncoding RNAs, which play significant roles as posttranscriptional regulators. The functions of animal miRNAs generally based on complementarity for their 5' components. Although several computational miRNA target-gene prediction methods have been proposed, they still limitations in revealing actual target genes. Results We implemented miTarget, a support vector machine (SVM) classifier gene prediction. It uses radial basis function kernel...
The intratumoral heterogeneity (ITH) and the evolution of genomic architectures associated with development distant metastases are not well understood in colorectal cancers.We performed multiregion biopsies primary liver metastatic regions from five cancers whole-exome sequencing copy number profiling.In addition to a substantial level genetic ITH, profiling identifies subclonal mutational architecture, leading region-based or spatial categorization somatic mutations inference evolutionary...
Abstract Surgical archives of tumor specimens are often impure. The presence RNA transcripts from nontumor cells, such as immune and stromal can impede analyses cancer expression profiles. To systematically analyze the impact purity, gene profiles purities were obtained for 7,794 across 21 types (available in Cancer Genome Atlas consortium). First, we observed that genes with roles immunity oxidative phosphorylation significantly inversely correlated respectively. implicated immunotherapy...
Human mesenchymal stromal cells (MSCs) have served as a major cellular resource for cell-based immunomodulatory and regenerative therapies. However, genomic instability may accumulate during ex vivo expansion of MSCs, thereby increasing the potential malignant transformation. Here, we performed whole genome sequencing two peripheral blood-derived MSC lines (MSC1 MSC2) at various passages (passage 1 [P1] to P9). The majority single-nucleotide variations (SNVs) occurred in later passages;...
The tumor microenvironment (TME) within mucosal neoplastic tissue in oral cancer (ORCA) is greatly influenced by tumor-infiltrating lymphocytes (TILs). Here, a clustering method was performed using CIBERSORT profiles of ORCA data that were filtered from the publicly accessible patients with head and neck Cancer Genome Atlas (TCGA) hierarchical where regrouped into binary risk groups based on clustering-measuring scores survival patterns associated individual groups. Based this analysis,...
Aberrant DNA methylation of CpG islands, island shores and first exons is known to play a key role in the altered gene expression patterns all human cancers. To date, systematic study on effect using high resolution data has not been reported. In this study, we conducted an integrated analysis MethylCap-sequencing Affymetrix microarray for 30 breast cancer cell lines representing different tumor phenotypes. As well-developed methods do currently exist, created series four methods. On...
Pancreatic ductal adenocarcinoma (PDAC) is the most challenging type of cancer to treat, with a 5-year survival rate <10%. Furthermore, because large portion inoperable cases, it difficult obtain specimens study biology tumors. Therefore, patient-derived xenograft (PDX) model an attractive option for preserving and expanding these tumors translational research. Here we report generation characterization 20 PDX models PDAC. The success initial graft was 74% were re-transplantable....
Somatic mutations in cancer genomes often show allelic imbalance (AI) of mutation abundance between the genome and transcriptome, but there is not yet a systematic understanding AI. In this study, we performed large-scale DNA RNA AI analyses >100,000 somatic >2,000 specimens across five tumor types using exome transcriptome sequencing data Cancer Genome Atlas consortium. First, analysis nonsense frameshift indels revealed that nonsense-mediated decay typical genomes, identified relationship...
Abstract Intraindividual tumoural heterogeneity (ITH) is a hallmark of solid tumours and impedes accurate genomic diagnosis selection proper therapy. The aim this study was to identify ITH ovarian high‐grade serous carcinomas (OSCs) determine the utility ascitic cancer cells as resource for mutation profiling in spite ITH. We performed whole‐exome sequencing, copy number DNA methylation four OSC genomes by using multiregional biopsies from 13 intraovarian lesions, 12 extraovarian tumour...
// Tae-Min Kim 1, 2, * , Chang Hyeok An 3, Je-Keun Rhee 2 Seung-Hyun Jung 4, 7 Sung Hak Lee 5 In-Pyo Baek Min 6 Sug Hyung Yeun-Jun Chung 1 Departments of Medical Informatics, College Medicine, The Catholic University Korea, Seoul, South Korea Cancer Evolution Research Center, 3 Surgery, 4 Integrated Center for Genome Polymorphism, Hospital Pathology, Microbiology, These authors have contributed equally to this work Correspondence to: Chung, e-mail: yejun@catholic.ac.kr Lee,...
The study of chromatin interactions has advanced considerably with technologies such as high-throughput chromosome conformation capture (Hi-C) sequencing, providing a genome-wide view physical within the nucleus. These techniques have revealed existence hierarchical structures compartments, topologically associating domains (TADs), and loops, which are crucial in genome organization regulation. However, identifying analyzing these structural features require computational methods. In recent...
The primary aim of this study was to investigate the genetic predisposition Internet gaming disorder (IGD), and secondary compare results those alcohol dependence (AD). Two independent case-control studies were conducted. A total 30 male participants with IGD, diagnosed according 5th edition Diagnostic Statistical Manual Mental Disorders (DSM-5) criteria, sex-matched controls participated in 1. We designed targeted exome sequencing (TES) test for 72 candidate genes that have been implicated...
Abstract Dacomitinib, an irreversible pan-HER inhibitor, had shown modest clinical activity in squamous cell carcinoma of head and neck (SCCHN) patients. Therefore, validated predictive biomarkers are required to identify patients most likely benefit from this therapeutic option. To characterize the genetic landscape cisplatin-treated SCCHN genomes potential for dacomitinib sensitivity, we performed whole exome sequencing on 18 cisplatin-resistant metastatic tumors their matched germline...
Abstract Predicting clinical responses to tumor immunotherapy is essential reduce side effects and the potential for sustained responses. Nevertheless, preselecting patients who are likely respond such treatments remains highly challenging. Here, we explored of microRNAs (miRNAs) as predictors immune checkpoint blockade using a machine learning approach. First, constructed random forest models predict response ICB therapy miRNA expression profiles across 19 cancer types. The contribution...
// Sung Hak Lee 1, * , Seung Hyun Jung 4, 6, Tae-Min Kim 2 Je-Keun Rhee Hyeon-Chun Park 3, 4 Min 5, 6 Soo 7 Chang Hyeok An 8 Sug Hyung Yeun-Jun Chung 5 1 Departments of Hospital Pathology, The Catholic University Korea, Seoul, Korea Medical Informatics, 3 Microbiology, Integrated Research Center for Genome Polymorphism, Cancer Evolution Center, Department Internal Medicine, General Surgery These two authors contributed equally to this work Correspondence to: Chung, email:...
Mutation profiles and intratumoral heterogeneity are not well understood for benign gastric adenomas, some of which progress into malignant adenocarcinomas. In this study, we performed whole-exome sequencing three microsatellite stable (MSS) two instability-high (MSI-H) adenomas with regional tumor biopsies per case. We observed that the mutation abundance was comparable to those adenocarcinomas, suggesting mutational makeup carcinogenesis may already be achieved in adenomas. The extent more...
Objectives: The cause of Meniere's disease (MD) is unclear but likely involves genetic and environmental factors. aim this study was to investigate the basis underlying MD by screening putative candidate genes for MD. Methods: Sixty-eight patients who met diagnostic criteria Barany Society were included. We performed targeted gene sequencing using next generation (NGS) panel composed 45 MD-associated genes. identified rare variants causing non-synonymous amino acid changes, stop codons,...
Pancreatic cancer is one of the most difficult cancers to cure due lack early diagnostic tools and effective therapeutic agents. In this study, we aimed isolate new bioactive compounds that effectively kill pancreatic ductal adenocarcinoma (PDAC) cells, but not untransformed, human epithelial (HPDE) cells. To end, established four primary PDAC cell lines screened 4141 from bioactive-compound libraries. Initial screening yielded 113 hit caused over a 50% viability reduction in all tested...
Background and aims Internet gaming disorder (IGD) has gained recognition as a potential new diagnosis in the fifth revision of Diagnostic Statistical Manual Mental Disorders, but genetic evidence supporting this remains scarce. Methods In study, targeted exome sequencing was conducted 30 IGD patients control subjects with focus on genes linked to various neurotransmitters associated substance non-substance addictions, depression, attention deficit hyperactivity disorder. Results rs2229910...
This study aimed to investigate the underlying pathogenesis of acute unilateral vestibulopathy (AUV) using gene expression profiling combined with bioinformatics analysis.Total RNA was extracted from peripheral blood mononuclear cells ten AUV patients in phase and controls. The differentially expressed genes (DEGs) between these two groups were screened microarray analysis cut-off criteria (|fold changes| > 1.5 p-value < 0.05). Functional enrichment DEGs performed Gene Ontology Kyoto...