A5101459219- Cancer Genomics and Diagnostics
- Genetic factors in colorectal cancer
- RNA modifications and cancer
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Genomics and Rare Diseases
- Renal cell carcinoma treatment
- Machine Learning in Bioinformatics
- Cancer-related molecular mechanisms research
- Helicobacter pylori-related gastroenterology studies
- Ubiquitin and proteasome pathways
- Medical Imaging Techniques and Applications
- Hearing, Cochlea, Tinnitus, Genetics
- Bioinformatics and Genomic Networks
- Genomic variations and chromosomal abnormalities
- Ferroptosis and cancer prognosis
- Veterinary Oncology Research
- Advanced Breast Cancer Therapies
- Biomedical Text Mining and Ontologies
- Colorectal Cancer Treatments and Studies
- Gene expression and cancer classification
- Colorectal Cancer Screening and Detection
- Retinal Imaging and Analysis
- Genetic Associations and Epidemiology
- Obesity, Physical Activity, Diet
- Infectious Diseases and Mycology
Seoul National University Bundang Hospital
2019-2025
Seoul National University
2024
Samsung Medical Center
2016-2019
Abstract Microsatellite instability (MSI) refers to the hypermutability of short repetitive sequences in genome caused by impaired DNA mismatch repair. Although MSI has been studied for decades, large amounts sequencing data now available allows us examine molecular fingerprints greater detail. Here, we analyse ∼8,000 exomes and ∼1,000 whole genomes cancer patients across 23 types. Our analysis reveals that frequency events is highly variable within tumour We also identify genes repair...
In many next-generation sequencing (NGS) studies, multiple samples or data types are profiled for each individual. An important quality control (QC) step in these studies is to ensure that datasets from the same subject properly paired. Given heterogeneity of types, file and depths a multi-dimensional study, robust program provides standardized metric genotype comparisons would be useful. Here, we describe NGSCheckMate, user-friendly software package verifying sample identities FASTQ, BAM...
Abstract Genomic and precision medicine research has afforded notable advances in human cancer treatment, yet applicability to other species remains uncertain. Through whole-exome transcriptome analyses of 191 spontaneous canine mammary tumors (CMTs) that exhibit the archetypal features breast cancers, we found a striking resemblance genomic characteristics including frequent PIK3CA mutations (43.1%), aberrations PI3K-Akt pathway (61.7%), key genes involved initiation progression. We also...
// Hyunchul Jung 1, 4, * , Hae Yong Yoo 2, Seung Ho Lee Sohyun Shin 3, Sang Cheol Kim Sejoon Je-Gun Joung Jae-Yong Nam Daeun Ryu Jae Won Yun 5, Kyoon Choi Ambarnil Ghosh Kyeong Kyu Seok Jin 6, Seog Woong-Yang Park 1 and Young Hyeh Ko 3 Department of Bio Brain Engineering, Korea Advanced Institute Science Technology (KAIST), Daejeon, Republic 2 Health Sciences Technology, Samsung for Sungkyunkwan University, Seoul, Pathology, Medical Center, University School Medicine, 4 Genome Institute,...
Next-generation sequencing (NGS) cancer profiling has gained traction in routine clinical practice South Korea. Here, we evaluated the use of NGS testing and genomically-matched therapies for patients with advanced solid tumors a real-world practice. We analyzed results from panel tests (SNUBH pan-cancer version 2) ordered June 2019 to 2020. Genomically-matched treatment was determined based on novel information obtained testing, while conventional molecular were excluded. A total 990...
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...
Studies of naturally occurring cancers in dogs, which share many genetic and environmental factors with humans, provide valuable information as a comparative model for studying the mechanisms human cancer pathogenesis. While individual small-scale studies canine are underway, more generalized multi-omics have not been attempted due to lack large-scale well-controlled genomic data. Here, we produced reliable whole-exome whole-transcriptome sequencing data 197 mammary their matched controls,...
Abstract Alzheimer’s disease (AD) is a progressive neurodegenerative associated with complex genetic etiology. Besides the apolipoprotein E ε4 ( APOE ε4) allele, few dozen other loci AD have been identified through genome-wide association studies (GWAS) conducted mainly in individuals of European ancestry. Recently, several GWAS performed ethnic groups shown importance replicating that identify previously established risk and searching for novel loci. -stratified yielded might be masked by,...
ABSTRACT Microsatellite instability (MSI) refers to the hypermutability of cancer genome due impaired DNA mismatch repair. Although MSI has been studied for decades, large amount sequencing data now available allows us examine molecular fingerprints in greater detail. Here, we analyze ~8000 exome and ~1000 whole-genome pairs across 23 types. Our pan-cancer analysis reveals that prevalence events is highly variable within tumor types including some which not typically examined. We also...
Background Common data models (CDMs) help standardize electronic health record and facilitate outcome analysis for observational longitudinal research. An of pathology reports is required to establish fundamental information infrastructure data-driven colon cancer The Observational Medical Outcomes Partnership (OMOP) CDM used in distributed research networks clinical data; however, it requires conversion free text–based into the CDM’s format. There are few use cases representing CDM....
Next-generation sequencing (NGS)-based tumor panel testing has been reimbursed by the Korean government since 2017. We evaluated use of NGS-based in real-world clinical practice, focusing on molecular profiling (MP)-guided breast cancer treatment.A total 137 patients underwent NGS between December 2017 and July 2020 at Seoul National University Bundang Hospital (SNUBH). Samples from were profiled using an in-house SNUBH pan-cancer panel. Sixty-four Pan_Cancer v1.0, targeting 89 genes, while...
Chromosomal instability (CIN) is known to be associated with prognosis and treatment response in breast cancer. This study was conducted determine whether copy number gain of centromere 17 (CEP17) reflects CIN, evaluate the prognostic predictive value CIN status determined by summing gains four centromeric probes (CEP1, CEP8, CEP11, CEP16) based on fluorescence situ hybridization scores were calculated using next generation sequencing data. High adverse clinicopatholgical parameters Among...
Abstract Background Next-generation sequencing (NGS) has been introduced to many Korean institutions support molecular diagnostics in cancer since 2017, when it became eligible for reimbursement by the National Health Insurance Service. However, uptake of molecularly guided treatment (MGT) based on NGS results limited because stringent regulations regarding prescriptions outside approved indications, a lack clinical trial opportunities, and access tumor boards (MTB) at most institutions. The...
Background: Colorectal cancer (CRC) is one of the leading causes cancer-related deaths worldwide. Although early diagnosis and treatment most successful strategy for improving patient survival, feasible sensitive blood biomarkers CRC screening remain elusive. Methods: Sixty-five patients thirty-three healthy individuals were enrolled. Peripheral (PB) tumor tissues from patients, PB subjected to immunophenotyping phospho-flow analysis cytokine-induced phosphorylated STAT (CIPS). Logistic...
We aimed to elucidate the evolutionary trajectories of gallbladder adenocarcinoma (GBAC) using multi-regional and longitudinal tumor samples. Using whole-exome sequencing data, we constructed phylogenetic trees in each patient analyzed mutational signatures. A total 11 patients including 2 rapid autopsy cases were enrolled. The most frequently altered gene primary tumors was ERBB2 TP53 (54.5%), followed by FBXW7 (27.3%). Most mutations genes detectable concurrent precancerous lesions...
Alterations of a genome can lead to changes in protein functions. Through these genetic mutations, lose its native function (loss-of-function, LoF), or it confer new (gain-of-function, GoF). However, when mutation occurs, is difficult determine whether will result LoF GoF. Therefore, this paper, we propose study that analyzes the genomic features and GoF instances find be used classify mutations. In order collect experimentally verified mutational information, obtained 816 mutations 474 from...
Sejoon Lee, Kil-yong Ji-Hwan Park, Duck-Woo Kim, Heung-Kwon Oh, Seong-Taek Jongbum Jeon, Dongyoon Soobok Joe, Hoang Bao Khanh Chu, Jisun Kang, Jin-Young Sheehyun Cho, Hyeran Shim, Si-Cho Hong Seok Young-Joon Jin Ok Yang, Jaeim Lee & Sung-Bum Kang. BMB Reports -0001;0:. https://doi.org/10.5483/BMBRep.2023-0103
Considering the recent increase in number of colorectal cancer (CRC) cases South Korea, we aimed to clarify molecular characteristics CRC unique Korean population. To gain insights into complexities and promote exchange critical data, RNA-sequencing analysis was performed reveal mechanisms that drive development progression CRC; this is for developing effective treatment strategies. We adjacent normal tissue samples from 214 participants (comprising a total 381 including 169 212 tumor...
Purpose: Homozygous hypomorphic variants of the RP1 gene, including c.5797C>T, p.Arg1933Ter, have traditionally been considered non-pathogenic. This study aimed to elucidate clinical manifestations late-onset, slowly progressive cone/macular dystrophy in patients homozygous for p.Arg1933Ter gene. Methods: Five with biallelic were retrospectively recruited, and their profiles analyzed. Copy number variation analysis Alu insertion assessment genes associated inherited retinal diseases...
The biological behavior of sebaceous carcinoma (SeC) is relatively indolent; however, local invasion or distant metastasis sometimes reported. Nevertheless, a lack understanding the genetic background SeC makes it difficult to apply effective systemic therapy. This study was designed investigate major alterations in SeCs Korean patients. A total 29 samples, including 20 ocular (SeC-Os) and 9 extraocular (SeC-EOs), were examined. Targeted next-generation sequencing tests 171 cancer-related...
Otoancorin (OTOA), encoded by OTOA, is required for the development of tectorial membrane in inner ear. Mutations this gene cause nonsyndromic hearing loss (DFNB22). The molecular mechanisms underlying most DFNB22 remain poorly understood. Disruption glycosylphosphatidylinositol (GPI) anchorage has been assumed to be pathophysiology mandating experimental validation. From a Korean deaf family, we identified two trans OTOA variants (c.1320 + 5 G>C and p.Gln589ArgfsX55 [NM_144672.3]) ....
Although American Thyroid Association guidelines offer a risk stratification scheme for thyroid cancer patients, there is continuous need more sophisticated biomarkers that can predict disease progression. In this study, we aim to evaluate the prognostic value of class III beta-tubulin (TUBB3) and uncover relationship between TUBB3 invasive potential in carcinoma. Immunohistochemistry (IHC) E-cadherin was performed on total 254 cases specimens. Tumor budding at margin evaluated. vitro...
Among the various types of breast cancer, luminal B subtype is most common in young women, and ESR1-CCDC170 (E:C) fusion frequent oncogenic driver subtype. Nevertheless, treatments targeting E:C has not been well established yet. Hence, aim this study to investigate potential therapies based on systematic bioinformatical analysis Cancer Genome Atlas (TCGA) data. One thousand related genes were extracted using transcriptome analysis, major signaling pathways associated with cancer identified...