A5102751360- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Radiomics and Machine Learning in Medical Imaging
- Machine Learning in Bioinformatics
- Genetics, Bioinformatics, and Biomedical Research
- Genomic variations and chromosomal abnormalities
- Glioma Diagnosis and Treatment
- Genetic factors in colorectal cancer
- Genomics and Rare Diseases
- Genomics and Chromatin Dynamics
- Advanced biosensing and bioanalysis techniques
- Bladder and Urothelial Cancer Treatments
- Innovative Microfluidic and Catalytic Techniques Innovation
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Urinary and Genital Oncology Studies
- Biosensors and Analytical Detection
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Industrial Vision Systems and Defect Detection
- Consumer Perception and Purchasing Behavior
- Myasthenia Gravis and Thymoma
- Acute Myeloid Leukemia Research
Illumina (United States)
2024-2025
Gwangju Institute of Science and Technology
2017-2024
<h3>Background</h3> Urachal cancer is a rare that develops in the urachus. Because of its rarity, standard treatment therapies for urachal are not established, and chemotherapeutic regimens bladder have been unsuccessful patients with cancer. Hence, we aim to understand systematic molecular characterisation <h3>Methods</h3> We identified somatic single-nucleotide variations (SNVs)/indels copy number aberrations (SCNAs) 17 by using whole-exome sequencing (WES) OncoScan platform (Affymetrix)...
Whole-genome sequencing (WGS) is increasingly preferred for clinical applications due to its comprehensive coverage, effectiveness in detecting copy number variants (CNVs), and declining costs. However, systematic evaluations of WGS CNV callers tailored germline testing-where high sensitivity confirmation reported CNVs are essential-remain necessary. Clinical reporting typically emphasizes affecting coding regions over precise breakpoint detection. This study benchmarks several short-read...
Thymic adenocarcinoma is an extremely rare subtype of thymic epithelial tumors. Due to its rarity, there currently no sequencing approach for adenocarcinoma. We performed whole exome and transcriptome on a case subsequent validation using Sanger sequencing. The showed aggressive behaviors with systemic bone metastases. identified high incidence genetic aberrations, which included somatic mutations in RNASEL, PEG10, TNFSF15, TP53, TGFB2, FAT1. Copy number analysis revealed complex chromosomal...
Abstract The 3D genome prediction in cancer is crucial for uncovering the impact of structural variations (SVs) on tumorigenesis, especially when they are present noncoding regions. We InfoHiC, a systemic framework predicting directly from whole-genome sequencing (WGS). InfoHiC utilizes contig-specific copy number encoding SV contig assembly, and performs contig-to-total Hi-C conversion multiple contigs. showed that can predict folding all types SVs using breast cell line data. applied it to...
Annotation of structural variations (SVs) and base-level karyotyping in cancer cells remains challenging. Here, we present Integrative Framework for Genome Reconstruction (InfoGenomeR)-a graph-based framework that can reconstruct individual SVs into karyotypes based on whole-genome sequencing data, by integrating SVs, total copy number alterations, allele-specific numbers, haplotype information. Using data sets patients with breast cancer, glioblastoma multiforme, ovarian demonstrate the...
Abstract Whole-genome sequencing (WGS) is increasingly favored over other genomic methods for clinical applications due to its comprehensive coverage and declining costs. WGS particularly useful the detection of copy number variants (CNVs), presumed be more accurate than targeted assays such as WES or gene panels, because it can identify breakpoints in addition changes depth. Recent advancements bioinformatics tools, including those employing hardware acceleration machine learning, have...
Abstract Although cancer genomes often contain complex genomic rearrangements, its impact on tumorigenesis is still unclear, especially when they are involved in non-coding regions. Understanding 3D genome architecture crucial for uncovering the impacts of rearrangements. Here, we present InfoHiC, a method predicting folding and Hi-C from InfoHiC provides distinct interaction views multiple contigs matrix. We then validated prediction using breast cell line data found contig-specific...