Biology subjects

Kim, B. C.

Publications and source records attributed to Kim, B. C..

5 recordsLinked to original sources

bioRxiv2022

Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups

We present 4,157 whole-genome sequences (Korea4K) coupled with 107 health check-up parameters as the largest whole genomic resource of Koreans. Korea4K provides 45,537,252 variants and encompasses most of the common and rare variants in Koreans. We identified 1,356 new geno-phenotype associations which were not found by the previous Korea1K dataset. Phenomics analyses revealed 24 genetic correlations, 1,131 pleiotropic variants, and 127 causal relationships from Mendelian randomization. Moreover, the Korea4K imputation reference panel showed a superior imputation performance to Korea1K. Collectively, Korea4K provides the most extensive genomic and phenomic data resources for discovering clinically relevant novel genome-phenome associations in Koreans.

genomics↗

bioRxiv2022

DeepParcellation: a novel deep learning method for robust brain magnetic resonance imaging parcellation in older East Asians

Accurate parcellation of cortical regions is crucial for distinguishing morphometric changes in aged brains, particularly in degenerative brain diseases. Normal aging and neurodegeneration precipitate brain structural changes, leading to distinct tissue contrast and shape in people aged > 60 years. Manual parcellation by trained radiologists can yield a highly accurate outline of the brain; however, analyzing large datasets is laborious and expensive. Alternatively, newly-developed computational models can quickly and accurately conduct brain parcellation, although thus far only for the brains of Caucasian individuals. DeepParcellation, our novel deep learning model for 3D magnetic resonance imaging (MRI) parcellation, was trained on 5,035 brains of older East Asians (Gwangju Alzheimers & Related Dementia) and 2,535 brains of Caucasians. We trained full 3D models for N-way individual regions of interest using memory reduction techniques. Our method showed the highest similarity and robust reliability among age-ethnicity groups, especially when parcellating the brains of older East Asians.

neuroscience↗

bioRxiv2019

Dynamic healing and remodeling of mandibular ramus in segmental mobility and cortical overlap after intraoral vertical osteotomy

The ramus immediately after intraoral vertical ramus osteotomy (IVRO) shows segmental mobility, cortical overlap, and projection, which yield smooth-surfaced continuity and stability after one year. This study aimed to elucidate the three-dimensional (3D) morphological changes driven by regional healing and remodeling 12 months postoperatively (Post) and their relationships with the immediate postoperative (Imm) segmental overlapping pattern. We performed a retrospective study of the morphological change of mandibular ramus in terms of time and amount of cortical overlap after IVRO. 3D computed tomography data of 108 hemi-mandibles were analyzed by independent superimposition of Imm proximal and distal segment to Post mandible. Analysis showed extensive regional bone resorption and apposition resulting in a relatively flat-surfaced and morphologically intact Post ramus. The middle ramal remodeling was significantly associated with Imm overlapping patterns and Post mandibular movement, new bony projections of various shapes being observed at the posterior border of the Post ramus. The ramus after IVRO underwent dynamic morphological changes during healing/remodeling which were partly associated with Imm overlap. Moreover, the Post functional and smooth-surfaced ramus seems to have been facilitated by the close surgical approximation of segments and the postoperative mandibular functional rehabilitation, even with segmental positional changes.

pathology↗

bioRxiv2019

Mutation profiling of both cfDNAs and CTCs in gynecological cancer patients

In the recent years, microRNAs (miRNAs) have been discovered to play a very important role in biological processes such as development, differentiation, and apoptosis. The miRNA expression levels in cells are associated with diverse diseases including cancers. MiRNA inhibitors have been widely employed for studying the functions and targets of miRNAs by transfecting the inhibitors into cells. The concentrations of miRNA inhibitors used for such studies can vary depending on the types of miRNAs being tested, the cell lines under study, and the analysis methods. Therefore, in order to obtain accurate results, appropriate amounts of miRNA inhibitors have to be used in the experiments. Apart from amounts, the evaluation of inhibitors may also have to be conducted for functional studies.\n\nHere we developed capillary electrophoresis with laser-induced fluorescence (CE-LIF) method for evaluating miRNA inhibitor and for optimizing miRNA inhibitor concentrations, in the A549 lung cancer cell line. The target miRNAs, miRNA-23a and miRNA-24 are biomarker candidates in lung cancer cell lines. Our results showed that miRNA-23a and miRNA-24 were effectively inhibited upon transfection with 20 nM miRNA inhibitors using CE-LIF method. Furthermore, these results demonstrated the potential of CE for fast, specific, sensitive and specific analyses for the evaluation and determination of the optimal concentration of miRNA inhibitors for functional studies.\n\nAbstract Graphics\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC=\"FIGDIR/small/566786v4_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (31K):\norg.highwire.dtl.DTLVardef@2bbfeeorg.highwire.dtl.DTLVardef@45b7e3org.highwire.dtl.DTLVardef@12ba79borg.highwire.dtl.DTLVardef@108ec2f_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2017

KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses

High-coverage whole-genome sequencing data of a single ethnicity can provide a useful catalogue of population-specific genetic variations. Herein, we report a comprehensive analysis of the Korean population, and present the Korean National Standard Reference Variome (KoVariome). As a part of the Korean Personal Genome Project (KPGP), we constructed the KoVariome database using 5.5 terabases of whole genome sequence data from 50 healthy Korean individuals with an average coverage depth of 31x. In total, KoVariome includes 12.7M single-nucleotide variants (SNVs), 1.7M short insertions and deletions (indels), 4K structural variations (SVs), and 3.6K copy number variations (CNVs). Among them, 2.4M (19%) SNVs and 0.4M (24%) indels were identified as novel. We also discovered selective enrichment of 3.8M SNVs and 0.5M indels in Korean individuals, which were used to filter out 1,271 coding-SNVs not originally removed from the 1,000 Genomes Project data when prioritizing disease-causing variants. CNV analyses revealed gene losses related to bone mineral densities and duplicated genes involved in brain development and fat reduction. Finally, KoVariome health records were used to identify novel disease-causing variants in the Korean population, demonstrating the value of high-quality ethnic variation databases for the accurate interpretation of individual genomes and the precise characterization of genetic variations.

genomics↗