KTED: a comprehensive web-based database for transposable elements in the Korean genome.

Summary: Transposable elements (TEs), commonly referred to as "mobile elements," constitute DNA segments capable of relocating within a genome. Initially disregarded as "junk DNA" devoid of specific functionality, it has become evident that TEs have diverse influences on an organism's biology and health. The impact of these elements varies according to their location, classification, and their effects on specific genes or regulatory components.

Detecting microsatellite instability by length comparison of microsatellites in the 3' untranslated region with RNA-seq.

Microsatellite instability (MSI), a phenomenon caused by deoxyribonucleic acid (DNA) mismatch repair system deficiencies, is an important biomarker in cancer research and clinical diagnostics. MSI detection often involves next-generation sequencing data, with many studies focusing on DNA. Here, we introduce a novel approach by measuring microsatellite lengths directly from ribonucleic acid sequencing (RNA-seq) data and comparing its distribution to detect MSI.

Otoconial Degeneration After Transient Ischemia Induced by Four-Vessel Occlusion in Rats.

Background And Purpose: Ischemia of the inner ear may damage the otoconia. However, no study has explored any changes in the configuration of otoconia after transient ischemia of the labyrinth.

Methods: Nineteen 7-week-old Sprague-Dawley rats were randomly assigned to either the sham (=5) or the experimental group (=14).

AS-CMC: a pan-cancer database of alternative splicing for molecular classification of cancer.

Alternative splicing (AS) is a post-transcriptional regulation that leads to the complexity of the transcriptome. Despite the growing importance of AS in cancer research, the role of AS has not been systematically studied, especially in understanding cancer molecular classification. Herein, we analyzed the molecular subtype-specific regulation of AS using The Cancer Genome Atlas data and constructed a web-based database, named Alternative Splicing for Cancer Molecular Classification (AS-CMC).

tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data.

Background: Recent deep sequencing technologies have proven to be valuable resources to gain insights into the expression profiles of diverse tRNAs. However, despite these technologies, the association of tRNAs with diverse diseases has not been explored in depth because analytical tools are lacking.

Results: We developed a user-friendly tool, tRNA Expression Analysis Software Utilizing R for Easy use (tReasure), to analyze differentially expressed tRNAs (DEtRNAs) from deep sequencing data of small RNAs using R packages.

Dissection of molecular and histological subtypes of papillary thyroid cancer using alternative splicing profiles.

Despite growing evidence of the relevance of alternative splicing (AS) to cancer development and progression, the biological implications of AS for tumor behaviors, including papillary thyroid cancer (PTC), remain elusive. With the aim of further understanding the molecular and histological subtypes of PTC, we in this study explored whether AS events might act as new molecular determinants. For this purpose, AS profiles were analyzed in RNA-sequencing data from The Cancer Genome Atlas (TCGA) and from a Korean patient dataset.

DBtRend: A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans.

Transfer RNA (tRNA), a key component of the translation machinery, plays critical roles in stress conditions and various diseases. While knowledge regarding the importance of tRNA function is increasing, its biological roles are still not well understood. There is currently no comprehensive database or web server providing the expression landscape of tRNAs across a variety of human tissues and diseases.

Whole Exome Sequencing in Patients with Phenotypically Associated Familial Intracranial Aneurysm.

Objective: Familial intracranial aneurysms (FIAs) are found in approximately 6%-20% of patients with intracranial aneurysms (IAs), suggesting that genetic predisposition likely plays a role in its pathogenesis. The aim of this study was to identify possible IA-associated variants using whole exome sequencing (WES) in selected Korean families with FIA.

Materials And Methods: Among the 26 families in our institutional database with two or more IA-affected first-degree relatives, three families that were genetically enriched (multiple, early onset, or common site involvement within the families) for IA were selected for WES.

Protective Effects of Deferoxamine on Vestibulotoxicity in Gentamicin-Induced Bilateral Vestibulopathy Rat Model.

Administration of aminoglycoside (AG) antibiotics is one of the most common causes of ototoxicity. This study aimed to determine the protective effects of deferoxamine, an iron-chelating agent, on vestibulotoxicity using an intratympanic gentamicin injection (ITGM)-induced bilateral vestibulopathy rat model. Fifteen Sprague-Dawley rats were randomly assigned to the ITGM only ( = 5), the ITGM combined with intramuscular deferoxamine (DFO) injection (ITGM+DFO, = 5), or the intratympanic normal saline (control, = 5) group.

Altered brain function in persistent postural perceptual dizziness: A study on resting state functional connectivity.

This study used resting state functional magnetic resonance imaging (rsfMRI) to investigate whole brain networks in patients with persistent postural perceptual dizziness (PPPD). We compared rsfMRI data from 38 patients with PPPD and 38 healthy controls using whole brain and region of interest analyses. We examined correlations among connectivity and clinical variables and tested the ability of a machine learning algorithm to classify subjects using rsfMRI results.

Diverse genetic aetiologies and clinical outcomes of paediatric hypoparathyroidism.

Context: Hypoparathyroidism is characterized by hypocalcaemia, hyperphosphataemia, and low or inappropriately normal parathyroid hormone (PTH) levels. Idiopathic or genetic drivers are the predominant causes of hypoparathyroidism in paediatric-age patients.

Objective: This study investigated the aetiology and clinical course of primary hypoparathyroidism in infancy and childhood.

Clinical and molecular characterisation of Holt-Oram syndrome focusing on cardiac manifestations.

Background: Holt-Oram syndrome is characterised by CHD and limb anomalies. Mutations in TBX5 gene, encoding the T-box transcription factor, are responsible for the development of Holt-Oram syndrome, but such mutations are variably detected in 30-75% of patients.

Methods: Clinically diagnosed eight Holt-Oram syndrome patients from six families were evaluated the clinical characteristics, focusing on the cardiac manifestations, in particular, and molecular aetiologies.

A de novo microdeletion of ANKRD11 gene in a Korean patient with KBG syndrome.

KBG syndrome is a very rare genetic disorder characterized by macrodontia of upper central incisors, global developmental delay, distinctive craniofacial features, short stature, and skeletal anomalies. Ankyrin repeat domain 11 gene (ANKRD11) has recently been identified as a causal factor of this syndrome. We describe a 6-yr-old Korean boy with features of KBG syndrome.

Clinical significance of previously cryptic copy number alterations and loss of heterozygosity in pediatric acute myeloid leukemia and myelodysplastic syndrome determined using combined array comparative genomic hybridization plus single-nucleotide polymorphism microarray analyses.

The combined array comparative genomic hybridization plus single-nucleotide polymorphism microarray (CGH+SNP microarray) platform can simultaneously detect copy number alterations (CNA) and copy-neutral loss of heterozygosity (LOH). Eighteen children with acute myeloid leukemia (AML) (n=15) or myelodysplastic syndrome (MDS) (n=3) were studied using CGH+SNP microarray to evaluate the clinical significance of submicroscopic chromosomal aberrations. CGH+SNP microarray revealed CNAs at 14 regions in 9 patients, while metaphase cytogenetic (MC) analysis detected CNAs in 11 regions in 8 patients.

RANBP2-ALK fusion combined with monosomy 7 in acute myelomonocytic leukemia.

Anaplastic lymphoma receptor tyrosine kinase (ALK) is located on chromosome 2p23; the chromosomal rearrangements of this gene are common genetic alterations, resulting in the creation of multiple fusion genes involved in tumorigenesis. However, the presence of an ALK fusion in myeloid malignancies is extremely rare. We report a case of acute myelomonocytic leukemia in a 31-year-old woman with an unusual rearrangement between RAN-binding protein 2 (RANBP2) and ALK and a karyotype of 45,XX,inv(2)(p23q21),-7[20].

Vulnerability of the vestibular organs to transient ischemia: implications for isolated vascular vertigo.

The aim of this study was to elucidate the mechanism of isolated vascular vertigo by determining selective and relative ischemic vulnerability of the vestibular structures using a global hypoperfusion model in rats. Sprague-Dawley male rats weighing 330-350 g were subjected to transient global ischemia of the brain using a 4-vessel-occlusion (4VO) model. After permanent occlusion of both vertebral arteries (VA) using electrocauterization, both common carotid arteries (CCAs) were occluded for 5-20 min with ligation.

Gentamicin-induced bilateral vestibulopathy in rabbits: vestibular dysfunction and histopathology.

Objectives/hypothesis: Bilateral vestibulopathy (BV) is a mostly persistent and disabling disorder causing dizziness, oscillopsia, and imbalance during locomotion. The animal model is a prerequisite for experimental investigation on prevention and treatment of this disorder. The aim of this study was to determine the vestibular dysfunction and histopathology in rabbits with gentamicin-induced BV.

OBFC2A/RARA: a novel fusion gene in variant acute promyelocytic leukemia.

Acute promyelocytic leukemia is characterized by the rearrangement of the retinoic acid receptor α (RARA) gene and its fusion with other genes. We report a novel case of variant acute promyelocytic leukemia with the karyotype der (2)t(2;17)(q32;q21). Array comparative genomic hybridization revealed distinct chromosome breakpoints within the RARA and oligonucleotide/oligosaccharide-binding fold containing 2A (OBFC2A) genes.

Molecular cytogenetic and clinical characterization of a patient with a 5.6-Mb deletion in 7p15 including HOXA cluster.

Here, we describe the clinical features of a boy with a 5.6-Mb deletion at chromosome 7p15.1-p15.

[Identification of a novel deletion region in 3q29 microdeletion syndrome by oligonucleotide array comparative genomic hybridization].

Background: The 3q29 microdeletion syndrome is a genomic disorder characterized by mental retardation, developmental delay, microcephaly, and slight facial dysmorphism. In most cases, the microdeletion spans a 1.6-Mb region between low-copy repeats (LCRs).