• Childhood Kidney Diseases
• /
• v.27 no.1
• /
• pp.11-18
• /
• 2023

Remarkable advances in genetic diagnosis expanded our knowledge about inherited tubulopathies and other genetic kidney diseases. This review suggests a simple categorization of inherited tubular disease, clarifies the concept of autosomal dominant tubulointerstitial kidney disease (ADTKD), and introduces novel therapies developed for tubulopathies. Facing patients with suspicious tubular disorders, clinicians should first evaluate the status of volume and acid-base. This step helps the clinicians to localize the affected segment and to confirm genetic diagnosis. ADTKD is a recently characterized disease entity involving tubules. The known causative genes are UMOD, MUC1, REN, and HNF1β. Still, only half of ADTKD patients show mutations for these four identified genes. Whole exome sequencing is a suitable diagnostic tool for tubulopathies, especially for ADTKD. Genetic approaches to treat tubulopathies have progressed recently. Despite the practical obstacles, novel therapies targeting inherited tubulopathies are currently in development.

• Genomics & Informatics
• /
• v.11 no.1
• /
• pp.46-51
• /
• 2013

Normal-karyotype acute myeloid leukemia (NK-AML) is a highly malignant and cytogenetically heterogeneous hematologic cancer. We searched for somatic mutations from 10 pairs of tumor and normal cells by using a highly efficient and reliable analysis workflow for whole-exome sequencing data and performed association tests between the NK-AML and somatic mutations. We identified 21 nonsynonymous single nucleotide variants (SNVs) located in a coding region of 18 genes. Among them, the SNVs of three leukemia-related genes (MUC4, CNTNAP2, and GNAS) reported in previous studies were replicated in this study. We conducted stepwise genetic risk score (GRS) models composed of the NK-AML susceptible variants and evaluated the prediction accuracy of each GRS model by computing the area under the receiver operating characteristic curve (AUC). The GRS model that was composed of five SNVs (rs75156964, rs56213454, rs6604516, rs10888338, and rs2443878) showed 100% prediction accuracy, and the combined effect of the three reported genes was validated in the current study (AUC, 0.98; 95% confidence interval, 0.92 to 1.00). Further study with large sample sizes is warranted to validate the combined effect of these somatic point mutations, and the discovery of novel markers may provide an opportunity to develop novel diagnostic and therapeutic targets for NK-AML.

• Journal of Genetic Medicine
• /
• v.17 no.2
• /
• pp.89-91
• /
• 2020

Charcot-Marie-Tooth (CMT) disease can be divided mainly into demyelination and axonopathy based on the results of the electrophysiological study. Mitofusin 2, encoded by MFN2 gene, has a crucial role in the fusion of mitochondria, which is known to associate with CMT type 2A as one of the axonal forms. We describe a 44-year-old man with progressive weakness on bilateral legs after noticing foot drop in his early teen. When we examined him at 45 years of age, he presented atrophy on entire legs and with distal muscle weakness on limbs. The nerve conduction study revealed severely decreased amplitude on motor nerve ranging from 0.2 to 4.5 mV, while conduction velocity remained more than 30.4 m/s. The whole-exome sequencing revealed a novel variant c.2228G>T in MFN2 by efficient genetic analysis tool, MutationDistiller. This report will not only expand the mutation spectrum of CMT2A but also introduce a time-saving genetic analysis tool.

• Childhood Kidney Diseases
• /
• v.25 no.2
• /
• pp.128-132
• /
• 2021

Morning glory syndrome (MGS) is a rare congenital optic disc anomaly with a characteristic fundal finding with severe visual impairment. It may occur in association with various systemic manifestations, even though most of the reported cases were isolated. A 6-year-old male visited the nephrology clinic with a history of microscopic hematuria and at the age of 12 years, he was diagnosed thin glomerular basement membrane nephropathy by kidney biopsy. After the following years, the patient had progressive deterioration of visual acuity, and diagnosed as MGS. Whole Exome Sequencing of this patient and his mother revealed heterozygous COL4A4 mutations [c.81_86del (p.Ile29_Leu30del)]. It is more reasonable to consider MGS seen in this patient as a coincidental finding of autosomal dominant Alport syndrome. To our knowledge, this case represents the first case report of autosomal dominant Alport syndrome associated with MGS.

• Korean Journal of Agricultural Science
• /
• v.49 no.3
• /
• pp.595-606
• /
• 2022

Industrial pig breeding has used the Duroc breed and terminal sires in a three-way crossbred system in Korea. This study identified the gene variation patterns related to carcass quality in crossbred pigs ([Landrace × Yorkshire] × Duroc) using whole-exome sequencing (WES). This study used crossbred pigs and divided them into two groups (first plus grade, n = 5; second grade, n = 5). Genomic DNA samples extracted from the loin muscles of both groups were submitted for WES. A set of validated single-nucleotide polymorphisms (SNPs: n = 102) were also subjected to the Kompetitive allele-specific polymerase chain reaction (KASP) to confirm the WES results in the loin muscles. Based on the WES, SNPs associated with meat quality were found on chromosomes 5, 10, and 15. We identified variations in three of the candidate genes, including kinesin family member 5B (KIF5B), GLI family zinc finger 2 (GLI2), and KIF26B, that were associated with meat color, marbling score, and backfat thickness. These genes were associated with meat quality and the mitogen-activated protein kinase (MAPK) and Hedgehog (Hh) signaling pathways in the crossbred pigs. These results may help clarify the mechanisms underlying high-quality meat in pigs.

• Genomics & Informatics
• /
• v.19 no.1
• /
• pp.2.1-2.10
• /
• 2021

BRAF inhibitors (e.g., vemurafenib) are widely used to treat metastatic melanoma with the BRAF V600E mutation. The initial response is often dramatic, but treatment resistance leads to disease progression in the majority of cases. Although secondary mutations in the mitogen-activated protein kinase signaling pathway are known to be responsible for this phenomenon, the molecular mechanisms governing acquired resistance are not known in more than half of patients. Here we report a genome- and transcriptome-wide study investigating the molecular mechanisms of acquired resistance to BRAF inhibitors. A microfluidic chip with a concentration gradient of vemurafenib was utilized to rapidly obtain therapy-resistant clones from two melanoma cell lines with the BRAF V600E mutation (A375 and SK-MEL-28). Exome and transcriptome data were produced from 13 resistant clones and analyzed to identify secondary mutations and gene expression changes. Various mechanisms, including phenotype switching and metabolic reprogramming, have been determined to contribute to resistance development differently for each clone. The roles of microphthalmia-associated transcription factor, the master transcription factor in melanocyte differentiation/dedifferentiation, were highlighted in terms of phenotype switching. Our study provides an omics-based comprehensive overview of the molecular mechanisms governing acquired resistance to BRAF inhibitor therapy.

• Clinical and Experimental Pediatrics
• /
• v.63 no.6
• /
• pp.195-202
• /
• 2020

Developments in next-generation sequencing (NGS) techogies have assisted in clarifying the diagnosis and treatment of developmental delay/intellectual disability (DD/ID) via molecular genetic testing. Advances in DNA sequencing technology have not only allowed the evolution of targeted panels but also, and more currently enabled genome-wide analyses to progress from research era to clinical practice. Broad acceptance of accuracy-guided targeted gene panel, whole-exome sequencing (WES), and whole-genome sequencing (WGS) for DD/ID need prospective analyses of the increasing cost-effectiveness versus conventional genetic testing. Choosing the appropriate sequencing method requires individual planning. Data are required to guide best-practice recommendations for genomic testing, regarding various clinical phenotypes in an etiologic approach. Targeted panel testing may be recommended as a firsttier testing approach for children with DD/ID. Family-based trio testing by WES/WGS can be used as a second test for DD/ID in undiagnosed children who previously tested negative on a targeted panel. The role of NGS in molecular diagnostics, treatment, prediction of prognosis will continue to increase further in the coming years. Given the rapid pace of changes in the past 10 years, all medical providers should be aware of the changes in the transformative genetics field.

• Genomics & Informatics
• /
• v.15 no.4
• /
• pp.136-141
• /
• 2017

Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) <1% can be identified, and any mutation with >3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation.

• Journal of Yeungnam Medical Science
• /
• v.38 no.2
• /
• pp.160-164
• /
• 2021

Oculocutaneous albinism (OCA) is a group of rare genetically heterogeneous disorders, characterized by hypopigmentation of the eyes, skin, and hair, which result in ocular abnormalities and a risk of developing skin cancer. Currently, there is no ophthalmologic procedure or drug that prevents the clinical features of OCA. Here, we report a new type of OCA in two, unrelated Korean families with the same OCA2 mutation. Affected individuals in this study are different from those of previous reports in two aspects: an inheritance pattern and clinical presentation. All reported patients with OCA have shown an autosomal recessive inheritance pattern, while our patients showed an autosomal dominant inheritance pattern. Small amounts of pigment can be acquired with age in OCA, but there is no substantial variation from adolescence to adulthood in this regard. A case where the patient attained normal pigmentation levels has never been reported. However, our patients displayed completely normal pigmentation in their late twenties. Whole exome sequencing and in-silico analysis revealed a novel mutation, OCA2 c.2338G>A p.(G780S) (NM_000275) with a high likelihood of pathogenicity. Sanger sequencing of p.G780S identified the same mutation in the affected individuals, which was not found in the family members with normal phenotype. We hypothesize that OCA2 G780S not only acts as a pathogenic variant of OCA but also induces pigmentation by enhancing the melanogenesis gene expression of other modifier genes, such as SLC45A2 and TPC2. These findings may provide further understanding of melanin biosynthesis and new treatment methods for OCA.

• Journal of Life Science
• /
• v.24 no.3
• /
• pp.311-317
• /
• 2014

Distal myopathy with rimmed vacuoles (DMRV) or hereditary inclusion body myopathy 2 is an autosomal recessive muscular disorder characterized by early adult-onset weakness of distal muscles and rimmed vacuoles in muscle biopsy. Mutations in the UDP-N-acetylglucosamine 2-epimerase/N-ace-tylmannosamine kinase (GNE) gene are associated with the development of DMRV. In this study, whole exome sequencing (WES) revealed compound heterozygous GNE mutations of p.Asp176Val and p.Val572Leu in a patient with distal limb weakness. Three hundred healthy controls did not show these mutations. All other variants found in distal myopathy-relevant genes were polymorphic. These findings confirmed that the patient had DMRV. This work underscores the usefulness of WES in improving the molecular diagnosis of myopathy.