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Genomic structural variations in myeloid, lymphoid, and plasma cell neoplasms can provide key diagnostic, prog‑ nostic, and therapeutic information while elucidating the underlying disease biology. Several molecular diagnostic approaches play a central role in evaluating hematological malignancies. Traditional cytogenetic diagnostic assays, such as chromosome banding and fluorescence in situ hybridization, are essential components of the current diag‑ nostic workup that guide clinical care for most hematologic malignancies. However, each assay has inherent limita‑ tions, including limited resolution for detecting small structural variations and low coverage, and can only detect alterations in the target regions. Recently, the rapid expansion and increasing availability of novel and comprehensive genomic technologies have led to their use in clinical laboratories for clinical management and translational research.This review aims to describe the clinical relevance of structural variations in hematologic malignancies and introduce genomic technologies that may facilitate personalized tumor characterization and treatment.
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Background@#Clonal hematopoiesis of indeterminate potential (CHIP), which is defined as the presence of blood cells originating from somatically mutated hematopoietic stem cells, is common among the elderly and is associated with an increased risk of hematologic malignancies. We investigated the clinical, mutational, and transcriptomic characteristics in elderly Korean individuals with CHIP mutations. @*Methods@#We investigated CHIP in 90 elderly individuals aged ≥60 years with normal complete blood counts at a tertiary-care hospital in Korea between June 2021 and February 2022. Clinical and laboratory data were prospectively obtained. Targeted next-generation sequencing of 49 myeloid malignancy driver genes and massively parallel RNA sequencing were performed to explore the molecular spectrum and transcriptomic characteristics of CHIP mutations. @*Results@#We detected 51 mutations in 10 genes in 37 (41%) of the study individuals. CHIP prevalence increased with age. CHIP mutations were observed with high prevalence in DNMT3A (26 individuals) and TET2 (eight individuals) and were also found in various other genes, including KDM6A, SMC3, TP53, BRAF, PPM1D, SRSF2, STAG1, and ZRSR2. Baseline characteristics, including age, confounding diseases, and blood cell parameters, showed no significant differences. Using mRNA sequencing, we characterized the altered gene expression profile, implicating neutrophil degranulation and innate immune system dysregulation. @*Conclusions@#Somatic CHIP driver mutations are common among the elderly in Korea and are detected in various genes, including DNMT3A and TET2. Our study highlights that chronic dysregulation of innate immune signaling is associated with the pathogenesis of various diseases, including hematologic malignancies.
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Background@#To investigate the clinical findings of choroideremia patients and perform genetic analysis by whole-exome sequencing (WES). @*Methods@#A total of 94 patients initially diagnosed with retinitis pigmentosa (RP) at another hospital, and who visited our hospital for genetic analysis by WES, were included in the study, along with 64 family members. All subjects underwent comprehensive ophthalmic evaluation, including best-corrected visual acuity, slit lamp examination, fundus photography, fundus autofluorescence (FAF), fluorescein angiography (FAG), visual field (VF), electroretinogram (ERG), and optical coherence tomography (OCT). @*Results@#In six male patients with suspected choroideremia, extensive retinal pigment epithelium (RPE) and severe loss of choroid were observed in the fundus, but not in the macula. CHM gene mutation was confirmed in five patients. A novel single nucleotide variant at a splice site was observed in one patient. OCT showed marked thinning of the outernuclear layer and choroid, except in the macula. FAF showed a small area of hyperfluorescence in the posterior pole. In addition, characteristic interlaminar bridges were observed in four patients. On FAG, hypofluorescence was seen up to the far-peripheral retina in five patients. @*Conclusion@#Of the 94 patients initially diagnosed with RP, CHM mutation was identified in five (5.3%) by WES. Choroideremia should be considered as a differential diagnosis of RP.WES would be useful for identifying the causes of hereditary retinal disease.
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We present the case of a healthy 28-day-old female full-term neonate who was admitted to the neonatal intensive care unit for severe metabolic acidosis, hypoglycemia, and an initial sinus rhythm. The first diagnostic hypothesis was hypovolemic shock, and fluid resuscitation was started immediately. During fluid therapy, cardiovascular collapse occurred with supraventricular tachycardia. The latter was successfully treated with adenosine and beta-blockers. After 8 days, electrocardiography showed ventricular pre-excitation, and Wolff-Parkinson-White syndrome was diagnosed. A novel variant of the MYL2 gene that is related to hypertrophic cardiomyopathy and conduction defect was found after discharge. Cardiogenic shock should be considered, despite being a rare cause of shock in neonates.
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We present the case of a healthy 28-day-old female full-term neonate who was admitted to the neonatal intensive care unit for severe metabolic acidosis, hypoglycemia, and an initial sinus rhythm. The first diagnostic hypothesis was hypovolemic shock, and fluid resuscitation was started immediately. During fluid therapy, cardiovascular collapse occurred with supraventricular tachycardia. The latter was successfully treated with adenosine and beta-blockers. After 8 days, electrocardiography showed ventricular pre-excitation, and Wolff-Parkinson-White syndrome was diagnosed. A novel variant of the MYL2 gene that is related to hypertrophic cardiomyopathy and conduction defect was found after discharge. Cardiogenic shock should be considered, despite being a rare cause of shock in neonates.
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Kyphoscoliotic Ehlers-Danlos syndrome (kEDS) is an autosomal recessive connective tissue disorder characterized by muscular hypotonia, hyperextensible skin, skin fragility, joint hypermobility, and progressive kyphoscoliosis. The disorder results from a deficiency of the enzyme collagen lysyl hydroxylase 1 due to mutations in the gene PLOD1. We describe the rare cases of kEDS in Korean siblings with two novel compound heterozygous variants, c.926_934del (p.Leu309_Leu311del) and c.2170_2172del (p.Phe724del) in the PLOD1 gene. They had congenital hypotonia, joint laxity, skin hyperextensibility, Marfanoid habitus, high myopia and atrophic scarring. The younger sibling had an early-onset progressive kyphoscoliosis, while the older sibling showed mild scoliosis during childhood. Intrafamilial variability of the clinical severity and age of kyphoscoliosis onset observed in our cases.
ABSTRACT
Kyphoscoliotic Ehlers-Danlos syndrome (kEDS) is an autosomal recessive connective tissue disorder characterized by muscular hypotonia, hyperextensible skin, skin fragility, joint hypermobility, and progressive kyphoscoliosis. The disorder results from a deficiency of the enzyme collagen lysyl hydroxylase 1 due to mutations in the gene PLOD1. We describe the rare cases of kEDS in Korean siblings with two novel compound heterozygous variants, c.926_934del (p.Leu309_Leu311del) and c.2170_2172del (p.Phe724del) in the PLOD1 gene. They had congenital hypotonia, joint laxity, skin hyperextensibility, Marfanoid habitus, high myopia and atrophic scarring. The younger sibling had an early-onset progressive kyphoscoliosis, while the older sibling showed mild scoliosis during childhood. Intrafamilial variability of the clinical severity and age of kyphoscoliosis onset observed in our cases.
ABSTRACT
Kyphoscoliotic Ehlers-Danlos syndrome (kEDS) is an autosomal recessive connective tissue disorder characterized by muscular hypotonia, hyperextensible skin, skin fragility, joint hypermobility, and progressive kyphoscoliosis. The disorder results from a deficiency of the enzyme collagen lysyl hydroxylase 1 due to mutations in the gene PLOD1. We describe the rare cases of kEDS in Korean siblings with two novel compound heterozygous variants, c.926_934del (p.Leu309_Leu311del) and c.2170_2172del (p.Phe724del) in the PLOD1 gene. They had congenital hypotonia, joint laxity, skin hyperextensibility, Marfanoid habitus, high myopia and atrophic scarring. The younger sibling had an early-onset progressive kyphoscoliosis, while the older sibling showed mild scoliosis during childhood. Intrafamilial variability of the clinical severity and age of kyphoscoliosis onset observed in our cases.
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BACKGROUND@#Poor reporting quality in diagnostic accuracy studies hampers an adequate judgment of the validity of the study. The Standards for Reporting of Diagnostic Accuracy Studies (STARD) statement was published to improve the reporting quality of diagnostic accuracy studies. This study aimed to evaluate the adherence of diagnostic accuracy studies published in Annals of Laboratory Medicine (ALM) to STARD 2015 and to identify directions for improvement in the reporting quality of these studies.@*METHODS@#Two independent authors assessed articles published in ALM between 2012–2018 for compliance with 30 STARD 2015 checklist items to identify all eligible diagnostic accuracy studies published during this period. We included 66 diagnostic accuracy studies. A total of the fulfilled STARD items were calculated, and adherence was analyzed on an individual-item basis.@*RESULTS@#The overall mean±SD number of STARD items reported for the included studies was 11.2±2.7. Only five (7.6%) studies adhered to more than 50% of the 30 items. No study satisfied more than 80% of the items. Large variability in adherence to reporting standards was detected across items, ranging from 0% to 100%.@*CONCLUSIONS@#Adherence to STARD 2015 is suboptimal among diagnostic accuracy studies published in ALM. Our study emphasizes the necessity of adherence to STARD to improve the reporting quality of future diagnostic accuracy studies to be published in ALM.
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Philadelphia-negative (Ph−) classical myeloproliferative neoplasms (MPNs) include polycythemia vera, essential thrombocythemia (ET), and primary myelofibrosis. Somatic driver mutations in the JAK2, CALR, and MPL genes serve as major diagnostic criteria of the Ph− MPNs and these mutations occur in a mutually exclusive manner. In this report, we describe the first case of ET harboring double mutations in JAK2 V617F and MPL. For MPL, the patient had multiple clones of MPL mutations: c.1543_1546delinsAGGG (p.Trp515_Gln516delinsArgGlu) and c.1546C>G (p.Gln516Glu). The JAK2 V617F allele burden in our patient is very low (4%) compared to the relatively high (17%–78%) allele frequency of MPL mutations. The low JAK2 mutant burden might be explained by preexisting clonal hematopoiesis before overt signs of MPNs, followed by the acquisition of a second oncogenic mutation of CALR or MPL leading to the MPN phenotype. This highlights that screening for a second driver mutation should be considered in patients with a low JAK2 mutant burden by reporting a 57-year-old Korean man with ET.
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Myeloproliferative neoplasms (MPNs) are a heterogeneous group of clonal disorders characterized by the overproduction of mature blood cells that have an increased risk of thrombosis and progression to acute myeloid leukemia. Next-generation sequencing studies have provided key insights regarding the molecular mechanisms of MPNs. MPN driver mutations in genes associated with the JAK-STAT pathway include JAK2 V617F, JAK2 exon 12 mutations and mutations in MPL, CALR, and CSF3R. Cooperating driver genes are also frequently detected and also mutated in other myeloid neoplasms; these driver genes are involved in epigenetic methylation, messenger RNA splicing, transcription regulation, and signal transduction. In addition, other genetic factors such as germline predisposition, order of mutation acquisition, and variant allele frequency also influence disease initiation and progression. This review summarizes the current understanding of the genetic basis of MPN, and demonstrates how molecular pathophysiology can improve both our understanding of MPN heterogeneity and clinical practice.
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Background@#The Laboratory Medicine Foundation (LMF) checklists explain the accreditation requirements of the program and reflect quality standards like those of the Clinical Laboratory Standards Institute (CLSI) or quality system essentials (QSE) of the World Health Organization (WHO). In this study, we have analyzed how the LMF checklists correlate with the 12 QSE elements of the WHO. @*Methods@#The LMF checklists for laboratory management (LM) (version 2019) were classified into the 12 specific QSE elements by five laboratory physicians. Each checklist item was classified into specific element if four or more participants agreed, and into overlapping elements when two or more of them agreed for two different items. Any changes in checklist items and chapter structuring of the checklist since 2009 were investigated. @*Results@#The LM checklists consisted of 183 checklist items, including 20 (10.9%) classified into overlapping QSE elements. The QSE element with the highest number of items was the facilities and safety (62, 33.9%), followed by the personnel (22, 12.0%), and the process control (17, 9.3%). In contrast, QSE elements with the lowest number of items were the customer service (4, 2.2%) and process improvement (4, 2.2%). Items belonging to the customer service and the organization elements have increased since 2017. @*Conclusions@#The LMF checklists reflect current quality goals for clinical laboratories and play a leading role in the laboratory's quality improvement. The results of our study will be of help in potentiating the quality leader role of LMF checklists, and international harmonization of our laboratory accreditation program.
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This erratum is being published to revise the website address of the Korean Reference Genome Database (KRGDB) and correct two typographical errors in the article.
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Cytogenetic dosimetry is useful for evaluating the absorbed dose of ionizing radiation based on analysis of radiation-induced chromosomal aberrations. We created two types of in vitro dose-response calibration curves for dicentric chromosomes (DC) and translocations (TR) induced by X-ray irradiation, using an electron linear accelerator, which is the most frequently used medical device in radiotherapy. We irradiated samples from four healthy Korean individuals and compared the resultant curves between individuals. Aberration yields were studied in a total of 31,800 and 31,725 metaphases for DC and TR, respectively, obtained from 11 X-ray irradiation dose-points (0, 0.05, 0.1, 0.25, 0.5, 0.75, 1, 2, 3, 4, and 5 Gy). The dose-response relationship followed a linear-quadratic equation, Y=C+αD+βD², with the coefficients C=0.0011 for DC and 0.0015 for TR, α=0.0119 for DC and 0.0048 for TR, and β=0.0617 for DC and 0.0237 for TR. Correlation coefficients between irradiation doses and chromosomal aberrations were 0.971 for DC and 0.6 for TR, indicating a very strong and a moderate correlation, respectively. This is the first study implementing cytogenetic dosimetry following exposure to ionizing X-radiation.
Subject(s)
Calibration , Chromosome Aberrations , Cytogenetics , In Vitro Techniques , Particle Accelerators , Radiation, Ionizing , RadiotherapyABSTRACT
BACKGROUND: False-positive fecal immunochemical test (FIT) results in the National Cancer Screening Program (NCSP) for colorectal cancer may lead to unnecessary procedures, such as colonoscopies, increasing the medical costs. We estimated reductions in the cost of National Health Insurance according to the accreditation status of screening facilities participating in the NCSP for colorectal cancer. METHODS: We used data collected between 2007 and 2010 from NCSP and the Korea Central Cancer Registry to identify patients with colorectal cancer. We also ascertained the history of the accreditation of each facility by the Korean Laboratory Accreditation Program (KLAP). Budget impact was defined as a reduction in medical costs achieved when the false-positive rate of the non-accredited facilities decreased relative to that of the accredited facilities. RESULTS: A total of 3,285 screening facilities participated in the NCSP. Of these, 196 were accredited by the KLAP. The false-positive rate of the accredited facilities was 2.47%, and that of the non-accredited facilities was 6.83%. Medical costs were estimated to be reduced by approximately 19 million US dollars (USD), and the cost of detecting one case of colorectal cancer was estimated to decrease from 9,212 USD to 7,332 USD if the false-positive rate of non-accredited facilities were decreased to that of the accredited facilities. Clinics were estimated to have the largest associated cost reduction. CONCLUSIONS: Quality assurance in clinical laboratories could lower false-positive rates and prevent the use of unnecessary procedures, ensuring patient safety and increasing the cost-effectiveness of FIT screening in the NCSP for colorectal cancer.
Subject(s)
Humans , Accreditation , Budgets , Colonoscopy , Colorectal Neoplasms , Early Detection of Cancer , Korea , Mass Screening , National Health Programs , Patient Safety , Quality Improvement , Unnecessary ProceduresABSTRACT
BACKGROUND: The identification of genetic abnormalities in patients with multiple myeloma (MM) has gained emphasis because genetics-based risk stratification significantly affects overall survival (OS). We investigated genetic abnormalities using conventional cytogenetics and FISH and analyzed the prognostic significance of the identified additional abnormalities in MM. METHODS: In total, 267 bone marrow samples were collected from February 2006 to November 2013 from patients who were newly diagnosed as having MM in a tertiary-care hospital in Korea. The clinical and laboratory data were retrospectively obtained. Cox proportional hazard regression was used to examine the relationship between clinical/genetic factors and survival outcome, using univariate and multivariate models. RESULTS: Using conventional cytogenetic analysis and FISH, 45% (120/267) and 69% (183/267) patients, respectively, were identified to harbor genetic abnormalities. In the univariate analysis, the following genetic variables were identified to affect OS: abnormal karyotype (P 65 years) (P=0.013) with an HR of 2.505 (95% CI, 1.218–5.151). CONCLUSIONS: Our findings highlight the importance of applying a comprehensive approach for detecting genetic abnormalities, which could be closely associated with the prognostic significance of MM.
Subject(s)
Humans , Abnormal Karyotype , Aneuploidy , Bone Marrow , Cytogenetic Analysis , Cytogenetics , Korea , Multiple Myeloma , Multivariate Analysis , Prognosis , Retrospective StudiesABSTRACT
The World Health Organization (WHO) Classification of Tumors of Haematopoietic and Lymphoid Tissues was recently published in a revised fourth edition. The categories of myeloproliferative neoplasms (MPNs) have not significantly changed since the 2008 fourth edition of the classification; however, newly discovered mutations including CALR and CSF3R and improved characterizations and standardizations of morphological features of some entities, particularly BCR-ABL1-negative MPNs, have impacted the diagnostic criteria of disease entities, increasing the reliability and reproducibility of diagnoses. The 2017 revised edition attempts to incorporate new clinical, prognostic, morphologic, and genetic data that have emerged since the last edition. This article reviews the major changes in the classification and their rationale for MPN classification within the revised 2017 WHO system.