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Background@#The three best-known NUP214 rearrangements found in leukemia (SET::NUP214, NUP214::ABL1, and DEK::NUP214) are associated with treatment resistance and poor prognosis. Mouse experiments have shown that NUP214 rearrangements alone are insufficient for leukemogenesis; therefore, the identification of concurrent mutations is important for accurate assessment and tailored patient management. Here, we characterized the demographic characteristics and concurrent mutations in patients harboring NUP214 rearrangements. @*Methods@#To identify patients with NUP214 rearrangements, RNA-sequencing results of diagnostic bone marrow aspirates were retrospectively studied. Concurrent targeted nextgeneration sequencing results, patient demographics, karyotypes, and flow cytometry information were also reviewed. @*Results@#In total, 11 patients harboring NUP214 rearrangements were identified, among whom four had SET::NUP214, three had DEK::NUP214, and four had NUP214::ABL1. All DEK::NUP214-positive patients were diagnosed as having AML. In patients carrying SET::NUP214 and NUP214::ABL1, T-lymphoblastic leukemia was the most common diagnosis (50%, 4/8). Concurrent gene mutations were found in all cases. PFH6 mutations were the most common (45.5%, 5/11), followed by WT1 (27.3%, 3/11), NOTCH1 (27.3%, 3/11), FLT3-internal tandem duplication (27.3%, 3/11), NRAS (18.2%, 2/11), and EZH2 (18.2%, 2/11) mutations. Two patients represented the second and third reported cases of NUP214::ABL1-positive AML. @*Conclusions@#We examined the characteristics and concurrent test results, including gene mutations, of 11 leukemia patients with NUP214 rearrangement. We hope that the elucidation of the context in which they occurred will aid future research on tailored monitoring and treatment.
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Background@#Structural variants (SVs) are currently analyzed using a combination of conventional methods; however, this approach has limitations. Optical genome mapping (OGM), an emerging technology for detecting SVs using a single-molecule strategy, has the potential to replace conventional methods. We compared OGM with conventional diagnostic methods for detecting SVs in various hematologic malignancies. @*Methods@#Residual bone marrow aspirates from 27 patients with hematologic malignancies in whom SVs were observed using conventional methods (chromosomal banding analysis, FISH, an RNA fusion panel, and reverse transcription PCR) were analyzed using OGM. The concordance between the OGM and conventional method results was evaluated. @*Results@#OGM showed concordance in 63% (17/27) and partial concordance in 37% (10/27) of samples. OGM detected 76% (52/68) of the total SVs correctly (concordance rate for each type of SVs: aneuploidies, 83% [15/18]; balanced translocation, 80% [12/15] unbalanced translocation, 54% [7/13] deletions, 81% [13/16]; duplications, 100% [2/2] inversion 100% [1/1]; insertion, 100% [1/1]; marker chromosome, 0% [0/1];isochromosome, 100% [1/1]). Sixteen discordant results were attributed to the involvement of centromeric/telomeric regions, detection sensitivity, and a low mapping rate and coverage. OGM identified additional SVs, including submicroscopic SVs and novel fusions, in five cases. @*Conclusions@#OGM shows a high level of concordance with conventional diagnostic methods for the detection of SVs and can identify novel variants, suggesting its potential utility in enabling more comprehensive SV analysis in routine diagnostics of hematologic malignancies, although further studies and improvements are required.
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Purpose@#We designed and evaluated the clinical performance of a plasma circulating tumor DNA (ctDNA) panel of 112 genes in various subtypes of lymphoma. @*Materials and Methods@#Targeted deep sequencing with an error-corrected algorithm was performed in ctDNA from plasma samples that were collected before treatment in 42 lymphoma patients. Blood buffy coat was utilized as a germline control. We evaluated the targeted gene panel using mutation detection concordance on the plasma samples with matched tissue samples analyzed the mutation profiles of the ctDNA. @*Results@#Next-generation sequencing analysis using matched tissue samples was available for 18 of the 42 patients. At least one mutation was detected in the majority of matched tissue biopsy samples (88.9%) and plasma samples (83.3%). A considerable number of mutations (40.4%) that were detected in the tissue samples were also found in the matched plasma samples. Majority of patients (21/42) were diffuse large B cell lymphoma patients. The overall detection rate of ctDNA in patients was 85.7% (36/42). The frequently mutated genes included PIM1, TET2, BCL2, KMT2D, KLHL6, HIST1H1E, and IRF8. A cutoff concentration (4,506 pg/mL) of ctDNA provided 88.9% sensitivity and 82.1% specificity to predict ctDNA mutation detection. The ctDNA concentration correlated with elevated lactate dehydrogenase level and the disease stage. @*Conclusion@#Our design panel can detect many actionable gene mutations, including those at low frequency. Therefore, liquid biopsy can be applied clinically in the evaluation of lymphoma patients, especially in aggressive lymphoma patients.
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Background@#AML is a heterogeneous disease, and despite intensive therapy, recurrence is still high in AML patients who achieve the criterion for cytomorphologic remission (residual tumor burden [measurable residual disease, MRD]0.99). The test reproducibly detected MRD in three dilution series samples, with a sensitivity of 0.25% for single-nucleotide variants. More than half of samples from patients with morphologic remission after one month of chemotherapy had detectable mutations. NGS-MRD positivity for samples collected after one month of chemotherapy tended to be associated with poor overall survival and progression-free survival. @*Conclusions@#Our highly sensitive and accurate NGS-MRD panel can be readily used to monitor most AML patients in clinical practice, including patients without gene rearrangement. In addition, this NGS-MRD panel may allow the detection of newly emerging clones during clinical relapse, leading to more reliable prognoses of AML.
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Background@#The incidence of early- and late-onset sepsis and meningitis in neonates due to maternal rectovaginal group B Streptococcus (GBS) colonization may differ with serotype distribution and clonal complex (CC). CC17 strains are associated with hypervirulence and poor disease outcomes. GBS serotypes are distinguished based on the polysaccharide capsule, the most important virulence factor. We determined the sequence type distribution of GBS isolates from pregnant women in Korea and validated whole-genome sequencing (WGS)-based prediction of antimicrobial susceptibility and capsular serotypes in GBS isolates. @*Methods@#Seventy-five GBS isolates collected from pregnant Korean women visiting Wonju Severance Christian Hospital, Wonju, Korea between 2017 and 2019 were subjected to WGS using the NovaSeq 6000 system (Illumina, San Diego, CA, USA). Multilocus sequence types, serotypes, antimicrobial resistance genes, and hemolysin operon mutations were determined by WGS, and the latter three were compared with the results of conventional phenotypic methods. @*Results@#The predominant lineage was CC1 (37.3%), followed by CC19 (32.0%), CC12 (17.3%), and CC17 (4.0%). All isolates were cps typeable (100%, (75/75), and 89.3% of cps genotypes (67/75) were concordant with serotypes obtained using latex agglutination. The cps genotypes of the 75 isolates were serotypes III (24.0%), V (22.7%), and VIII (17.3%). All isolates harboring intact ermB and tet were non-susceptible to erythromycin and tetracycline, respectively. Three non-hemolytic strains had 1-bp frameshift insertions in cylE. @*Conclusions@#The low prevalence of CC17 GBS colonization may explain the low frequency of neonatal GBS infections. WGS is a useful tool for simultaneous genotyping and antimicrobial resistance determination.
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Background@#Pheochromocytoma and paragangliomas (PPGL) are hereditary in approximately 30% to 40% cases. With the advancement of genetic analysis techniques, including next-generation sequencing (NGS), there were attempts to classify PPGL into molecular clusters. With NGS being applied to clinical settings recently, we aimed to review the results of genetic analysis, including NGS, and investigate the association with clinical characteristics in Korean PPGL patients. @*Methods@#We reviewed the medical records of PPGL patients who visited Severance hospital from 2006 to 2019. We documented the clinical phenotype of those who underwent targeted NGS or had known germline mutations of related genes. @*Results@#Among 57 PPGL patients, we found 28 pathogenic germline mutations of susceptibility genes. Before the targeted NGS was implemented, only obvious syndromic feature lead to the Sanger sequencing for the specific genes. Therefore, for the exact prevalence, only patients after the year 2017, when targeted NGS was added, were included (n=43). The positive germline mutations were found in 14 patients; thus, the incidence rate is 32.6%. Patients with germline mutations had a higher likelihood of family history. There were significant differences in the type of PPGLs, percentage of family history, metastasis rate, presence of other tumors, and biochemical profile among three molecular clusters: pseudohypoxic tricarboxylic acid cycle-related, pseudohypoxic von Hippel-Lindau (VHL)/endothelial PAS domain-containing protein 1-related, and kinase-signaling group. Germline mutations were identified in seven PPGL-related genes (SDHB, RET, VHL, NF1, MAX, SDHA, and SDHD). @*Conclusion@#We report the expected prevalence of germline mutations in Korean PPGL patients. NGS is a useful and accessible tool for genetic analysis in patients with PPGLs, and further research on molecular classification is needed for precise management.
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Background@#Pheochromocytoma and paragangliomas (PPGL) are hereditary in approximately 30% to 40% cases. With the advancement of genetic analysis techniques, including next-generation sequencing (NGS), there were attempts to classify PPGL into molecular clusters. With NGS being applied to clinical settings recently, we aimed to review the results of genetic analysis, including NGS, and investigate the association with clinical characteristics in Korean PPGL patients. @*Methods@#We reviewed the medical records of PPGL patients who visited Severance hospital from 2006 to 2019. We documented the clinical phenotype of those who underwent targeted NGS or had known germline mutations of related genes. @*Results@#Among 57 PPGL patients, we found 28 pathogenic germline mutations of susceptibility genes. Before the targeted NGS was implemented, only obvious syndromic feature lead to the Sanger sequencing for the specific genes. Therefore, for the exact prevalence, only patients after the year 2017, when targeted NGS was added, were included (n=43). The positive germline mutations were found in 14 patients; thus, the incidence rate is 32.6%. Patients with germline mutations had a higher likelihood of family history. There were significant differences in the type of PPGLs, percentage of family history, metastasis rate, presence of other tumors, and biochemical profile among three molecular clusters: pseudohypoxic tricarboxylic acid cycle-related, pseudohypoxic von Hippel-Lindau (VHL)/endothelial PAS domain-containing protein 1-related, and kinase-signaling group. Germline mutations were identified in seven PPGL-related genes (SDHB, RET, VHL, NF1, MAX, SDHA, and SDHD). @*Conclusion@#We report the expected prevalence of germline mutations in Korean PPGL patients. NGS is a useful and accessible tool for genetic analysis in patients with PPGLs, and further research on molecular classification is needed for precise management.
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Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS), which is caused by mutations in SACS gene, is a very rare neurodegenerative disorder characterized by the clinical triad of early onset cerebellar ataxia, pyramidal tract features, and sensorimotor polyneuropathy. Herein, we report a 35-year-old Korean male who presented with gait disturbance and lower extremity weakness. Neuroimaging and ophthalmologic evaluation revealed features consistent with ARSACS. Mutation in SACS gene was demonstrated in clinical exome sequence analysis and the patient was finally diagnosed as ARSACS.
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Adulto , Humanos , Masculino , Ataxia , Ataxia Cerebelosa , Exoma , Marcha , Extremidad Inferior , Espasticidad Muscular , Enfermedades Neurodegenerativas , Neuroimagen , Polineuropatías , Tractos Piramidales , Análisis de Secuencia , Degeneraciones EspinocerebelosasRESUMEN
PURPOSE@#Mutations in the cyclin-dependent kinase-like 5 (CDKL5) gene are associated with epileptic encephalopathy and severe cognitive impairment. We aim to characterize the association between this gene and treatment efficacy.@*METHODS@#We retrospectively analyzed 10 patients who were treated at Severance Children's Hospital for epileptic encephalopathy who were subsequently diagnosed with a CDKL5 mutation using next-generation sequencing.@*RESULTS@#Electroencephalography (EEG) results showed generalized pattern abnormalities in 60% (6/10) of patients with CDKL5 mutations. We analyzed the effects of three treatments, namely antiepileptic drugs (AEDs), ketogenic diet (KD), and steroids. A more than 50% reduction in seizures was observed in 12% (1/8) of patients treated with clobazam. KD treatment proved ineffective in most cases. In addition, a more than 50% reduction in seizures was observed in 57% (4/7) of patients treated with steroids. EEG analysis of patients treated effectively with steroids revealed that 75% (3/4) showed hypsarrhythmia and 25% (1/4) showed focal epileptiform.@*CONCLUSION@#In this study, as in other studies, AEDs and KD did not effectively control seizures in most patients with a CDKL5 mutation. However, steroid therapy reduced the frequency of seizures in patients who also exhibited hypsarrhythmia. This suggests that steroid treatment is helpful in cases of hypsarrhythmia with CDKL5 mutations.
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In both 2016 and 2017, the cytogenetic and molecular cytogenetic programs conducted three assessments for the Korean Association of External Quality Assessment Service. A total of six cases with chromosomal aberrations were distributed in 2016, and nine cases were examined in 2017 in the chromosome surveys. For the fluorescence in situ hybridization surveys, six cases and nine cases were assessed in 2016 and 2017, respectively. A total of 38 laboratories in 2016 and 39 laboratories in 2017 participated in the cytogenetics program. In the molecular cytogenetics program, a total of 32 laboratories participated in 2016, and 31 laboratories participated in 2017. Most of the participating laboratories showed acceptable results for the cytogenetics and molecular cytogenetics programs. For the unacceptable results, there were various annotation errors, suggesting the need for continuous education and quality control.
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Aberraciones Cromosómicas , Citogenética , Educación , Fluorescencia , Hibridación in Situ , Corea (Geográfico) , Ensayos de Aptitud de Laboratorios , Control de CalidadRESUMEN
KBG syndrome is a rare neurodevelopmental disorder characterized by intellectual disability, skeletal anomalies, short stature, craniofacial dysmorphism, and macrodontia. ANKRD11 gene mutation and 16q24.3 microdeletion have been reported to cause KBG syndrome. Here, we report two patients with ANKRD11 mutations who initially presented with neurologic symptoms such as developmental delay and seizures. Patient 1 was a 23-month-old boy who presented with a global developmental delay. Language delay was the most dominant feature. He had hypertelorism, hearing impairment, and behavior problems characterized as hyperactivity. A c.1903_1907delAAACA (p.Lys635GInfsTer26) mutation in ANKRD11 was identified with diagnostic exome sequencing. Patient 2 was a 14-month-old boy with developmental delay and seizure. He also had atrial septum defect, and ventricular septal defect. Generalized tonic seizures began at the age of 8 months. Electroencephalography showed generalized sharp and slow wave pattern. Seizures did not respond to antiepileptic drugs. A loss of function mutation c.5350_5351delTC (p.ser1784HisfsTer12) in ANKRD11 was identified with diagnostic exome sequencing. In both cases, characteristic features of KBG syndrome such as short stature or macrodontia, were absent, and they visited the hospital due to neurological symptoms. These findings suggest that more patients with mild phenotypes of KBG syndrome are being recognized with advances in diagnostic exome sequencing genetic technologies.
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Humanos , Lactante , Masculino , Anticonvulsivantes , Tabique Interatrial , Discapacidades del Desarrollo , Diagnóstico Precoz , Electroencefalografía , Exoma , Pérdida Auditiva , Defectos del Tabique Interventricular , Hipertelorismo , Discapacidad Intelectual , Trastornos del Desarrollo del Lenguaje , Trastornos del Neurodesarrollo , Manifestaciones Neurológicas , Fenotipo , ConvulsionesRESUMEN
Minimal residual disease (MRD) following B-lymphoblastic leukemia (B-ALL) treatment has gained prognostic importance. Clonal immunoglobulin heavy chain (IGH) gene rearrangement is a useful follow-up marker in B-ALL owing to its high positivity rate. We evaluated the performance and clinical applicability of a next-generation sequencing (NGS) assay for IGH rearrangement in B-ALL MRD monitoring. IGH rearrangement was tested by using fluorescence PCR-fragment analysis and the NGS assay in eight B-ALL patients. The NGS assay was run on two platforms: the Ion Torrent PGM (Thermo Fisher Scientific, USA) (18 samples from 1st to 7th patients) and the MiSeq system (Illumina, USA) (four samples from 8th patient). All initial diagnostic samples and four follow-up samples were positive for clonal IGH rearrangement with fluorescence PCR-fragment analysis and the NGS assay, and six follow-up samples were positive only with NGS. In one case with BCR-ABL1 translocation, BCR-ABL1 quantitative PCR was negative but the NGS IGH assay was positive just prior to full-blown relapse, suggesting the high sensitivity and clinical utility of the NGS assay. The NGS assay is proposed for MRD monitoring in B-ALL Additional studies are needed to confirm the clinical implications of cases showing positive results only in NGS.
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Humanos , Fluorescencia , Estudios de Seguimiento , Reordenamiento Génico , Cadenas Pesadas de Inmunoglobulina , Inmunoglobulinas , Leucemia , Neoplasia Residual , Reacción en Cadena de la Polimerasa , RecurrenciaRESUMEN
No abstract available.
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Anciano , Humanos , Masculino , Citidina Desaminasa/genética , Dasatinib/uso terapéutico , Progresión de la Enfermedad , Resistencia a Antineoplásicos , Proteínas de Fusión bcr-abl/genética , Mesilato de Imatinib/uso terapéutico , Hibridación Fluorescente in Situ , Cariotipo , Leucemia Mielógena Crónica BCR-ABL Positiva/tratamiento farmacológico , Proteínas de Microfilamentos/genética , Proteínas Oncogénicas/genética , Inhibidores de Proteínas Quinasas/uso terapéuticoRESUMEN
No abstract available.
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Anciano , Femenino , Humanos , Protocolos de Quimioterapia Combinada Antineoplásica/efectos adversos , Células de la Médula Ósea/citología , Citometría de Flujo , Proteínas de Fusión bcr-abl/genética , Factor Estimulante de Colonias de Granulocitos/uso terapéutico , Inmunofenotipificación , Leucemia/diagnóstico , Linfoma de Células B Grandes Difuso/tratamiento farmacológico , Fenotipo , Rituximab/administración & dosificaciónRESUMEN
Epilepsy of infancy with migrating focal seizure (MFEI) is an early-onset epileptic encephalopathy characterized by randomly migrating focal seizures and psychomotor deterioration. It is associated with mutations in a variety of genes, with potassium sodium-activated channel subfamily T member 1 (KCNT1) being an example. Previously reported KCNT1 mutations in MFEI are gain-of-function mutations. Therefore, quinidine therapy targeted at reduction of pathologically increased KCNT1 channel-mediated potassium conductance has been proposed as a target treatment for MEFI with KCNT1 mutation. The authors report a case involving a patient with MFEI and a missense mutation in KCNT1 (c.7129G>A; p.Phe346Leu) treated with quinidine therapy. Seizure activity was poorly responsive to quinidine.
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Humanos , Encefalopatías , Epilepsia , Mutación Missense , Potasio , Quinidina , ConvulsionesRESUMEN
BACKGROUND: Grafts survive despite blood group antigens on the transplant being continuously exposed to antibodies in the blood of recipients in ABO-incompatible kidney transplantation (ABOi KT), owing to the mechanism of accommodation. We analyzed the immunodynamics of soluble ABH antigens in allografts from secretor donors and the influence of such immunodynamics on accommodation and subsequent graft survival in ABOi KT. METHODS: The genotype of a known human β-galactoside α-1,2-fucosyltransferase gene (FUT2), which determines soluble ABH antigen secretor status, was established in 32 donors for ABOi KT at the Severance Hospital, from June 2010 to July 2015. Clinical outcomes of recipients, such as anti-A/B antibody titer change, renal function, and graft survival, were evaluated. RESULTS: Twenty-five donors were secretors (78.1%), and seven were nonsecretors (21.9%). The frequency of anti-A/B IgG or IgM antibody titer elevation or reduction post-transplantation was not significantly related to donor secretor status. However, IgM titer was rapidly reduced in recipients transplanted from nonsecretor donors (P=0.01), which could be explained by the lack of absorption effect of soluble antigens, enhancing the binding of antibodies to antigens in the allografts. Interestingly, soluble ABH antigens did not affect rejection-free graft survival, which may be due to the nature of β-galactoside α-1,2-fucosyltransferase. CONCLUSIONS: Soluble ABH antigens produced by transplanted kidneys from secretor donors played a role in inducing accommodation within three months of KT through neutralization; however, major graft outcomes were not affected.
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Humanos , Absorción , Aloinjertos , Anticuerpos , Antígenos de Grupos Sanguíneos , Incompatibilidad de Grupos Sanguíneos , Genotipo , Supervivencia de Injerto , Inmunoglobulina G , Inmunoglobulina M , Trasplante de Riñón , Riñón , Donantes de Tejidos , TrasplantesRESUMEN
PURPOSE: We evaluated the clinical role of rapid next-generation sequencing (NGS) for identifying BRCA1/2 mutations compared to traditional Sanger sequencing. METHODS: Twenty-four paired samples from 12 patients were analyzed in this prospective study to compare the performance of NGS to the Sanger method. Both NGS and Sanger sequencing were performed in 2 different laboratories using blood samples from patients with breast cancer. We then analyzed the accuracy of NGS in terms of variant calling and determining concordance rates of BRCA1/2 mutation detection. RESULTS: The overall concordance rate of BRCA1/2 mutation identification was 100%. Variants of unknown significance (VUS) were reported in two cases of BRCA1 and 3 cases of BRCA2 after Sanger sequencing, whereas NGS reported only 1 case of BRCA1 VUS, likely due to differences in reference databases used for mutation identification. The median turnaround time of Sanger sequencing was 22 days (range, 14–26 days), while the median time of NGS was only 6 days (range, 3–21 days). CONCLUSION: NGS yielded comparably accurate results to Sanger sequencing and in a much shorter time with respect to BRCA1/2 mutation identification. The shorter turnaround time and higher accuracy of NGS may help clinicians make more timely and informed decisions regarding surgery or neoadjuvant chemotherapy in patients with breast cancer.
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Humanos , Neoplasias de la Mama , Mama , Toma de Decisiones Clínicas , Quimioterapia , Secuenciación de Nucleótidos de Alto Rendimiento , Métodos , Estudios ProspectivosRESUMEN
No abstract available.
