27 results on '"Lee, Seung Tae"'
Search Results
2. Analysis of BRCA1/2 variants of unknown significance in the prospective Korean Hereditary Breast Cancer study.
- Author
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Kim JH, Park S, Park HS, Park JS, Lee ST, Kim SW, Lee JW, Lee MH, Park SK, Noh WC, Choi DH, Han W, and Jung SH
- Subjects
- Adult, Breast Neoplasms epidemiology, Breast Neoplasms genetics, Female, Hereditary Breast and Ovarian Cancer Syndrome epidemiology, Hereditary Breast and Ovarian Cancer Syndrome genetics, Humans, Prospective Studies, Republic of Korea epidemiology, BRCA1 Protein genetics, BRCA2 Protein genetics, Breast Neoplasms pathology, Genetic Testing methods, Hereditary Breast and Ovarian Cancer Syndrome pathology, Mutation
- Abstract
Genetic testing for BRCA1 and BRCA2 is crucial in diagnosing hereditary breast and ovarian cancer syndromes and has increased with the development of multigene panel tests. However, results classified as variants of uncertain significance (VUS) present challenges to clinicians in attempting to choose an appropriate management plans. We reviewed a total of 676 breast cancer patients included in the Korean Hereditary Breast Cancer (KOHBRA) study with a VUS on BRCA mutation tests between November 2007 and April 2013. These results were compared to the ClinVar database. We calculated the incidence and odds ratios for these variants using the Korean Reference Genome Database. A total of 58 and 91 distinct VUS in BRCA1 and BRCA2 were identified in the KOHBRA study (comprising 278 and 453 patients, respectively). A total of 27 variants in the KOHBRA study were not registered in the Single Nucleotide Polymorphism database. Among BRCA1 VUSs, 20 were reclassified as benign or likely benign, four were reclassified as pathogenic or likely pathogenic, and eight remained as VUSs according to the ClinVar database. Of the BRCA2 VUSs, 25 were reclassified as benign or likely benign, two were reclassified as pathogenic or likely pathogenic, and 33 remained as VUS according to the ClinVar database. There were 12 variants with conflicting interpretations of pathogenicity for BRCA1 and 18 for BRCA2. Among them, p.Leu1780Pro showed a particularly high odds ratio. Six pathogenic variants and one conflicting variant identified using ClinVar could be reclassified as pathogenic variants in this study. Using updated ClinVar information and calculating odds ratios can be helpful when reclassifying VUSs in BRCA1/2.
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- 2021
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3. Mutant Thr95Ile Transthyretin-Related Cardiac Amyloidosis With Polyneuropathy.
- Author
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Kim K, Oh J, Lee ST, Shim HS, and Kang SM
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- Aged, Amyloid Neuropathies, Familial diagnostic imaging, Amyloid Neuropathies, Familial physiopathology, Amyloid Neuropathies, Familial therapy, Cardiomyopathies diagnostic imaging, Cardiomyopathies physiopathology, Cardiomyopathies therapy, Defibrillators, Implantable, Electric Countershock instrumentation, Genetic Predisposition to Disease, Humans, Male, Phenotype, Stroke Volume, Ventricular Dysfunction, Left diagnostic imaging, Ventricular Dysfunction, Left physiopathology, Ventricular Dysfunction, Left therapy, Ventricular Function, Left, Amyloid Neuropathies, Familial genetics, Cardiomyopathies genetics, Mutation, Prealbumin genetics, Ventricular Dysfunction, Left genetics
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- 2019
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4. Targeted panel sequencing identifies a novel NR2F1 mutations in a patient with Bosch-Boonstra-Schaaf optic atrophy syndrome.
- Author
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Park SE, Lee JS, Lee ST, Kim HY, Han SH, and Han J
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- Child, Developmental Disabilities genetics, Genetic Testing, Humans, Intellectual Disability genetics, Male, Optic Atrophy genetics, Prognosis, Vision, Low genetics, COUP Transcription Factor I genetics, Developmental Disabilities diagnosis, High-Throughput Nucleotide Sequencing methods, Intellectual Disability diagnosis, Mutation, Optic Atrophy diagnosis, Vision, Low diagnosis
- Abstract
Background : Nuclear hormone receptor gene, NR2F1 , plays a key role in brain and eye development. Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS, MIM #615772) is an autosomal dominant hereditary disorder caused by mutations in this gene. However, there have been few studies describing fundus and optical coherence tomography findings on BBSOAS. Materials and methods : The patient underwent a detailed clinical evaluation and ophthalmic imaging followed by targeted panel next-generation sequencing analysis. Results : A 7-year-old Korean boy, with a history of delayed development and borderline intellectual functioning, was referred to our clinic for evaluation of low vision. He was born full-term with no perinatal insults. Best-corrected visual acuity was 20/100 in both eyes, and latent nystagmus was noted. Dilated fundus examinations revealed optic atrophy in both eyes, and optical coherence tomography showed diffuse thinning of retinal nerve fiber layers. Targeted panel next-generation sequencing showed novel c.513C>G; p.Tyr171Ter (NM_005654.4) in NR2F1 gene. This stop-gain mutation was predicted to be deleterious by in silico prediction programs, and was absent in the current population genomic database. Conclusions : We highlighted the value of genetic testing in definite diagnosis of BBSOAS in patients with unexplained optic atrophy.
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- 2019
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5. Next-generation sequencing with comprehensive bioinformatics analysis facilitates somatic mosaic APC gene mutation detection in patients with familial adenomatous polyposis.
- Author
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Kim B, Won D, Jang M, Kim H, Choi JR, Kim TI, and Lee ST
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- Adenomatous Polyposis Coli blood, Adult, Aged, Humans, Middle Aged, Adenomatous Polyposis Coli genetics, Adenomatous Polyposis Coli Protein genetics, Computational Biology, DNA Mutational Analysis, High-Throughput Nucleotide Sequencing, Mutation
- Abstract
Background: Familial adenomatous polyposis (FAP) is an autosomal dominant colorectal tumor characterized by numerous adenomatous colonic polyps that often lead to colon cancer. Although most patients with FAP harbored germline mutations in APC gene, it was recently recognized that patients with clinical FAP, but without detectable pathogenic mutations, could be associated with somatic mosaic APC mutation., Methods: We reanalyzed the nest-generation sequencing (NGS) gene panel testing results of patients who were diagnosed with FAP, but did not have APC mutations, at Yonsei Cancer Prevention Center between July 2016 and March 2018. We tested several variant calling algorithms to identify low level mosaic variants. In one patient with a low frequency APC mutation, NGS analysis was performed together with endoscopic biopsy. Variant calling tools HaplotypeCaller, MuTect2, VarScan2, and Pindel were used. We also used 3'-Modified Oligonucleotides (MEMO)-PCR or conventional PCR for confirmation., Results: Among 28 patients with clinical suspicion of FAP but no detectable pathogenic variants of colonic polyposis associated genes, somatic mosaic pathogenic variants were identified in seven patients. The variant allele frequency ranged from 0.3 to 7.7%. These variants were mostly detected through variant caller MuTect2 and Pindel, and were further confirmed using mutant enrichment with MEMO-PCR., Conclusions: The NGS with an adequate combination of bioinformatics tools is effective to detect low level somatic variants in a single assay. Because mosaic APC mutations are more frequent than previously thought, the presence of mosaic mutations must be considered when analyzing genetic tests of patients with FAP.
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- 2019
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6. The TECTA mutation R1890C is identified as one of the causes of genetic hearing loss: a case report.
- Author
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Nam GS, Rim JH, Choi JY, Gee HY, Choi JR, Lee ST, and Jung J
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- Child, Preschool, Female, GPI-Linked Proteins genetics, Genes, Dominant, High-Throughput Nucleotide Sequencing, Humans, Extracellular Matrix Proteins genetics, Hearing Loss, Sensorineural genetics, Mutation
- Abstract
Background: Many mutations in the α-tectorin gene (TECTA) have been reported to cause non-syndromic hearing loss (NSHL) in either a dominant or recessive inheritance pattern. Among the identified TECTA mutations, H1400Y has been associated with NSHL in two independent studies. However, its exact role in contributing to genetic hearing loss remains elusive., Case Presentation: We herein report the whole-exome sequencing of a proband presenting with prelingual, non-progressive, mild-to-moderate hearing loss in a simplex family. By using trio-based whole-exome sequencing, we found two heterozygous mutations of R1890C and H1400Y in the ZP and ZA domains of TECTA, respectively. R1890C, previously reported as a pathogenic autosomal dominant mutation of genetic hearing loss, was found to be inherited in a de novo pattern, causing hearing loss in the proband. By contrast, H1400Y was not segregated in this family, and one family member with normal hearing also carried the H1400Y mutation., Conclusion: According to the hearing loss-specific American College of Medical Genetics and Genomics (ACMG) guidelines, we conclude that H1400Y should be disqualified as a cause of genetic hearing loss. True pathogenic variants causing genetic hearing loss should be more deliberately reported in accordance with ACMG guidelines.
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- 2019
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7. Distinct Clinical Courses of Epithelial Ovarian Cancer with Mutations in BRCA1 5' and 3' Exons.
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Eoh KJ, Park HS, Park JS, Lee ST, Han JW, Lee JY, Kim S, Kim SW, Kim YT, and Nam EJ
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- 3' Flanking Region genetics, 5' Flanking Region genetics, Adult, Aged, Carcinoma, Ovarian Epithelial mortality, Carcinoma, Ovarian Epithelial pathology, Disease Progression, Exons genetics, Female, Follow-Up Studies, Genes, BRCA1, Humans, Middle Aged, Ovarian Neoplasms mortality, Ovarian Neoplasms pathology, Retrospective Studies, Survival Analysis, BRCA1 Protein genetics, Carcinoma, Ovarian Epithelial genetics, Mutation, Ovarian Neoplasms genetics
- Abstract
Background/aim: This study aimed to determine the effect of different BRCA1 exonal mutations on the clinical course of epithelial ovarian cancer (EOC)., Patients and Methods: Clinicopathological variables and survival outcomes were compared among 53 primary EOC patients with pathogenic BRCA1 mutations in exons 1-11 (5' mutations) and in exons 12-24 (3' mutations)., Results: BRCA1 5' exonal mutations were found in 35 (66.0%) patients. The median follow-up period was 40 months. Clinicopathological variables remained unchanged between the two groups. Patients with 5' mutations had a significantly longer progression-free survival than those with C-terminal mutations (p=0.034), better predicting progression-free survival [2.923 (1.402-6.093), p=0.004], but not overall survival in cases of multiple relapses (p=0.497)., Conclusion: N-terminal BRCA1 mutations in EOC patients are associated with favourable primary progression-free survival, a trend observed only in primary progression-free survival, not in overall survival., (Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.)
- Published
- 2018
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8. Mowat-Wilson syndrome presenting with fever-associated seizures.
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Seo SE, Kim SH, Lee ST, Choi JR, Lee JS, Kim HD, and Kang HC
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- Child, Preschool, DNA Mutational Analysis, Facies, Female, Hirschsprung Disease complications, Hirschsprung Disease genetics, Humans, Intellectual Disability complications, Intellectual Disability genetics, Male, Microcephaly complications, Microcephaly genetics, Seizures, Febrile genetics, Hirschsprung Disease diagnosis, Intellectual Disability diagnosis, Microcephaly diagnosis, Mutation, Seizures, Febrile etiology, Zinc Finger E-box Binding Homeobox 2 genetics
- Abstract
Mowat-Wilson syndrome (MWS) is a disorder caused by mutations or deletions of the zinc finger E-box-binding homeobox 2 (ZEB2) gene. Diagnosis of MWS can be challenging to neurologists, because its manifestations are diverse and the spectrum of genetic mutations are broad. Here, we describe two patients with MWS who initially showed atypical forms of fever-triggered seizures during childhood. Both had characteristic facial features, cognitive impairment, and genito-urinary anomalies consistent with MWS. By performing targeted next-generation sequencing (NGS) using a gene panel for epilepsy, we were able to identify a nonsense mutation (c.1965C>A) in the ZEB2 gene of one patient and a frameshift mutation (c.2348dupC) in the other patient. Fever-induced seizures can be presenting signs of MWS. MWS should be considered in the differential diagnosis of fever-induced seizures, especially when the patient has distinctive facial features and multiple anomalies, including cardiac, genito-urinary, and eye defects.
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- 2017
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9. Identification of a Novel BRCA1 Pathogenic Mutation in Korean Patients Following Reclassification of BRCA1 and BRCA2 Variants According to the ACMG Standards and Guidelines Using Relevant Ethnic Controls.
- Author
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Park JS, Nam EJ, Park HS, Han JW, Lee JY, Kim J, Kim TI, and Lee ST
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- Adult, Biomarkers, Tumor, Computational Biology methods, Databases, Genetic, Female, Founder Effect, Genetic Variation, Hereditary Breast and Ovarian Cancer Syndrome epidemiology, Hereditary Breast and Ovarian Cancer Syndrome genetics, Humans, Middle Aged, Models, Molecular, Odds Ratio, Protein Conformation, Republic of Korea epidemiology, Structure-Activity Relationship, Exome Sequencing, Ethnicity genetics, Genes, BRCA1, Genes, BRCA2, Genetic Association Studies, Genetic Predisposition to Disease, Mutation, Population Surveillance
- Abstract
Purpose: Comparison of variant frequencies in the general population has become an essential part of the American College of Medical Genetics and Genomics (ACMG) standards and guidelines for interpreting sequence variants. We determined the optimal number of relevant ethnic controls that should be used to accurately calculate the odds ratio (OR) of genetic variants., Materials and Methods: Using the ACMG guidelines, we reclassified BRCA1 and BRCA2 mutations and variants of unknown significance in 745 Korean patients susceptible to hereditary breast and ovarian cancer compared with 1,314 Korean population controls., Results: We observed that the ORs were falsely inflated when we analyzed several variants using non-Korean population data. Our simulation indicated that the number of controls needed for the lower limit of a 95% confidence interval to exceed 1.0 varied according to the frequency of the variant in each patient group, with more than 820 controls needed for a variant existing in 1% of cases. Using a sufficient number of relevant population data, we could efficiently classify variants and identified the BRCA1 p.Leu1780Pro mutation as a possible pathogenic founder mutation in Korean patients., Conclusion: Our study suggests that BRCA1 p.Leu1780Pro is a novel pathogenic mutation found in Korean patients. We also determined the optimal number of relevant ethnic controls needed for accurate variant classification according to the ACMG guidelines.
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- 2017
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10. BRCA1 and BRCA2 mutation predictions using the BRCAPRO and Myriad models in Korean ovarian cancer patients.
- Author
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Eoh KJ, Park JS, Park HS, Lee ST, Han J, Lee JY, Kim SW, Kim S, Kim YT, and Nam EJ
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- Adult, Aged, Aged, 80 and over, Breast Neoplasms genetics, Decision Support Techniques, Female, Genetic Predisposition to Disease, Genetic Testing, Hereditary Breast and Ovarian Cancer Syndrome diagnosis, Hereditary Breast and Ovarian Cancer Syndrome epidemiology, Humans, Middle Aged, Models, Theoretical, Probability, ROC Curve, Republic of Korea, Risk Assessment, Adenocarcinoma, Clear Cell genetics, Asian People genetics, Carcinoma, Endometrioid genetics, Genes, BRCA1, Genes, BRCA2, Hereditary Breast and Ovarian Cancer Syndrome genetics, Mutation, Neoplasms, Cystic, Mucinous, and Serous genetics, Ovarian Neoplasms genetics
- Abstract
Objective: To evaluate the predictive efficacies including sensitivity and positive predictive value of the genetic risk prediction model BRCAPRO and the Myriad BRCA risk calculator in Korean ovarian cancer patients., Methods: Individuals undergoing genetic testing for BRCA mutations from November 2010-August 2016 were recruited from the Department of Obstetrics and Gynecology at a single institute in Korea. The observed BRCA1 and BRCA2 mutation statuses were compared with the predicted carrier probabilities using BRCAPRO and the Myriad BRCA risk calculator., Results: Two hundred thirty-two patients were recruited, of whom 99.1% (230/232) were of Korean ethnicity. Of the 232 individuals, 206 and 26 had ovarian and double primary breast/ovarian cancer, respectively. Thirty-six individuals had a family history of breast/ovarian cancer in first-degree relatives. Fifty-seven patients (24.6%) tested positive for BRCA mutation (41 BRCA1, 16 BRCA2). The mean BRCAPRO and Myriad scores for all patients were 6.4% and 7.7%, respectively. The scores were significantly higher for patients with positive BRCA mutation status (29.0% vs. 6.1%, P<0.001, 12.1% vs. 7.7%, P<0.001, respectively). For all patients, the respective areas under the receiver operating characteristics curves were 0.720 and 0.747 for the BRCAPRO and Myriad models to predict the risk of carrying a BRCA mutation. Both models overestimated the mutation probability in patients with a family history of breast/ovarian cancer (1.55-fold and 1.50-fold, respectively) and underestimated the probability in patients without a family history (both, 0.54-fold)., Conclusion: BRCAPRO and Myriad seem to be acceptable risk assessment tools for determining the risk of carrying BRCA mutations in Korean ovarian cancer patients., (Copyright © 2017 Elsevier Inc. All rights reserved.)
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- 2017
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11. Comparison of Clinical Outcomes of BRCA1/2 Pathologic Mutation, Variants of Unknown Significance, or Wild Type Epithelial Ovarian Cancer Patients.
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Eoh KJ, Park HS, Park JS, Lee ST, Han J, Lee JY, Kim SW, Kim S, Kim YT, and Nam EJ
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- Adult, Aged, Alleles, Carcinoma, Ovarian Epithelial, Combined Modality Therapy, Female, Humans, Middle Aged, Multimodal Imaging methods, Neoplasm Grading, Neoplasm Staging, Neoplasms, Glandular and Epithelial diagnosis, Neoplasms, Glandular and Epithelial therapy, Ovarian Neoplasms diagnosis, Ovarian Neoplasms therapy, Prognosis, Sequence Analysis, DNA, Survival Analysis, Treatment Outcome, Genes, BRCA1, Genes, BRCA2, Mutation, Neoplasms, Glandular and Epithelial genetics, Neoplasms, Glandular and Epithelial mortality, Ovarian Neoplasms genetics, Ovarian Neoplasms mortality
- Abstract
Purpose: The purpose of this study was to investigate the clinical features of epithelial ovarian cancer (EOC) patients according to BRCA1/2 mutation status (mutation, variant of uncertain significance [VUS], or wild type)., Materials and Methods: We analyzed 116 patients whose BRCA1/2 genetic test results were available for mutation type and clinical features, including progression-free survival (PFS), overall survival (OS), and response rate. These characteristics were compared according to BRCA1/2 mutation status., Results: Thirty-seven (37/116, 31.9%) BRCA1/2 mutations were identified ( BRCA1 , 30; BRCA2 , 7). Mutation of c.3627_3628insA (p.Leu1209_Glu1210?fs) in BRCA1 was observed in five patients (5/37, 13.5%). Twenty-five patients had BRCA1/2 VUSs (25/116, 21.6%). Personal histories of breast cancer were observed in 48.6% of patients with BRCA1/2 mutation (18/37), 16.0% of patients with BRCA1/2 VUS (4/25), and 7.4% of patients with BRCA wild type (4/54) (p < 0.001). Patients with BRCA1/2 mutation showed longer OS than those with BRCA1/2 wild type (p=0.005). No significant differences were detected in PFS, OS, or response rates between patients with BRCA1/2 VUS and BRCA1/2 mutation (p=0.772, p=0.459, and p=0.898, respectively)., Conclusion: Patientswith BRCA1/2 mutation had longer OS than thosewith BRCA1/2 wild type. Patients with BRCA1/2 mutation and BRCA1/2 VUS displayed similar prognoses.
- Published
- 2017
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12. Mutation profiling of 19 candidate genes in acute myeloid leukemia suggests significance of DNMT3A mutations.
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Shin SY, Lee ST, Kim HJ, Cho EH, Kim JW, Park S, Jung CW, and Kim SH
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- Acute Disease, Adolescent, Adult, Aged, DNA Methyltransferase 3A, DNA Mutational Analysis methods, Disease-Free Survival, Female, Humans, Karyotype, Leukemia, Myeloid pathology, Male, Middle Aged, Nucleophosmin, Young Adult, DNA (Cytosine-5-)-Methyltransferases genetics, Genetic Predisposition to Disease genetics, Leukemia, Myeloid genetics, Mutation
- Abstract
We selected 19 significantly-mutated genes in AMLs, including FLT3, DNMT3A, NPM1, TET2, RUNX1, CEBPA, WT1, IDH1, IDH2, NRAS, ASXL1, SETD2, PTPN11, TP53, KIT, JAK2, KRAS, BRAF and CBL, and performed massively parallel sequencing for 114 patients with acute myeloid leukemias, mainly including those with normal karyotypes (CN-AML). More than 80% of patients had at least one mutation in the genes tested. DNMT3A mutation was significantly associated with adverse outcome in addition to conventional risk stratification such as the European LeukemiaNet (ELN) classification. We observed clinical usefulness of mutation testing on multiple target genes and the association with disease subgroups, clinical features and prognosis in AMLs.
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- 2016
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13. Challenges in assessing pathogenicity based on frequency of variants in mismatch repair genes: an extreme case of a MSH2 variant and a meta-analysis.
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Woo HI, Woo YM, Kim S, Lee ST, Ki CS, and Kim JW
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- Alleles, Female, Humans, Male, Middle Aged, Colonic Neoplasms genetics, DNA Mismatch Repair, Databases, Nucleic Acid, Gene Frequency, MutS Homolog 2 Protein genetics, Mutation, Polymorphism, Genetic
- Abstract
The clinical interpretation of variants in mismatch repair (MMR) genes associated with Lynch syndrome can be confusing when the functional nature of the variant is not clearly defined. We report an extreme case where a polymorphism in the MSH2 gene which had a low minor allele frequency, was misclassified as a mutation based on low evidential methods in the database and previous publications. We expanded this experience to perform a systematic meta-analysis in order to investigate other variants that have potentially been misclassified. Our results suggested that the interpretation of pathogenicity should be more cautious and emphasized the need for solid validation through multiple analyses including functional analysis for variants in MMR genes., (Copyright © 2014 Elsevier B.V. All rights reserved.)
- Published
- 2014
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14. Distinct frequencies and mutation spectrums of genetic thrombophilia in Korea in comparison with other Asian countries both in patients with thromboembolism and in the general population.
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Kim HJ, Seo JY, Lee KO, Bang SH, Lee ST, Ki CS, Kim JW, Jung CW, Kim DK, and Kim SH
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- Adult, Antithrombin III genetics, Asia, Blood Proteins genetics, Female, Humans, Male, Middle Aged, Protein C genetics, Protein S, Republic of Korea, Thromboembolism diagnosis, Venous Thromboembolism diagnosis, Venous Thromboembolism epidemiology, Venous Thromboembolism genetics, Genetic Predisposition to Disease, Mutation, Thromboembolism epidemiology, Thromboembolism genetics
- Abstract
Hereditary natural anticoagulant deficiencies are the major cause of genetic thrombophilia in Asia. Given the growing acknowledgment of the risk of venous thromboembolism in Asian populations, we investigated the frequency and mutation spectrums of natural anticoagulant deficiency in Korea. The group of patients consisted of consecutive patients with venous thromboembolism screened for thrombophilia. Genetic tests were performed on suspicion of natural anticoagulant deficiency. For the population group, >3,000 individuals were screened from routine check-ups, and those with a low level (<1(st) percentile) of natural anticoagulant underwent genetic tests. Mutations were detected by direct sequencing of PROC, PROS1, and SERPINC1, followed by additional multiplex ligation-dependent probe amplification for PROS1 and SERPINC1 for dosage mutations. Among 500 patients screened, 127 were suspected of having a natural anticoagulant deficiency, and this was genetically confirmed in 71: protein C deficiency in 36 (50.7%), antithrombin deficiency in 21 (29.6%), and protein S deficiency in 14 (19.7%). Among 3,129 individuals from the population who were screened, the frequency of natural anticoagulant deficiency was ~1.0%: antithrombin deficiency 0.49%, protein C deficiency 0.35%, and protein S deficiency 0.16%. Two PROC mutations causing type I protein C deficiency were prevalent (Arg211Trp and Met406Ile in patients and Arg211Trp in the population). Two SERPINC1 mutations causing type II antithrombin deficiency, Arg79Cys and Ser158Pro, were prevalent in the population group. This is the first study on the genetic epidemiology of natural anticoagulant deficiencies in Korea. The results demonstrated that the frequencies and spectrum of mutations underlying genetic thrombophilia in Korea are different not only from those in Caucasians but also those in other Asian populations.
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- 2014
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15. Identification of a novel splicing mutation in the ARSA gene in a patient with late-infantile form of metachromatic leukodystrophy.
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Kang DH, Lee DH, Hong YH, Lee ST, Jeon BR, Lee YK, Ki CS, and Lee YW
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- Exons, Heterozygote, Humans, Infant, Introns, Leukodystrophy, Metachromatic diagnosis, Magnetic Resonance Imaging, Male, Mutation, Missense, RNA, Messenger genetics, Cerebroside-Sulfatase genetics, Leukodystrophy, Metachromatic genetics, Mutation, RNA Splicing
- Abstract
Metachromatic leukodystrophy (MLD; MIM 250100), a severe neurodegenerative disorder inherited as an autosomal recessive trait, is caused by mutations in the arylsulfatase A (ARSA) gene. Although several germ line ARSA mutations have been identified in patients with MLD of various ethnic backgrounds elsewhere in the world, no genetically confirmed cases of MLD have been reported in Korea. Recently, we identified a mutation in the ARSA gene of a Korean male with MLD. A male infant with late-infantile form of MLD had been admitted to our hospital for further examination. His neuromuscular symptoms, which included inability to walk at the age of 12 months, gradually worsened, even after allograft bone marrow transplantation; he died at the age of 9 yr. His elder brother had also been diagnosed with MLD. To confirm the presence of a genetic abnormality, all the coding exons of the ARSA gene and the flanking introns were amplified by PCR. A molecular analysis of the ARSA gene revealed both a novel heterozygous splicing mutation (c.1101+1G>T) in intron 6 and a heterozygous missense mutation in exon 2 (c.296G>A; Gly99Asp). The patient's elder brother who had MLD is believed to have had the same mutation, which may be correlated with a rapidly deteriorating clinical course. This study identified a novel mutation in the ARSA gene, related to a late-infantile form of MLD with a lethal clinical course and suggested that molecular diagnosis of patients may be useful in early diagnosis and for deciding intervention measures for their family members.
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- 2010
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16. Therapy-related myeloid neoplasm in a patient with TP53 mutation: a dilemma in allogeneic stem cell transplant.
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Kim MK, Cho HS, Bae YK, Lee KH, Ki CS, Lee ST, and Hyun MS
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- Acute Disease, Adult, Base Sequence, Diagnosis, Differential, Female, Humans, Risk Assessment, Sequence Analysis, DNA, Stem Cell Transplantation methods, Transplantation, Homologous, Leukemia, Myeloid diagnosis, Mutation, Neoplasms, Second Primary diagnosis, Tumor Suppressor Protein p53 genetics
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- 2010
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17. UNC13D is the predominant causative gene with recurrent splicing mutations in Korean patients with familial hemophagocytic lymphohistiocytosis.
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Yoon HS, Kim HJ, Yoo KH, Sung KW, Koo HH, Kang HJ, Shin HY, Ahn HS, Kim JY, Lim YT, Bae KW, Lee KO, Shin JS, Lee ST, Chung HS, Kim SH, Park CJ, Chi HS, Im HJ, and Seo JJ
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- Adolescent, Child, Child, Preschool, DNA analysis, DNA genetics, Exons genetics, Female, Homozygote, Humans, Infant, Infant, Newborn, Korea, Lymphohistiocytosis, Hemophagocytic pathology, Lymphohistiocytosis, Hemophagocytic therapy, Male, Perforin, Pore Forming Cytotoxic Proteins genetics, Prognosis, Qa-SNARE Proteins genetics, Recurrence, Alternative Splicing genetics, Genetic Predisposition to Disease, Lymphohistiocytosis, Hemophagocytic genetics, Membrane Proteins genetics, Mutation genetics
- Abstract
Background: Familial hemophagocytic lymphohistiocytosis is a fatal disease characterized by immune dysregulation from defective function of cytotoxic lymphocytes. Three causative genes have been identified for this autosomal recessive disorder (PRF1, UNC13D, and STX11). We investigated the molecular genetics of familial hemophagocytic lymphohistiocytosis in Korea., Design and Methods: Pediatric patients who fulfilled the HLH-2004 criteria were recruited from the Korean Registry for Histiocytosis. Molecular genetic studies were performed on the patients' DNA samples by direct sequencing of all coding exons and flanking sequences of PRF1, UNC13D, and STX11., Results: Forty patients were studied and familial hemophagocytic lymphohistiocytosis mutations were identified in nine; eight patients had UNC13D mutations (89%) and one had a mutation in PRF1. No patient had a STX11 mutation. Notably, four patients had only one UNC13D mutant allele, suggesting that the other mutation was missed by conventional direct sequencing. All UNC13D mutations were deleterious in nature. One known splicing mutation, c.754-1G>C, was recurrent, accounting for 58% of all the mutant alleles (7/12). Five UNC13D mutations were novel (p.Gln98X, p.Glu565SerfsX7, c.1993-2A>G, c.2367+1G>A, and c.2954+5G>A). The one patient with PRF1 mutation was homozygous for a frameshift mutation (p.Leu364GlufsX93), which was previously reported to be the most frequent PRF1 mutation in Japan., Conclusions: This is the first investigation on the molecular genetics of familial hemophagocytic lymphohistiocytosis in Korea. The data showed that UNC13D is the predominant causative gene in the Korean population. The identification of mutations missed by conventional sequencing would better delineate the mutation spectrum and help to establish the optimal molecular diagnostic strategy for familial hemophagocytic lymphohistiocytosis in Korea, which might need an RNA-based screening strategy.
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- 2010
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18. Novel PANK2 gene mutations in korean patient with pantothenate kinase-associated neurodegeneration presenting unilateral dystonic tremor.
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Yoon WT, Lee WY, Shin HY, Lee ST, and Ki CS
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- Arm physiopathology, Dystonic Disorders physiopathology, Hand physiopathology, Humans, Korea, Male, Middle Aged, Tremor physiopathology, Dystonic Disorders genetics, Mutation, Pantothenate Kinase-Associated Neurodegeneration genetics, Pantothenate Kinase-Associated Neurodegeneration physiopathology, Phosphotransferases (Alcohol Group Acceptor) genetics, Tremor genetics
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- 2010
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19. A novel mutation Ala57Val of the ELA2 gene in a Korean boy with severe congenital neutropenia.
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Lee ST, Yoon HS, Kim HJ, Lee JH, Park JH, Kim SH, Seo JJ, and Im HJ
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- Alanine genetics, Alanine metabolism, Child, Preschool, Computational Biology, Humans, Korea, Leukocyte Elastase metabolism, Male, Neutropenia enzymology, Neutropenia pathology, Leukocyte Elastase genetics, Mutation genetics, Neutropenia congenital, Neutropenia genetics
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- 2009
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20. Clinical features and mutations in the ENG, ACVRL1, and SMAD4 genes in Korean patients with hereditary hemorrhagic telangiectasia.
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Lee ST, Kim JA, Jang SY, Kim DK, Do YS, Suh GY, Kim JW, and Ki CS
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- Adult, Alleles, Angiography, Base Sequence, Endoglin, Female, Genetic Predisposition to Disease, Humans, Korea, Male, Middle Aged, Pedigree, Telangiectasia, Hereditary Hemorrhagic diagnosis, Telangiectasia, Hereditary Hemorrhagic pathology, Tomography, X-Ray Computed, Young Adult, Activin Receptors, Type II genetics, Antigens, CD genetics, Asian People genetics, Mutation, Receptors, Cell Surface genetics, Smad4 Protein genetics, Telangiectasia, Hereditary Hemorrhagic genetics
- Abstract
Hereditary hemorrhagic telangiectasia (HHT) is an inherited disorder that is characterized by abnormal communication between the arteries and veins in the skin, mucosa, and various organs. HHT has been reported to show significant phenotypic variability and genetic heterogeneity with wide ethnic and geographic variations. Although mutations in the endoglin (ENG) and activin A receptor type II-like 1 (ACVRL1) genes have been known to cause HHT for more than 10 yr, little is known about the clinical features or genetic background of Korean patients with HHT. In addition, mutations in mothers against decapentaplegic homolog 4 (SMAD4) are also seen in patients with the combined syndrome of juvenile polyposis and HHT. This study examined five Korean patients with the typical manifestations of HHT such as frequent epistaxis and pulmonary arteriovenous malformations. Direct sequencing of the ENG and ACVRL1 genes revealed one known mutation, ENG c.277C>T, in one patient and two novel mutations, ENG c.992-1G>C and ACVRL1 c.81dupT in two patients, respectively. The remaining two patients with negative results were screened for SMAD4 mutations as well as gross deletions of ENG and ACVRL1 using multiple ligation-dependent probe amplification, but none was detected. Despite the small number of patients investigated, we firstly report Korean patients with genetically confirmed HHT, and show the genetic and allelic heterogeneity underlying HHT.
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- 2009
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21. High oxygen-affinity hemoglobin variant associated with high-level venous oxygen saturation.
- Author
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Lee YW, Ki CS, Kim HJ, Lee ST, Kim CK, Shin HB, Hong DS, and Lee YK
- Subjects
- Chromatography, Humans, Male, Middle Aged, Polycythemia genetics, Polycythemia metabolism, Sequence Analysis, DNA, Hemoglobins genetics, Hemoglobins metabolism, Mutation, Oxygen metabolism, Veins metabolism
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- 2008
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22. Genetic analysis of three Korean patients with clinical features of Ehlers-Danlos syndrome type IV.
- Author
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Yang JH, Lee ST, Kim JA, Kim SH, Jang SY, Ki CS, and Kim DK
- Subjects
- Adult, Aged, Amino Acid Sequence, Base Sequence, DNA Mutational Analysis, Female, Genetic Heterogeneity, Humans, Korea, Male, Molecular Sequence Data, Pedigree, Tomography, X-Ray Computed, Collagen Type III genetics, Ehlers-Danlos Syndrome genetics, Ehlers-Danlos Syndrome pathology, Mutation
- Abstract
Ehlers-Danlos syndrome (EDS) is a hereditary disorder of the connective tissue. EDS type IV (EDS IV), the vascular type of the disease, is characterized by easy bruising, thin skin with visible veins, and spontaneous rupture of the large arteries, uterus, or bowel. EDS IV is caused by mutations in the gene for type III procollagen (COL3A1). However, recent studies suggest that the causative mutation of EDS IV is not homogeneous. We report our experience with three patients presenting with clinical features of type IV EDS. A 48-yr-old woman presented with acute aortic dissection (patient 1) and 36-yr-old and 21-yr-old women presented with carotidcavernous fistula (patients 2 and 3, respectively). All three patients bruised easily. Two patients (patients 1 and 3) had thin transparent skin with visible veins. Genetic analysis of COL3A1 revealed a Gly732Val (c.2195G>T) mutation in patient 1 and a duplication of 15 base pairs (c.3221_3235dup) which resulted in an interposition of five amino acids (p.Gly1074_Pro1078dup) in patient 2. However, no mutations were observed in COL3A1 or transforming growth factor beta receptors 1 and 2 in patients 3, which might be either due to a deletion of single or multiple exons in the COL3A1 gene or due to a genetic heterogeneity. This is the first report of genetically confirmed cases of EDS IV in Korea.
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- 2007
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23. PTPRG inhibition by DNA methylation and cooperation with RAS gene activation in childhood acute lymphoblastic leukemia
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Xiao, Jianqiao, Lee, Seung‐Tae, Xiao, Yuanyuan, Ma, Xiaomei, Houseman, E Andres, Hsu, Ling‐I, Roy, Ritu, Wrensch, Margaret, de Smith, Adam J, Chokkalingam, Anand, Buffler, Patricia, Wiencke, John K, and Wiemels, Joseph L
- Subjects
Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Genetics ,Human Genome ,Pediatric ,Hematology ,Rare Diseases ,Pediatric Cancer ,Cancer ,Childhood Leukemia ,Pediatric Research Initiative ,Aetiology ,2.1 Biological and endogenous factors ,Cell Transformation ,Neoplastic ,Child ,Child ,Preschool ,DNA Methylation ,DNA-Binding Proteins ,Enzyme Activation ,Epigenesis ,Genetic ,Extracellular Signal-Regulated MAP Kinases ,Gene Expression Regulation ,Leukemic ,HEK293 Cells ,Humans ,Mutation ,Phosphorylation ,Precursor Cell Lymphoblastic Leukemia-Lymphoma ,Promoter Regions ,Genetic ,Receptor-Like Protein Tyrosine Phosphatases ,Class 5 ,Transcription Factors ,Transcriptional Activation ,ras Proteins ,childhood acute lymphoblastic leukemia ,RAS ,PTPRG ,DNA methylation ,Oncology & Carcinogenesis ,Oncology and carcinogenesis - Abstract
While the cytogenetic and genetic characteristics of childhood acute lymphoblastic leukemias (ALL) are well studied, less clearly understood are the contributing epigenetic mechanisms that influence the leukemia phenotype. Our previous studies and others identified gene mutation (RAS) and DNA methylation (FHIT) to be associated with the most common cytogenetic subgroup of childhood ALL, high hyperdiploidy (having five more chromosomes). We screened DNA methylation profiles, using a genome-wide high-dimension platform of 166 childhood ALLs and 6 normal pre-B cell samples and observed a strong association of DNA methylation status at the PTPRG locus in human samples with levels of PTPRG gene expression as well as with RAS gene mutation status. In the 293 cell line, we found that PTPRG expression induces dephosphorylation of ERK, a downstream RAS target that may be critical for mutant RAS-induced cell growth. In addition, PTPRG expression is upregulated by RAS activation under DNA hypomethylating conditions. An element within the PTPRG promoter is bound by the RAS-responsive transcription factor RREB1, also under hypomethylating conditions. In conclusion, we provide evidence that DNA methylation of the PTPRG gene is a complementary event in oncogenesis induced by RAS mutations. Evidence for additional roles for PTPR family member genes is also suggested. This provides a potential therapeutic target for RAS-related leukemias as well as insight into childhood ALL etiology and pathophysiology.
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- 2014
24. Analysis of copy number variation using whole genome exon-focused array CGH in Korean patients with primary congenital glaucoma
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Lee, Ji Hyun, Ki, Chang-Seok, Kim, Hee-Jung, Suh, Wool, Lee, Seung-Tae, Kim, Jong-Won, and Kee, Changwon
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Adult ,Male ,animal structures ,genetic structures ,DNA Copy Number Variations ,Gene Dosage ,Genes, Recessive ,macromolecular substances ,Asian People ,Gene Duplication ,Republic of Korea ,Humans ,Child ,Aged ,Comparative Genomic Hybridization ,Genome, Human ,fungi ,Infant ,Glaucoma ,Exons ,body regions ,Genetic Loci ,Child, Preschool ,Cytochrome P-450 CYP1B1 ,Mutation ,Female ,Aryl Hydrocarbon Hydroxylases ,Gene Deletion ,Research Article - Abstract
Purpose Primary congenital glaucoma (PCG) is an autosomal recessive form of glaucoma that manifests within the first year of life and if left untreated, leads to irreversible blindness. Cytochrome P450 1B1 (CYP1B1) is the major gene known to be associated with PCG. The role of the CYP1B1 gene in disease pathogenesis and the relatively low detection rate of CYP1B1 mutations in some populations, especially Asians, remain unexplained. We hypothesized that altered gene dosage of CYP1B1 or anterior segmental dysgenesis causative genes may be involved in the pathogenesis of PCG. Methods We performed whole genome exon-focused array comparative genome hybridization (aCGH) to identify copy number variation (CNV) in 20 Korean PCG patients and their parents. Results We identified 12 patients with at least one rare gene-containing copy number variation each, corresponding to 25 CNVs (5 deletions and 20 duplications) at frequencies of 5-30% in PCG patients and 0% in controls. The 25 CNVs were not located at known chromosomal loci for PCG, namely GLC3A, which harbors CYP1B1 (2p21), GLC3B (1p36.2-p36.1), or GLC3C (14q23), and did not include any target genes associated with PCG or anterior segmental dysgenesis. Conclusions Further genetic studies with larger cohorts of patients are necessary to validate our results and to elucidate other genetic mechanisms underlying PCG, because the identified CNVs might be PCG-specific pathogenic variants and may explain the disease pathogenesis of PCG.
- Published
- 2011
25. Somatic mosaic truncating mutations of PPM1D in blood can result from expansion of a mutant clone under selective pressure of chemotherapy.
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Kim, Borahm, Won, Dongju, Lee, Seung-Tae, and Choi, Jong Rak
- Subjects
CANCER chemotherapy ,CIRCULATING tumor DNA ,PHOSPHOPROTEIN phosphatases ,OVARIAN cancer ,CANCER treatment ,BLOOD testing - Abstract
Background: PPM1D (Protein phosphatase magnesium-dependent 1δ) is known as a damage response regulator, a part of the p53 negative feedback loop. Truncating mutations of PPM1D, resulting in overexpression, are frequently found in the blood of patients with breast or ovarian cancer. To identify whether the PPM1D mutation predisposes patients to such cancers or if it results from the cancer and therapy, somatic PPM1D mutations in association with previous cancer and chemotherapy need to be explored. Methods: We performed next-generation sequencing (NGS) analysis of blood samples from patients suspected to have hereditary cancer. We grouped the patients according to their diagnoses and history of chemotherapy. For the patients with PPM1D mutations in blood, tumor tissue specimens were examined for the PPM1D mutation using conventional sequencing. Results: A total of 1,195 patients, including 719 patients with breast cancer and 240 with ovarian cancer, were tested, and four (~0.3%) had the truncating mutation in PPM1D. All truncating mutations were in exon 6, in mosaic form, with a mean allele fraction of 11.15%. While 395 out of the 1,195 patients had undergone chemotherapy, the four with the truncating mutation had a history of cisplatin-based chemotherapy. No corresponding mutations were identified in the tumor tissues. Conclusions: We investigated the frequency of the somatic mosaic PPM1D mutation, in patients with breast or ovarian cancer, which is suggested to be low and related to a history of cisplatin-based chemotherapy. It may be a marker of previous exposure to selective pressure for cells with an impaired DNA damage response. [ABSTRACT FROM AUTHOR]
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- 2019
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26. Targeted next generation sequencing can serve as an alternative to conventional tests in myeloid neoplasms.
- Author
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Kim, Borahm, Lee, Hyeonah, Jang, Jieun, Kim, Soo-Jeong, Lee, Seung-Tae, Cheong, June-Won, Lyu, Chuhl Joo, Min, Yoo Hong, and Choi, Jong Rak
- Subjects
MYELOID leukemia ,SOMATIC mutation ,CANCER genetics ,CANCER susceptibility ,BIOINFORMATICS ,DNA copy number variations - Abstract
The 2016 World Health Organization classification introduced a number of genes with somatic mutations and a category for germline predisposition syndromes in myeloid neoplasms. We have designed a comprehensive next-generation sequencing assay to detect somatic mutations, translocations, and germline mutations in a single assay and have evaluated its clinical utility in patients with myeloid neoplasms. Extensive and specified bioinformatics analyses were undertaken to detect single nucleotide variations, FLT3 internal tandem duplication, genic copy number variations, and chromosomal copy number variations. This enabled us to maximize the clinical utility of the assay, and we concluded that, as a single assay, it can be a good supplement for many conventional tests, including Sanger sequencing, RT-PCR, and cytogenetics. Of note, we found that 8.4–11.6% of patients with acute myeloid leukemia and 12.9% of patients with myeloproliferative neoplasms had germline mutations, and most were heterozygous carriers for autosomal recessive marrow failure syndromes. These patients often did not respond to standard chemotherapy, suggesting that germline predisposition may have distinct and significant clinical implications. [ABSTRACT FROM AUTHOR]
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- 2019
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27. Identification of an Arg35X mutation in the PDCD10 gene in a patient with cerebral and multiple spinal cavernous malformations
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Lee, Seung-Tae, Choi, Ki-Whan, Yeo, Hyung-Tae, Kim, Jong-Won, Ki, Chang-Seok, and Cho, Young-Dae
- Subjects
- *
GENETIC mutation , *SPINAL cord , *CENTRAL nervous system , *BRAIN stem - Abstract
Abstract: Although cerebral cavernous malformations (CCMs) are not uncommon, the concurrent finding of cavernous malformations (CMs) both in the brain and spinal cord is quite rare. Furthermore, multiple spinal cord CMs are extremely rare with only a few cases being reported thus far. Recently, we encountered a 33-year-old Korean male with both CCM and multiple spinal intramedullary CMs. The patient complained of seizure and right chest paresthesia. The lesions were located throughout the neuraxis including the cerebral hemisphere, brain stem, and cervical and thoracic spinal cords. Molecular analysis of the KRIT1 (CCM1), CCM2, and PDCD10 (CCM3) genes identified a heterozygous nonsense mutation (c.103C>T; Arg35X) in the PDCD10 gene, which was reported previously in a CCM family. The patient denied a family history, however, his daughter had an identical mutation, but was asymptomatic. Three months later, after identifying the mutation in the father and the daughter, the daughter presented with seizure. To the best of our knowledge, this is the first report of an association between a mutation in the PDCD10 gene and spinal CMs. [Copyright &y& Elsevier]
- Published
- 2008
- Full Text
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