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1.
Article in English | WPRIM | ID: wpr-875471

ABSTRACT

Background/Aims@#Understanding leukemic stem cell (LSC) is important for acute myeloid leukemia (AML) treatment. However, association of LSC with patient prognosis and genetic information in AML patients is unclear. @*Methods@#Here we investigated the associations between genetic information and the various LSC phenotypes, namely multipotent progenitor (MPP)-like, lymphoid primed multipotent progenitor (LMPP)-like and granulocyte-macrophage progenitors (GMP)-like LSC in 52 AML patients. @*Results@#In secondary AML patients, MPP-like LSC was significantly higher than de novo AML (p = 0.0037). The proportion of MPP-like LSC was especially high in post-myeloproliferative neoplasm AML (p = 0.0485). There was no correlation between age and LSC phenotype. Mutations of KRAS and NRAS were observed in MPP-like LSC dominant patients, TP53 and ASXL1 mutations in LMPP-like LSC dominant patients, and CEBPA, DNMT3A and IDH1 mutations in GMP-like LSC dominant patients. Furthermore, KRAS mutation was significantly associated with MPP-like LSC expression (p = 0.0540), and TP53 mutation with LMPP-like LSC expression (p = 0.0276). When the patients were separated according to the combined risk including next generation sequencing data, the poorer the prognosis, the higher the LMPP-like LSC expression (p = 0.0052). This suggests that the dominant phenotype of LSC is one of the important factors in predicting the prognosis and treatment of AML. @*Conclusions@#LSC phenotype in AML is closely associated with the recurrent mutations which has prognostic implication. Further research to confirm the meaning of LSC phenotype in the context of genetic aberration is warranted.

2.
Article in English | WPRIM | ID: wpr-874151

ABSTRACT

Background@#Conventional diagnosis of fragile X syndrome (FXS) is based on a combination of fragment analysis (FA) and Southern blotting (SB); however, this diagnostic approach is time- and labor-intensive and has pitfalls such as the possibility of missing large number alleles. Triplet repeat primed PCR (TP-PCR) is a current alternative used to overcome these limitations. We evaluated the diagnostic usefulness of TP-PCR compared with the conventional diagnostic protocol consisting of FA and/or SB in terms of allele categorization, repeat number correlation, and zygosity concordance in female genetic carriers. @*Methods@#From November 2013 to March 2018, 458 patients (326 males, 132 females) were simultaneously examined using FA and/or SB and TP-PCR by detecting CGG repeat numbers in FMR gene and diagnosed as per American College of Medical Genetics guidelines. @*Results@#The TP-PCR results showed high concordance with the FA and/or SB results for all three aspects (allele categorization, repeat number correlation, and zygosity concordance in female genetic carriers). TP-PCR detected CGG expansions ≥ 200 in all full mutation (FM) allele cases in male patients, as well as both the normal allele (NL) and FM allele in female carriers. In premutation (PM) allele carriers, the TP-PCR results were consistent with the FA and/or SB results. In terms of zygosity concordance in female genetic carriers, 12 NL cases detected by TP-PCR showed a merged peak consisting of two close heterozygous peaks; however, this issue was resolved using a 10-fold dilution. @*Conclusions@#TP-PCR may serve as a reliable alternative method for FXS diagnosis.

3.
Blood Research ; : S39-S43, 2021.
Article in English | WPRIM | ID: wpr-897352

ABSTRACT

Thalassemia is characterized by the impaired synthesis of globin chains due to disease-causing variants in α- or β-globin genes. In this review, we provide an overview of the molecular basis underlying α- and β-thalassemia, and of the current technologies used to characterize these disease-causing variants for the diagnosis of thalassemia.Understanding these molecular basis and technologies will prove to be beneficial for the accurate diagnosis of thalassemia.

4.
Blood Research ; : S39-S43, 2021.
Article in English | WPRIM | ID: wpr-889648

ABSTRACT

Thalassemia is characterized by the impaired synthesis of globin chains due to disease-causing variants in α- or β-globin genes. In this review, we provide an overview of the molecular basis underlying α- and β-thalassemia, and of the current technologies used to characterize these disease-causing variants for the diagnosis of thalassemia.Understanding these molecular basis and technologies will prove to be beneficial for the accurate diagnosis of thalassemia.

5.
Article in English | WPRIM | ID: wpr-898131

ABSTRACT

Background@#Pheochromocytoma and paragangliomas (PPGL) are known as tumors with the highest level of heritability, approximately 30% of all cases. Clinical practice guidelines of PPGL recommend genetic testing for germline variants in all patients. In this study, we used whole exome sequencing to identify novel causative variants associated with PPGL to improve the detection of rare genetic variants in our cohort. @*Methods@#Thirty-six tested negative for pathogenic variants in previous Sanger sequencing or targeted gene panel testing for PPGL underwent whole exome sequencing. Whole exome sequencing was performed using DNA samples enriched using TruSeq Custom Enrichment Kit and sequenced with MiSeq (Illumina Inc.). Sequencing alignment and variant calling were performed using SAMtools. @*Results@#Among previously mutation undetected 36 patients, two likely pathogenic variants and 13 variants of uncertain significance (VUS) were detected in 32 pheochromocytoma-related genes. SDHA c.778G>A (p.Gly260Arg) was detected in a patient with head and neck paraganglioma, and KIF1B c.2787-2A>C in a patient with a bladder paraganglioma. Additionally, a likely pathogenic variant in BRCA2, VUS in TP53, and VUS in NFU1 were detected. @*Conclusion@#Exome sequencing further identified genetic alterations by 5.6% in previously mutation undetected patients in PPGL. Implementation of targeted gene sequencing consisted of extended genes of PPGL in routine clinical screening can support the level of comprehensive patient assessment.

6.
Article | WPRIM | ID: wpr-836056

ABSTRACT

Background@#Next-generation sequencing is a powerful technology thatallows simultaneous analysis of several genes but also demands a welldesignedquality management system owing to its complexity. We aimed toanalyze the results of next-generation sequencing (NGS)-germline proficiencytesting (PT) survey performed by the Korean Association of External QualityAssessment Service during 2017–2019 to assess the current status of theNGS-based genetic testing in Korea. @*Methods@#The recent 3-year results from the PT survey were investigated.During this period, PT survey was performed twice every year with two orthree challenges per round. Correct results (%) were calculated from alltested regions; the trend by year and variation type was analyzed and theprobable causes estimated. @*Results@#During this period, the number of participating laboratoriesincreased from 5 to 22. The correct results were 97.2% in average andshowed a gradual increase with year. The most common ‘unacceptable’results were false-negative or false-positive, followed by inappropriatenomenclature and zygosity assignment. @*Conclusions@#The PT survey shows that the overall performance of NGSlaboratories in Korea is highly confident, although some improvements maybe needed. A method-based PT survey for the NGS test serves as a usefulapproach to assess the performance of NGS laboratories.

7.
Article | WPRIM | ID: wpr-835777

ABSTRACT

Purpose@#Duchenne muscular dystrophy (DMD) is the most common lethal muscular dystrophy and is caused by the genetic variants of DMD gene. Because DMD is X-linked recessive and shows familial aggregates, prenatal diagnosis is an important role in the management of DMD family. We present our experience of prenatal molecular diagnosis and carrier detection based on multiplex polymerase chain reaction (PCR), multiplex ligation-dependent probe amplification (MLPA), and linkage analysis. @*Materials and Methods@#During study period, 34 cases of prenatal diagnosis and 21 cases of carrier detection were performed at the Seoul National University Hospital. Multiplex PCR and MLPA was used to detect the exon deletions or duplications. When the DMD pathogenic variant in the affected males is unknown and no DMD pathogenic variant is detected in atrisk females, linkage analysis was used. @*Results@#The prenatal molecular diagnosis was offered to 34 fetuses. Twenty-five fetuses were male and 6 fetuses (24.0%) were affected. Remaining cases had no pathogenic mutation. We had 24 (80.0%) cases of known proband results; exon deletion mutation in 19 (79.2%) cases and duplication in 5 (20.8%) cases. Linkage analysis was performed in 4 cases in which 2 cases (50.0%) were found to be affected. In the carrier testing, among 21 cases including 15 cases of mother and 6 cases of female relative, 9 (42.9%) cases showed positive results and 12 (57.1%) cases showed negative results. @*Conclusion@#Prenatal molecular diagnosis and carrier detection of DMD are effective and feasible. They are useful in genetic counseling for DMD families.

8.
Article in English | WPRIM | ID: wpr-890427

ABSTRACT

Background@#Pheochromocytoma and paragangliomas (PPGL) are known as tumors with the highest level of heritability, approximately 30% of all cases. Clinical practice guidelines of PPGL recommend genetic testing for germline variants in all patients. In this study, we used whole exome sequencing to identify novel causative variants associated with PPGL to improve the detection of rare genetic variants in our cohort. @*Methods@#Thirty-six tested negative for pathogenic variants in previous Sanger sequencing or targeted gene panel testing for PPGL underwent whole exome sequencing. Whole exome sequencing was performed using DNA samples enriched using TruSeq Custom Enrichment Kit and sequenced with MiSeq (Illumina Inc.). Sequencing alignment and variant calling were performed using SAMtools. @*Results@#Among previously mutation undetected 36 patients, two likely pathogenic variants and 13 variants of uncertain significance (VUS) were detected in 32 pheochromocytoma-related genes. SDHA c.778G>A (p.Gly260Arg) was detected in a patient with head and neck paraganglioma, and KIF1B c.2787-2A>C in a patient with a bladder paraganglioma. Additionally, a likely pathogenic variant in BRCA2, VUS in TP53, and VUS in NFU1 were detected. @*Conclusion@#Exome sequencing further identified genetic alterations by 5.6% in previously mutation undetected patients in PPGL. Implementation of targeted gene sequencing consisted of extended genes of PPGL in routine clinical screening can support the level of comprehensive patient assessment.

10.
Article in English | WPRIM | ID: wpr-739103

ABSTRACT

Long QT syndrome (LQTS) is an inherited cardiac disease characterized by a prolonged heart rate-corrected QT (QTc) interval. We investigated the genetic causes in patients with prolonged QTc intervals who were negative for pathogenic variants in three major LQTS-related genes (KCNQ1, KCNH2, and SCN5A). Molecular genetic testing was performed using a panel including 13 LQTS-related genes and 67 additional genes implicated in other cardiac diseases. Overall, putative genetic causes of prolonged QTc interval were identified in three of the 30 patients (10%). Among the LQTS-related genes, we detected a previously reported pathogenic variant, CACNA1C c.1552C>T, responsible for cardiac-only Timothy syndrome. Among the genes related to other cardiac diseases, a likely pathogenic variant, RYR2 c.11995A>G, was identified in a patient with catecholaminergic polymorphic ventricular tachycardia. Another patient who developed dilated cardiomyopathy with prolonged QTc interval was found to carry a likely pathogenic variant, TAZ c.718G>A, associated with infantile dilated cardiomyopathy. Comprehensive screening of genetic variants using multigene panel sequencing enables detection of genetic variants with a possible involvement in QTc interval prolongation, thus uncovering unknown molecular mechanisms underlying LQTS.


Subject(s)
Cardiomyopathy, Dilated , Heart , Heart Diseases , Humans , Long QT Syndrome , Mass Screening , Molecular Biology , Ryanodine Receptor Calcium Release Channel , Tachycardia, Ventricular
11.
Article in Korean | WPRIM | ID: wpr-718773

ABSTRACT

Quality control for genetic analysis has become more important with a drastic increase in testing volume and clinical demands. The molecular diagnostics division of the Korean Association of Quality Assurance for Clinical Laboratory conducted two trials in 2017 on the basis of molecular diagnostics surveys, involving 53 laboratories. The molecular diagnostics surveys included 37 tests: gene rearrangement tests for leukemia (BCR-ABL1, PML-RARA, AML1-ETO, and TEL-AML1), genetic tests for Janus kinase 2, FMS-like tyrosine kinase 3-internal tandem duplication, FMS-like tyrosine kinase 3-tyrosine kinase domain, nucleophosmin, cancer-associated genes (KRAS, EGFR, KIT, and BRAF), hereditary breast and ovarian cancer genes (BRCA1 and BRCA2), Li-Fraumeni syndrome (TP53), Wilson disease (ATP7B), achondroplasia (FGFR3), hearing loss and deafness (GJB2), Avellino (TGFBI), multiple endocrine neoplasia 2 (RET), Huntington disease, spinocerebellar ataxia, spinal and bulbar muscular atrophy, mitochondrial encephalopathy with lactic acidosis and stroke-like episodes, myoclonic epilepsy ragged red fibre, Leber hereditary optic neuropathy, Prader-raderd Angelman syndrome, Duchenne muscular dystrophy, spinal muscular atrophy, fragile X syndrome, apolipoprotein E genotyping, methylenetetrahydrofolate reductase genotyping, and ABO genotyping. Molecular genetic surveys revealed excellent results for most participants. The external quality assessment program for genetic analysis in 2017 proved useful for continuous education and the evaluation of quality improvement.


Subject(s)
Achondroplasia , Acidosis, Lactic , Angelman Syndrome , Apolipoproteins , Brain Diseases , Breast , Deafness , Education , Epilepsies, Myoclonic , Fragile X Syndrome , Gene Rearrangement , Hearing Loss , Hepatolenticular Degeneration , Huntington Disease , Janus Kinase 2 , Korea , Laboratory Proficiency Testing , Leukemia , Li-Fraumeni Syndrome , Methylenetetrahydrofolate Reductase (NADPH2) , Molecular Biology , Multiple Endocrine Neoplasia , Muscular Atrophy, Spinal , Muscular Disorders, Atrophic , Muscular Dystrophy, Duchenne , Optic Atrophy, Hereditary, Leber , Ovarian Neoplasms , Pathology, Molecular , Phosphotransferases , Quality Control , Quality Improvement , Spinocerebellar Ataxias , Vascular Endothelial Growth Factor Receptor-1
12.
Article in English | WPRIM | ID: wpr-714432

ABSTRACT

BACKGROUND: The major genetic cause of Currarino syndrome (CS), a congenital malformation syndrome typically characterized by sacral agenesis, anorectal malformation, and presence of a pre-sacral mass, is known to be pathogenic variants in motor neuron and pancreas homeobox 1 (MNX1), which exist in almost all familial cases and 30% of sporadic cases. Less commonly, a large deletion or a complex rearrangement involving the 7q36 region is associated with CS. We investigated the spectrum of MNX1 pathogenic variants and associated clinical features in the Korean patients with CS. METHODS: We enrolled 25 patients with CS, including 24 sporadic cases and one familial case. Direct sequencing of MNX1 and multiplex ligation-dependent probe amplification were performed. We also analyzed clinical phenotypes and evaluated genotype-phenotype correlations. RESULTS: We identified six novel variants amongst a total of six null variants, one missense variant, and one large deletion. The null variants included four frameshift variants (p.Gly98Alafs*124, p.Gly145Alafs*77, p.Gly151Leufs*67, and p.Ala216Profs*5) and two nonsense variants (p.Tyr186* and p.Gln212*). The missense variant, p.Lys295Gln, was located in the highly-conserved homeobox domain and was predicted to be deleterious. A large deletion involving the 7q36 region was detected in one patient. Pathogenic variants in MNX1 were detected in 28% of all CS cases and 25% of sporadic cases. The clinical phenotype was variable in patients with and without pathogenic variants; no significant genotype-phenotype correlation was observed. CONCLUSIONS: This study revealed the spectrum and phenotypic variability of MNX1 pathogenic variants in the Korean population.


Subject(s)
Genes, Homeobox , Genetic Association Studies , Humans , Motor Neurons , Multiplex Polymerase Chain Reaction , Pancreas , Phenotype
13.
Article in Korean | WPRIM | ID: wpr-194390

ABSTRACT

The Diagnostic Genetics Subcommittee of Korean Association of External Quality Assessment Service conducted two trials in 2015 based on cytogenetics and molecular genetics surveys. A total of 43 laboratories participated in the chromosome surveys, 31 laboratories participated in the fluorescence in situ hybridization surveys, and 133 laboratories participated in the molecular genetics surveys. All except one laboratory showed acceptable results in the cytogenetics surveys. The molecular genetics surveys included the following tests: Mycobacterium tuberculosis detection, hepatitis B and C virus detection and quantification, human papilloma virus genotyping, gene rearrangement tests for leukaemias and lymphomas, genetic tests for JAK2, FMS-like tyrosine kinase 3, nucleophosmin, cancer-associated genes (KRAS, EGFR, KIT, and BRAF), hereditary breast and ovarian cancer genes (BRCA1 and BRCA2), Li-Fraumeni syndrome (TP53), Wilson disease (ATP7B), achondroplasia (FGFR3), hearing loss and deafness (GJB2 ), multiple endocrine neoplasia 2 (RET), Huntington disease, spinocerebellar ataxia, spinal and bulbar muscular atrophy, mitochondrial encephalopathy with lactic acidosis and stroke like episodes, myoclonic epilepsy ragged red fibre, Leber hereditary optic neuropathy, Prader-Willi/Angelman syndrome, Duchenne muscular dystrophy, spinal muscular atrophy, fragile X syndrome (FMR1), apolipoprotein E genotyping, methylenetetrahydrofolate reductase genotyping, ABO genotyping, cytochrome P450 2C9 genotyping, cytochrome P450 2C19 genotyping, and DNA sequencing analysis. The molecular genetics surveys showed excellent results for most of the participants. The external quality assessment program for genetics analysis in 2015 proved to be helpful for continuous education and the evaluation of quality improvement.


Subject(s)
Achondroplasia , Acidosis, Lactic , Apolipoproteins , Breast , Cytochrome P-450 Enzyme System , Cytogenetics , Deafness , Education , Epilepsies, Myoclonic , Fluorescence , fms-Like Tyrosine Kinase 3 , Fragile X Syndrome , Gene Rearrangement , Genetics , Hearing Loss , Hepatitis B , Hepatolenticular Degeneration , Humans , Huntington Disease , In Situ Hybridization , Korea , Li-Fraumeni Syndrome , Lymphoma , Methylenetetrahydrofolate Reductase (NADPH2) , Molecular Biology , Multiple Endocrine Neoplasia , Muscular Atrophy, Spinal , Muscular Disorders, Atrophic , Muscular Dystrophy, Duchenne , Mycobacterium tuberculosis , Optic Atrophy, Hereditary, Leber , Ovarian Neoplasms , Papilloma , Quality Improvement , Sequence Analysis, DNA , Spinocerebellar Ataxias , Stroke
14.
Article in English | WPRIM | ID: wpr-56704

ABSTRACT

BACKGROUND: The largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection outside Middle East Asia in 2015 has necessitated the rapid expansion of laboratories that conduct MERS-CoV molecular testing in Korea, together with external quality assessment (EQA) to evaluate the assays used. METHODS: The EQA program consisted of two phases; self-validation and blind assessment. For the first EQA phase, in vitro transcribed upstream region of the envelope gene (upE) and the open reading frame (ORF)1a RNAs were used at a concentration of 1,000 copies/microL. The test panel for the second EQA phase consisted of RNA extracts from three samples, which were obtained from two MERS-CoV positive patients and one MERS-CoV negative patient. RESULTS: The first EQA phase results for 46 participants showed a linear relationship between the threshold cycle (CT) values of RNA materials and the logarithmic concentrations for both upE and ORF1a gene targets (R2=0.73 and 0.75, respectively). The mean CT value for each concentration was different depending on which commercial kit was used for the assay. Among the three commonly used kits, PowerChek MERS Real-Time PCR kit (KogeneBiotech, Korea) showed the lowest CT values at all concentrations of upE and most concentrations of ORF1a. The second EQA phase results for 47 participants were 100% correct for all tested samples. CONCLUSIONS: This EQA survey demonstrates that the MERS-CoV molecular testing performed in Korea during the 2015 outbreak is of robust capability. However, careful establishment and validation of a cut-off value are recommended to ensure good analytical sensitivity.


Subject(s)
Coronavirus Infections/diagnosis , Disease Outbreaks , Humans , Middle East Respiratory Syndrome Coronavirus/genetics , Molecular Diagnostic Techniques/standards , Quality Assurance, Health Care , RNA, Viral/analysis , Real-Time Polymerase Chain Reaction , Republic of Korea/epidemiology , Surveys and Questionnaires
15.
Article in English | WPRIM | ID: wpr-56700

ABSTRACT

Rapid and accurate identification of an influenza outbreak is essential for patient care and treatment. We describe a next-generation sequencing (NGS)-based, unbiased deep sequencing method in clinical specimens to investigate an influenza outbreak. Nasopharyngeal swabs from patients were collected for molecular epidemiological analysis. Total RNA was sequenced by using the NGS technology as paired-end 250 bp reads. Total of 7 to 12 million reads were obtained. After mapping to the human reference genome, we analyzed the 3-4% of reads that originated from a non-human source. A BLAST search of the contigs reconstructed de novo revealed high sequence similarity with that of the pandemic H1N1 virus. In the phylogenetic analysis, the HA gene of our samples clustered closely with that of A/Senegal/VR785/2010(H1N1), A/Wisconsin/11/2013(H1N1), and A/Korea/01/2009(H1N1), and the NA gene of our samples clustered closely with A/Wisconsin/11/2013(H1N1). This study suggests that NGS-based unbiased sequencing can be effectively applied to investigate molecular characteristics of nosocomial influenza outbreak by using clinical specimens such as nasopharyngeal swabs.


Subject(s)
Databases, Genetic , Genotype , High-Throughput Nucleotide Sequencing , Humans , Influenza A Virus, H1N1 Subtype/classification , Influenza, Human/diagnosis , Nasopharynx/virology , Nucleic Acid Amplification Techniques , Phylogeny , RNA, Viral/analysis , Sequence Analysis, RNA , Viral Proteins/genetics
16.
Article in English | WPRIM | ID: wpr-59851

ABSTRACT

BACKGROUND: Next-generation sequencing (NGS) can detect many more microorganisms of a microbiome than traditional methods. This study aimed to analyze the vaginal microbiomes of Korean women by using NGS that included bacteria and other microorganisms. The NGS results were compared with the results of other assays, and NGS was evaluated for its feasibility for predicting vaginitis. METHODS: In total, 89 vaginal swab specimens were collected. Microscopic examinations of Gram staining and microbiological cultures were conducted on 67 specimens. NGS was performed with GS junior system on all of the vaginal specimens for the 16S rRNA, internal transcribed spacer (ITS), and Tvk genes to detect bacteria, fungi, and Trichomonas vaginalis. In addition, DNA probe assays of the Candida spp., Gardnerella vaginalis, and Trichomonas vaginalis were performed. Various predictors of diversity that were obtained from the NGS data were analyzed to predict vaginitis. RESULTS: ITS sequences were obtained in most of the specimens (56.2%). The compositions of the intermediate and vaginitis Nugent score groups were similar to each other but differed from the composition of the normal score group. The fraction of the Lactobacillus spp. showed the highest area under the curve value (0.8559) in ROC curve analysis. The NGS and DNA probe assay results showed good agreement (range, 86.2-89.7%). CONCLUSIONS: Fungi as well as bacteria should be considered for the investigation of vaginal microbiome. The intermediate and vaginitis Nugent score groups were indistinguishable in NGS. NGS is a promising diagnostic tool of the vaginal microbiome and vaginitis, although some problems need to be resolved.


Subject(s)
Area Under Curve , Bacteria/genetics , Bacterial Proteins/genetics , Candida/genetics , Female , Fungal Proteins/genetics , Gardnerella vaginalis/genetics , High-Throughput Nucleotide Sequencing , Humans , Microbiota , RNA, Ribosomal, 16S/chemistry , ROC Curve , Sequence Analysis, DNA , Trichomonas vaginalis/genetics , Vagina/microbiology , Vaginitis/diagnosis
17.
Article in English | WPRIM | ID: wpr-64356

ABSTRACT

CHARGE syndrome MIM #214800 is an autosomal dominant syndrome involving multiple congenital malformations. Clinical symptoms include coloboma, heart defects, choanal atresia, retardation of growth or development, genital hypoplasia, and ear anomalies or deafness. Mutations in the chromodomain helicase DNA binding protein 7 (CHD7) gene have been found in 65-70% of CHARGE syndrome patients. Here, we describe a 16-month-old boy with typical CHARGE syndrome, who was referred for CHD7 gene analysis. Sequence analysis and multiplex ligation-dependent probe amplification were performed. A heterozygous 38,304-bp deletion encompassing exon 3 with a 4-bp insertion was identified. There were no Alu sequences adjacent to the breakpoints, and no sequence microhomology was observed at the junction. Therefore, this large deletion may have been mediated by non-homologous end joining. The mechanism of the deletion in the current case differs from the previously suggested mechanisms underlying large deletions or complex genomic rearrangements in the CHD7 gene, and this is the first report of CHD7 deletion by this mechanism worldwide.


Subject(s)
Alu Elements/genetics , Base Sequence , CHARGE Syndrome/diagnosis , DNA/chemistry , DNA End-Joining Repair , DNA Helicases/genetics , DNA-Binding Proteins/genetics , Exons , Gene Dosage , Heterozygote , Humans , Infant , Male , Multiplex Polymerase Chain Reaction , Mutation , Sequence Analysis, DNA , Sequence Deletion
18.
Article in Korean | WPRIM | ID: wpr-104674

ABSTRACT

Quality control for genetic tests has become more important as testing volume and clinical demands have increased dramatically. The diagnostic genetics subcommittee of Korean Association of External Quality Assessment Service conducted two trials in 2014 based on cytogenetics and molecular genetics surveys. A total of 44 laboratories participated in the chromosome surveys, 33 laboratories participated in the fl uorescence in situ hybridization (FISH) surveys, and 130 laboratories participated in the molecular genetics surveys as a part of these trials. All laboratories showed acceptable results in the chromosome and FISH surveys. The molecular genetics surveys included various tests: Mycobacterium tuberculosis detection, hepatitis B and C virus detection and quantification, human papilloma virus genotyping, gene rearrangement tests for leukaemia and lymphomas, genetic tests for JAK2, FMS-like tyrosine kinase 3, nucleophosmin, cancer-associated genes (KRAS, EGFR, KIT, and BRAF), hereditary breast and ovarian cancer genes (BRCA1 and BRCA2), Li-Fraumeni syndrome (TP53), Wilson disease (ATP7B), achondroplasia (FGFR3), Huntington disease, spinocerebellar ataxia, spinal and bulbar muscular atrophy, mitochondrial encephalopathy with lactic acidosis and stroke like episodes, myoclonic epilepsy ragged red fibre, Prader-Willi/Angelman syndrome, Duchenne muscular dystrophy, spinal muscular atrophy, fragile X syndrome, nonsyndromic hearing loss and deafness (GJB2), multiple endocrine neoplasia 2 (RET), Leber hereditary optic neuropathy (major mutation), apolipoprotein E genotyping, methylenetetrahydrofolate reductase genotyping, ABO genotyping, and DNA sequencing analysis. Molecular genetic surveys showed excellent results for most of the participants. The external quality assessment program for genetic analysis in 2014 proved to be helpful for continuous education and the evaluation of quality improvement.


Subject(s)
Achondroplasia , Acidosis, Lactic , Apolipoproteins , Breast , Cytogenetics , Deafness , Education , Epilepsies, Myoclonic , fms-Like Tyrosine Kinase 3 , Fragile X Syndrome , Gene Rearrangement , Genetics , Hearing Loss , Hepatitis B , Hepatolenticular Degeneration , Humans , Huntington Disease , In Situ Hybridization , Korea , Li-Fraumeni Syndrome , Lymphoma , Methylenetetrahydrofolate Reductase (NADPH2) , Molecular Biology , Molecular Diagnostic Techniques , Multiple Endocrine Neoplasia , Muscular Atrophy, Spinal , Muscular Disorders, Atrophic , Muscular Dystrophy, Duchenne , Mycobacterium tuberculosis , Optic Atrophy, Hereditary, Leber , Ovarian Neoplasms , Papilloma , Quality Assurance, Health Care , Quality Control , Quality Improvement , Sequence Analysis, DNA , Spinocerebellar Ataxias , Stroke
19.
Neurology Asia ; : 357-362, 2014.
Article in English | WPRIM | ID: wpr-628548

ABSTRACT

Background & Objective: Recently, mutations in PRRT2 have been found to cause paroxysmal kinesigenic dyskinesia (PKD). However, only several reports have described the detailed clinical features of patients with the PRRT2 mutation compared to those without the mutation. Furthermore, 16p11.2 microdeletions including PRRT2 also have been reported in patients with PKD; however, it is unknown to what extent the PRRT2 deletion contributes to the development of PKD. Methods: We performed mutation screening in 29 Korean patients with PKD analyzing the sequence and gene dosage of PRRT2 and their clinical features. Results: Overall, genetic abnormalities in PRRT2 were identified in 7 patients (24%): 3 from the 6 familial cases (50%) and 4 from the 23 sporadic cases (17%). The previously reported c.649dupC and c.649delC were found in 5 and 1 patient, respectively, and a novel mutation c.323_324delCA was found in 1 patient. No patients had deletions involving the PRRT2 gene. Compared with the mutation-negative cases, the age of PKD onset was earlier in the mutation-positive cases. However, there were no differences in the other clinical features. A dystonia-only phenotype was reported only in the mutation-negative cases. Contrary to common belief that patients with PKD have an excellent response to carbamazepine, 3 mutation-positive patients taking carbamazepine reported only a partial response. Conclusions: PRRT2 is a common causative gene for Korean patients with PKD. Our results show that the incomplete response to carbamazepine does not exclude the PRRT2 mutation.

20.
Article in English | WPRIM | ID: wpr-65814

ABSTRACT

BACKGROUND: The need for genotyping single nucleotide polymorphisms (SNPs) in genes encoding drug-metabolizing enzymes is increasing. Therefore, the recent focus has been on developing fully automated methods for the rapid and accurate measurement of SNPs. METHODS: We used the quenching probe (QP) method and i-densy IS-5310 to genotype 200 DNA specimens from 200 healthy Koreans and 100 whole blood from another 100 for the SNPs CYP2C19*2 and CYP2C19*3. We also performed genotyping of UGT1A1*6 and UGT1A1*28 with the above mentioned 200 DNA samples and 81 whole blood samples. The results of the assay were then compared to conventional direct sequencing. RESULTS: The allele frequencies of CYP2C19 were 25.7% for *2 and 10.3% for *3, and those of UGT1A1 were 17.3% for *6 and 11.2% for *28. These results are similar to those reported in previous studies on Korean populations. The CYP2C19 and UGT1A1 genotypes determined by the QP method perfectly matched (100.0%, K=1.000, P<0.001 for CYP2C19, and 99.6%, K=0.992, P<0.001 for UGT1A1) those determined by direct sequencing, barring a single exception for the UGT1A1 genotype in 1 DNA specimen. CONCLUSIONS: Our results suggest that the QP method, owing to its speed and ease of use, will enable rapid and sensitive diagnosis in clinical laboratories.


Subject(s)
Diagnosis , DNA , Gene Frequency , Genotype , Polymorphism, Single Nucleotide
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