Mutation Analysis of the TGFBI Gene in Consecutive Korean Patients With Corneal Dystrophies

Background

Mutations in the transforming growth factor β-induced gene (TGFBI) are major causes of genetic corneal dystrophies (CDs), which can be grouped into TGFBI CDs. Although a few studies have reported the clinical and genetic features of Korean patients with TGFBI CD, no data are available regarding the frequency and spectrum of TGFBI mutations in a consecutive series of Korean patients with clinically diagnosed CDs.

Methods

Patients with any type of CD, who underwent both ophthalmologic examination and TGFBI gene analysis by Sanger sequencing at a tertiary care hospital in Seoul, Korea from 2006 to 2013, were enrolled in this study.

Results

Among a total of 89 patients, 77 (86.5%) were diagnosed as having clinical TGFBI CD. Seventy-three out of 74 patients (98.6%) with granular CD type 2 (GCD2), had the p.R124H mutation. Of particular note, one patient with rapidly progressive CD had the p.R124H mutation as well as a novel nonsense variant with unknown clinical significance (p.A179*). In three patients with lattice CD type 1 (LCD1), one known mutation (p.R124C) and two novel variants (p.L569Q and p.T621P) in the TGFBI gene were identified.

Conclusions

This study provides epidemiological insight into CDs in a Korean population and reaffirms that GCD2 is the most common TGFBI CD phenotype and that p.R124H is the only mutation identified in patients with GCD2. In addition, we broaden the spectrum of TGFBI mutations by identifying two novel missense variants in patients with LCD1.

Identification of a Novel De Novo Variant in the PAX3 Gene in Waardenburg Syndrome by Diagnostic Exome Sequencing: The First Molecular Diagnosis in Korea

Waardenburg syndrome (WS) is a clinically and genetically heterogeneous hereditary auditory pigmentary disorder characterized by congenital sensorineural hearing loss and iris discoloration. Many genes have been linked to WS, including PAX3, MITF, SNAI2, EDNRB, EDN3, and SOX10, and many additional genes have been associated with disorders with phenotypic overlap with WS. To screen all possible genes associated with WS and congenital deafness simultaneously, we performed diagnostic exome sequencing (DES) in a male patient with clinical features consistent with WS. Using DES, we identified a novel missense variant (c.220C>G; p.Arg74Gly) in exon 2 of the PAX3 gene in the patient. Further analysis by Sanger sequencing of the patient and his parents revealed a de novo occurrence of the variant. Our findings show that DES can be a useful tool for the identification of pathogenic gene variants in WS patients and for differentiation between WS and similar disorders. To the best of our knowledge, this is the first report of genetically confirmed WS in Korea.

Intermittent antibiotic therapy for nodular bronchiectatic Mycobacterium avium complex lung disease

RATIONALE

Although intermittent, three-times-weekly therapy is recommended for the initial treatment of noncavitary nodular bronchiectatic Mycobacterium avium complex (MAC) lung disease, supporting data are limited.

OBJECTIVES

To evaluate the clinical efficacy of intermittent therapy compared with daily therapy for nodular bronchiectatic MAC lung disease.

METHODS

A retrospective cohort study of 217 patients with treatment-naive noncavitary nodular bronchiectatic MAC lung disease. All patients received either daily (n = 99) or intermittent therapy (n = 118) that included clarithromycin or azithromycin, rifampin, and ethambutol.

MEASUREMENTS AND MAIN RESULTS

Modification of the initial antibiotic therapy occurred more frequently in the daily therapy group than in the intermittent therapy group (46 vs. 21%; P < 0.001); in particular, ethambutol was more frequently discontinued in the daily therapy group than in the intermittent therapy group (24 vs. 1%; P ≤ 0.001). However, the rates of symptomatic improvement, radiographic improvement, and sputum culture conversion were not different between the two groups (daily therapy vs. intermittent therapy: 75 vs. 82%, P = 0.181; 68 vs. 73%, P = 0.402; 76 vs. 67%, P = 0.154, respectively). In addition, the adjusted proportion of sputum culture conversion was similar between the daily therapy (71.3%; 95% confidence interval, 59.1-81.1%) and the intermittent therapy groups (73.6%; 95% confidence interval, 62.9-82.2%; P = 0.785).

CONCLUSIONS

These results suggest that intermittent three-times-weekly therapy with a macrolide, rifampin, and ethambutol is a reasonable initial treatment regimen for patients with noncavitary nodular bronchiectatic MAC lung disease. Clinical trial registered with www.clinicaltrials.gov (NCT 00970801).

A novel missense mutation in GCH1 gene in a Korean family with Segawa disease

Segawa disease is a rare disorder presenting gait disturbance and dystonia with marked fluctuation, and caused by GTP cyclohydrolase 1 (GCH1) deficiency. Our 15-year-old patient was admitted for fluctuating gait disturbance lasted for 4years. Administration of levodopa resulted in a dramatic improvement, and positron emission tomography using 18F-FP-CIT showed normal striatal dopamine transporter activity. Genetic study revealed a novel missense mutation in the exon 5 of GCH1 gene at c.623C>A in the proband and his father, and in silico analysis predicted that the protein function was probably damaged. Mutation analysis and searching with genetic databases might help diagnosing Segawa disease and predicting protein function.

Mutations in DDX58, which encodes RIG-I, cause atypical Singleton-Merten syndrome

Singleton-Merten syndrome (SMS) is an autosomal-dominant multi-system disorder characterized by dental dysplasia, aortic calcification, skeletal abnormalities, glaucoma, psoriasis, and other conditions. Despite an apparent autosomal-dominant pattern of inheritance, the genetic background of SMS and information about its phenotypic heterogeneity remain unknown. Recently, we found a family affected by glaucoma, aortic calcification, and skeletal abnormalities. Unlike subjects with classic SMS, affected individuals showed normal dentition, suggesting atypical SMS. To identify genetic causes of the disease, we performed exome sequencing in this family and identified a variant (c.1118A>C [p.Glu373Ala]) of DDX58, whose protein product is also known as RIG-I. Further analysis of DDX58 in 100 individuals with congenital glaucoma identified another variant (c.803G>T [p.Cys268Phe]) in a family who harbored neither dental anomalies nor aortic calcification but who suffered from glaucoma and skeletal abnormalities. Cys268 and Glu373 residues of DDX58 belong to ATP-binding motifs I and II, respectively, and these residues are predicted to be located closer to the ADP and RNA molecules than other nonpathogenic missense variants by protein structure analysis. Functional assays revealed that DDX58 alterations confer constitutive activation and thus lead to increased interferon (IFN) activity and IFN-stimulated gene expression. In addition, when we transduced primary human trabecular meshwork cells with c.803G>T (p.Cys268Phe) and c.1118A>C (p.Glu373Ala) mutants, cytopathic effects and a significant decrease in cell number were observed. Taken together, our results demonstrate that DDX58 mutations cause atypical SMS manifesting with variable expression of glaucoma, aortic calcification, and skeletal abnormalities without dental anomalies.

Spinal Stenosis with Paraparesis in a Korean Boy with Albright's Hereditary Osteodystrophy: Identification of a Novel Nonsense Mutation in the GNAS

Children with Albright's hereditary osteodystrophy (AHO) suffering from spinal cord compression are rarely reported worldwide. The association of compressive myelopathy with AHO is not still well known. AHO is a rare heterogeneous group of inherited disorders and results from the GNAS mutation. AHO manifests in two different phenotypes, pseudohypoparathyroidism type Ia (PHP-Ia) and pseudopsedohypoparthyroidim (PPHP), which may happen in the same family members. We present the case of a 15-year-old boy with AHO features, who was later diagnosed with PHP-Ia. He suffered from cervical myelopathy with paraparesis due to spinal stenosis. His mother with AHO phenotype was diagnosed with PPHP without spinal stenosis. Genetic analysis revealed a novel heterozygous nonsense mutation within exon 1 of GNAS(c.49A>T; p.Lys17*) in both of them. This is the first clinically, biochemically, and genetically identified child case of spinal stenosis and paraparesis associated with PHP-Ia, having a novel GNAS mutation in Korea.

A novel splice site mutation in the PAX6 gene in a Korean family with isolated aniridia

Aniridia is a rare congenital ocular disorder of complete or partial iris hypoplasia. Frequently associated ocular changes include corneal abnormalities, cataract, glaucoma, and foveal hypoplasia. In most cases, aniridia is caused by decreased dosage of the paired box 6 (PAX6) gene, which is located in chromosome 11p13. We report the case of a Korean family with isolated aniridia inherited in an autosomal dominant manner. The proband was a one-month-old boy. He presented with bilateral complete aniridia and congenital glaucoma. His four-year-old sister had bilateral complete aniridia, glaucoma, and a corneal ulcer. His father had bilateral microcornea and cataract without aniridia. Using PAX6 sequencing analysis, we identified a deletion at the splice donor site of intron 8 in the proband (c.357+1delG). To our knowledge, this variant has not been previously described.

Hypoparathyroidism in a 3-year-old Korean boy with Sotos syndrome and a novel mutation in NSD1

Sotos syndrome is a common genetic overgrowth syndrome caused by a mutation of the NSD1 gene, which is located at chromosome 5q35 and normally encodes a histone methyltransferase protein. The general characteristics of this syndrome include a characteristic facial appearance, developmental delay, and overgrowth, resulting in macrocephaly and tall stature. We describe rhabdomyolysis and hypocalcemia due to hypoparathyroidism in a 3-year-old Korean boy with Sotos syndrome. He was diagnosed with Sotos syndrome based on the typical phenotype and has a heterozygous nonsense mutation (c.4710C>A [p.Cys1570*]) of the NSD1 gene, which causes a premature stop codon and a truncating protein mutation. Hypoparathyroidism has never been described in Sotos syndrome. This report may therefore expand the phenotypic spectrum of this syndrome.

Letter to the Editor: A Novel Mutation in the CREBBP Gene of a Korean Girl with Rubinstein-Taybi syndrome

Rubinstein-Taybi syndrome (RTS) is a rare congenital disorder characterized by broad thumbs and halluces, dysmorphic facial features, mental retardation, and short stature. Mutations in the cAMP-response element binding protein-BP (CREBBP) gene (50-60% of cases) and E1A-binding protein (EP300, 3%) are known genetic causes in affected individuals. Here, we describe a genetically confirmed Korean RTS patient with atypical features, including Hirschsprung disease and growth hormone deficiency. Mutational analysis revealed a novel heterozygous frameshift mutation, c.2064_2077del14 (p.Gly689Cysfs*32) in the CREBBP gene.

Osteogenesis imperfecta Type I caused by a novel mutation in the start codon of the COL1A1 gene in a Korean family

Osteogenesis imperfecta (OI) comprises a heterogeneous group of disorders characterized by susceptibility to bone fractures ranging in severity from perinatal death to a subtle increase in fracture frequency. We report the case of a patient who appeared healthy at birth and did not experience any fractures until 12 months of age. We observed blue sclera, frequent fractures without commensurate trauma, nearly normal stature, the absence of dentinogenesis imperfecta, no bony deformity, and no limitation of mobility in the patient--all characteristics suggestive of OI Type I. The patient's mother also had blue sclera and a history of frequent fracture episodes until the age of 15 years. A novel COL1A1 missense mutation (c.2T>G) disrupting the start codon of the gene (ATG to AGG (Met1Arg)) was found in the patient and his mother.

Identification of novel PKD1 and PKD2 mutations in Korean patients with autosomal dominant polycystic kidney disease

Background

Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disorder. It is caused by mutations in the PKD1 and PKD2 genes, and manifests as progressive cyst growth and renal enlargement, resulting in renal failure. Although there have been a few studies on the frequency and spectrum of mutations in PKD1 and PKD2 in Korean patients with ADPKD, only exons 36–46, excluding the duplicated region, were analyzed, which makes it difficult to determine accurate mutation frequencies and mutation spectra.

Methods

We performed sequence analysis of 20 consecutive unrelated ADPKD patients using long-range polymerase chain reaction (PCR) to avoid pseudogene amplification, followed by exon-specific PCR and sequencing of the all exons of these two genes. Multiplex ligation-dependent probe amplification was performed in patients in whom pathogenic mutations in PKD1 or PKD2 were not identified by LR-PCR and direct sequencing to detect large genomic rearrangements.

Results

All patients met the diagnostic criteria of ADPKD, and pathogenic mutations were found in 18 patients (90.0%), comprising 15 mutations in PKD1 and three in PKD2. Among 10 novel mutations, eight mutations were found in the PKD1 gene while two mutations were found in the PKD2 gene. Eight of 14 PKD1 mutations (57.1%) were located in the duplicated region.

Conclusions

This study expands the spectra of mutations in the PKD1 and PKD2 genes and shows that the mutation frequencies of these genes in Korean ADPKD patients are similar to those reported in other ethnicities. Sequence analysis, including analysis of the duplicated region, is essential for molecular diagnosis of ADPKD.

Evaluation of the iNtRON VRE vanA/vanB real-time PCR assay for detection of vancomycin-resistant enterococci

BACKGROUND

Recently, the iNtRON VRE vanA/vanB real-time PCR (iNtRON; iNtRON Biotechnology, Korea) assay, a multiplex real-time PCR method, was introduced. In this prospective study, we compared the iNtRON assay with the Seeplex VRE ACE detection kit (Seeplex; Seegene, Korea), a conventional multiplex PCR assay.

METHODS

A chromogenic agar-based culture, in which pre-selected vancomycin-resistant enterococci (VRE) was grown and subsequently plated on blood agar with vancomycin disks, was regarded as the reference method. A total of 304 consecutive rectal swab specimens were tested for VRE by culture and by iNtRON and Seeplex PCR assays. For the PCR assays, specimens were enriched for 16-24 hr before PCR.

RESULTS

VRE were isolated from 44 (14.5%) specimens by chromogenic agar-based culture. The clinical sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the iNtRON assay were 100% (95% confidence interval: 89.8%-100%), 99.2% (96.9%-99.9%), 95.6% (83.6%-99.2%), and 100% (98.2%-100%), respectively, while those of the Seeplex assay were 97.7% (86.2%-99.9%), 99.6% (97.5%-99.9%), 97.7% (86.2%-99.9%), and 99.6% (97.5%-99.9%), respectively. The iNtRON assay had a detection limit of 3,159 copies/µL and 13,702 copies/µL for the vanA and vanB genes, respectively. No cross-reactivity was observed in 11 non-VRE bacterial culture isolates.

CONCLUSIONS

The overall performance of the iNtRON assay was comparable to that of a chromogenic agar-based culture method for prompt identification of VRE-colonized patients in hospitals. This assay could be an alternative or supportive method for the effective control of nosocomial VRE infection.

Does type I truly dominate hepatic glycogen storage diseases in Korea?: a single center study

PURPOSE

There are no studies of hepatic glycogen storage diseases (GSDs) other than type I and III in Korea. We aimed on investigating the characteristics of hepatic GSDs in Korea diagnosed and followed at a single center.

METHODS

We retrospectively analyzed patients who were diagnosed as GSD and followed at Samsung Medical Center from January, 1997 to December, 2013. Clinical manifestations, laboratory results, treatment, and prognosis were investigated.

RESULTS

Twenty-one patients were included in the study. The types of 17 patients were confirmed by enzyme activity tests and/or gene analysis. GSD Ia was diagnosed in 7 patients (33.3%), Ib in 1 patient (4.8%), III in 2 patients (9.5%), IV in 1 patient (4.8%), and IX in 6 patients (28.6%). Types other than GSD I constituted 52.9% (9/17) of the patients diagnosed with a specific type of hepatic GSD. The median age at presentation was 2 years. Hepatomegaly was observed in 95.2%, elevated liver transaminases in 90.5%, and hyperlactacidemia in 81.0% of the patients. The duration for follow-up was 77±62.0 months. Uncooked corn starch was initiated in all the patients. No mortality was observed during the follow-up period, and liver transplantation was performed in 14.3%.

CONCLUSION

Types other than GSD I comprised more than half of the patients diagnosed with a specific type of hepatic GSD. Clinical suspicion and thorough evaluation of hepatic GSDs in Korea should be focused not only on GSD I, but also on other types.

Autosomal dominant familial neurohypophyseal diabetes insipidus caused by a mutation in the arginine-vasopressin II gene in four generations of a Korean family

Autosomal dominant neurohypophyseal diabetes insipidus is a rare form of central diabetes insipidus that is caused by mutations in the vasopressin-neurophysin II (AVP-NPII) gene. It is characterized by persistent polydipsia and polyuria induced by deficient or absent secretion of arginine vasopressin (AVP). Here we report a case of familial neurohypophyseal diabetes insipidus in four generations of a Korean family, caused by heterozygous missense mutation in exon 2 of the AVP-NPII gene (c.286G>T). This is the first report of such a case in Korea.

Performance evaluation of the Xpert MTB/RIF assay according to its clinical application

Background

The Xpert MTB/RIF assay (Xpert assay; Cepheid, Sunnyvale, CA) is becoming the test of choice for the rapid diagnosis of tuberculosis and rifampin (RIF) resistance. The aim of this study was to evaluate the performance of the Xpert assay with respect to its clinical application at a tertiary care hospital in Korea, a country with an intermediate tuberculosis burden and high-resource.

Methods

A total of 303 Xpert assay results from 109 smear-positive and 194 smear-negative respiratory specimens were retrospectively reviewed. Based on patients’ medical records, four categories of clinical applications of the Xpert assay were identified: (1) the diagnosis of pulmonary tuberculosis in patients with a high probability of pulmonary tuberculosis according to their clinical and radiological features; (2) the exclusion of tuberculosis in clinically indeterminate patients for pulmonary tuberculosis; (3) the differentiation of Mycobacterium tuberculsosis (MTB) from nontuberculous mycobacteria in a smear-positive specimen; and (4) the diagnosis of RIF resistance. Standard culture and drug susceptibility tests were used as reference methods.

Results

The sensitivity of the Xpert assay for MTB detection in category 1 was 89.8% (95% confidence interval [CI], 78.5-95.8%), but 66.7% (95% CI, 12.5-98.2%) in category 2. The positive predictive values ranged from 33.3% (95% CI, 6.0-75.9%) in category 2 to 91.3% and 91.7% in categories 1 and 3, respectively. The negative predictive values were over 90% in all categories. The Xpert assay correctly detected RIF resistance in six of the seven (85.7%) isolates tested.

Conclusions

The Xpert assay exhibited variable performance according to its clinical application; this finding cautions that careful interpretation for the results of this assay would be needed according to its intended purpose.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-014-0589-x) contains supplementary material, which is available to authorized users.

Mutant Enrichment with 3'-Modified Oligonucleotides (MEMO)-Quantitative PCR for Detection of NPM1 Mutations in Acute Myeloid Leukemia

BACKGROUND

Detection of NPM1 mutations in acute myeloid leukemia (AML) is important for risk stratification, treatment decision, and therapeutic monitoring. We have designed a real-time PCR method implementing the Mutant enrichment with 3'-modified oligonucleotides (MEMO) technique to detect NPM1 mutations and validated its utility in clinical samples.

METHODS

Sensitivity and linearity were evaluated using serially diluted NPM1-positive samples. Clinical usefulness was assessed by measuring the levels of mutant alleles in 29 patients at diagnosis and in ten patients after induction chemotherapy.

RESULTS

Excellent linear relationships between the mutant allele proportion and the threshold cycle (Ct) values (r = 0.999) were observed in a range of 1:1-1:10(3) . MEMO-PCR was able to detect NPM1 mutations regardless of mutant type and also detected novel mutants (964_967delTGGAinsATGATGTC, 957_959delCTGinsATGCATG, 960insTAAG, and 960insTCAG). The concentrations of NPM1 mutant alleles decreased after induction chemotherapy in accordance with the reduction of tumor cells, and in one case, NPM1 mutant alleles were detectable about 7 months before morphological relapse.

CONCLUSION

MEMO-quantitative PCR was shown to detect virtually all types of NPM1 mutants with high sensitivity and specificity. This novel method may be useful in the diagnosis of AML with an NPM1 mutation, the detection of minimal residual disease, and the monitoring of treatment response.

Midbrain hypometabolism in fatal familial insomnia: a case report and a statistical parametric mapping analysis of a korean family

Background and Methods

Fatal familial insomnia (FFI) is a rare genetic disease characterized by intractable insomnia, dysautonomia, and dementia. Herein we describe a patient with FFI. In order to study brain glucose hypometabolism in the patient, we used statistical parametric mapping (SPM) analysis of [¹⁸F]-fluorodeoxyglucose positron emission tomography (FDG-PET).

Case Report

The patient was a 34-year-old Korean man. He presented with intractable insomnia, rapidly progressive dementia and autonomic disturbances. A comprehensive clinical investigation was conducted, including brain MRI, electroencephalography, polysomnography, neuropsychological tests, FDG-PET and genomic tests. SPM analysis was performed using 7 healthy controls. Direct sequencing of the PRNP gene identified a heterozygous p. Asp179Asn mutation homozygous for methionine at codon 129 and for glutamate at codon 219. The results of the SPM analysis showed marked hypometabolism in the deep cerebral nuclei (including the bilateral thalami, caudate nuclei, and hypothalamus), association cortices (including the frontal, lateral temporal, inferior parietal lobule and posterior cingulate gyri), and midbrain.

Conclusions

This is the first Korean report of FFI, in which the family showed male phenotypic predominance. The patient's SPM analysis demonstrated brain hypometabolism in the midbrain and the hypothalamus, as well as the thalami, caudate nuclei, and multiple cortical regions. These results contribute further to the overall understanding of the pathophysiology of FFI.