Moon Woo Seong

The Alu-Rich Genomic Architecture of SPAST Predisposes to Diverse and Functionally Distinct Disease-Associated CNV Alleles

Intragenic copy-number variants (CNVs) contribute to the allelic spectrum of both Mendelian and complex disorders. Although pathogenic deletions and duplications in SPAST (mutations in which cause autosomal-dominant spastic paraplegia 4 [SPG4]) have been described, their origins and molecular consequences remain obscure. We mapped breakpoint junctions of 54 SPAST CNVs at nucleotide resolution. Diverse combinations of exons are deleted or duplicated, highlighting the importance of particular exons for spastin function. Of the 54 CNVs, 38 (70%) appear to be mediated by an Alu-based mechanism, suggesting that the Alu-rich genomic architecture of SPAST renders this locus susceptible to various genome rearrangements. Analysis of breakpoint Alus further informs a model of Alu-mediated CNV formation characterized by small CNV size and potential involvement of mechanisms other than homologous recombination. Twelve deletions (22%) overlap part of SPAST and a portion of a nearby, directly oriented gene, predicting novel chimeric genes in these subjects genomes. cDNA from a subject with a SPAST final exon deletion contained multiple SPAST:SLC30A6 fusion transcripts, indicating that SPAST CNVs can have transcriptional effects beyond the gene itself. SLC30A6 has been implicated in Alzheimer disease, so these fusion gene data could explain a report of spastic paraplegia and dementia cosegregating in a family with deletion of the final exon of SPAST. Our findings provide evidence that the Alu genomic architecture of SPAST predisposes to diverse CNV alleles with distinct transcriptional--and possibly phenotypic--consequences. Moreover, we provide further mechanistic insights into Alu-mediated copy-number change that are extendable to other loci.

Usefulness of a Rapid Real-time PCR Assay in Prenatal Screening for Group B Streptococcus Colonization

Background Group B streptococcus (GBS) infection is a leading cause of neonatal morbidity and mortality worldwide. Here, we present the analytical and diagnostic usefulness of a new real-time PCR-based assay (Xpert GBS; Cepheid, USA) for rapid and accurate prenatal GBS screening. Methods We enrolled 175 pregnant women who were between 35 and 39 weeks of gestation. The analytical performance of the Xpert GBS assay was first tested using a reference GBS strain. Next, to test diagnostic performance, rectovaginal swabs were obtained from pregnant women who visited the hospital for regular antenatal screening after 34 weeks of gestation. The results of the Xpert GBS assay were compared to those of standard culture for the detection of prenatal GBS colonization. Results When any positive result from Xpert GBS or culture was considered a true positive, the sensitivity of the Xpert GBS assay and culture were 91% (20/22; 95% CI [confidence interval], 72-98) and 68% (15/22; 95% CI, 47-84), respectively. The specificity of both methods was 100% (153/153; 95% CI, 97-100). The sensitivity and specificity of the Xpert GBS assay, using the culture results as a reference, were 86.7% and 95.6%, respectively. In the Xpert GBS assay, the median threshold cycle of vaginally colonized samples was significantly lower than rectally colonized samples (P<0.01). Conclusions The Xpert GBS assay is an accurate, rapid, easy-to-use test for the detection of maternal GBS colonization in prenatal screening that might be especially useful in clinical settings where standard culture is not feasible.

Monochorionic dizygotic twins with discordant sex and confined blood chimerism.

Monochorionic (MC) pregnancy in humans is usually considered to be associated only with monozygotic twinning. However, several reports have revealed that dizygotic (DZ) twins can also share a chorion during pregnancy. A chimera is defined as an organism that contains different cells derived from two or more distinct zygotes. As artificial reproductive techniques develop, it can be predicted that the occurrence of MC DZ twins will increase, and DNA-fingerprinting methods, such as short tandem repeat (STR) analysis, will be essential for their accurate diagnosis. We report the first Korean case of MC DZ twins with blood chimerism, 46,XX/46,XY, as a consequence of in vitro fertilization/embryo transfer. The clinical phenotypes of the twins’ genitalia were complete female and male, respectively. Monochorionicity was confirmed by pathological analysis of the placenta after delivery. The dizygosity and confined blood chimerism of the twins were confirmed by STR analysis using their peripheral lymphocytes and skin fibroblasts. The confined blood chimerism of the twins can be considered similar to the status of the hematopoietic system in patients after allogenic bone marrow transplantation. Conclusion: When MC twins with discordant sex are expected during pregnancy, it is important to consider the possibility of DZ twins showing normal sexual development, especially in twins who were fertilized using artificial reproductive techniques.

Revisit of multiple epiphyseal dysplasia: ethnic difference in genotypes and comparison of radiographic features linked to the COMP and MATN3 genes.

Multiple epiphyseal dysplasia (MED) is a genetically heterogeneous group of diseases characterized by variable degrees of epiphyseal abnormality primarily involving the hip and knee joints. The purpose of this study was to investigate the frequency of mutations in individuals with a clinical and radiographic diagnosis of MED and to test the hypothesis that characteristic radiological findings may be helpful in predicting the gene responsible. The radiographs of 74 Korean patients were evaluated by a panel of skeletal dysplasia experts. Six genes known to be associated with MED (COMP, MATN3, COL9A1, COL9A2, COL9A3, and DTDST) were screened by sequencing. Mutations were found in 55 of the 63 patients (87%). MATN3 mutations were found in 30 patients (55%), followed by COMP mutations in 23 (41%), and COL9A2 and DTDST mutations in one patient (2%) each. Comparisons of radiographic findings in patients with COMP and MATN3 mutations showed that albeit marked abnormalities in hip and knee joints were observed in both groups, the degree of involvement and the morphology of dysplastic epiphyses differed markedly. The contour of the pelvic acetabulum, the presence of metaphyseal vertical striations, and/or the brachydactyly of the hand were also found to be highly correlated with the genotypes. The study confirms that MATN3 and COMP are the genes most frequently responsible for MED and that subtle radiographic signs may give precious indications on which gene(s) should be prioritized for mutational screening in a given individual.

Analysis of the Vaginal Microbiome by Next-Generation Sequencing and Evaluation of its Performance as a Clinical Diagnostic Tool in Vaginitis

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.

COQ6 Mutations in Children With Steroid-Resistant Focal Segmental Glomerulosclerosis and Sensorineural Hearing Loss

The phenotypic combination of steroid-resistant focal segmental glomerulosclerosis (SR-FSGS) and sensorineural hearing loss has been mainly reported in patients with mitochondrial cytopathies, including primary coenzyme Q10 (CoQ10) deficiency. In this report of 10 children with SR-FSGS and sensorineural hearing loss, we found 6 patients with biallelic COQ6 mutations. Median age at the onset of nephrotic syndrome was 29 (range, 15-47) months. All patients progressed to end-stage renal disease within a median of 13 (range, 1-27) months after the onset. Kidney biopsy revealed abnormal mitochondrial proliferation in podocytes in all 6 patients. None of the 5 patients who underwent kidney transplantation developed recurrence of FSGS. Primary CoQ10 deficiency due to COQ6 mutations should be considered in children presenting with both SR-FSGS and sensorineural hearing loss. An early diagnosis of COQ6 mutations is essential because the condition is treatable when CoQ10 supplementation is started at the early stage. We recommend early kidney biopsy because detection of abnormal mitochondrial proliferation in podocytes might provide an earlier diagnostic clue.

Chimerism Monitoring after Allogeneic Hematopoietic Stem Cell Transplantation Using Quantitative Real-Time PCR of Biallelic Insertion/Deletion Polymorphisms

An accurate and sensitive determination of chimerism status is mandatory after allogeneic hematopoietic stem cell transplantation. We evaluated the performance of the AlleleSEQR Chimerism Assay, which is based on quantitative real-time PCR of biallelic indel markers, using 79 recipient-donor pairs. When the informativeness of the screening panel composed of 34 markers was determined using 130 unrelated individuals, it presented a >99.9% probability of selecting at least one informative marker. The analytic sensitivity of the indel marker assay was estimated using a serially diluted DNA mixture. The detection limit of the quantitative assay approached 0.024% when 250 ng of DNA was used. We used 175 samples that had undergone hematopoietic stem cell transplantation to compare the quantitative real-time PCR assay with short tandem repeat quantitation. Results from the AlleleSEQR Chimerism Assay showed excellent correlation with those from the short tandem repeat method (r(2) = 0.931). Moreover, in some patients with relapsed leukemia, the AlleleSEQR Chimerism Assay was able to detect an early increase in recipient DNA levels that was undetectable using the short tandem repeat method. The indel marker-based AlleleSEQR Chimerism Assay can be a useful tool for following up patients after hematopoietic stem cell transplantation because of its high sensitivity compared with the conventional short tandem repeat method.

Neonatal invasive Streptococcus gallolyticus subsp. pasteurianus infection with delayed central nervous system complications

Group D streptococci are known to cause newborn septicemia and meningitis, but the Streptococcus bovis group strains rarely cause serious neonatal infections in Korea. Central nervous system (CNS) complications of neonatal S. bovis group infection have rarely been reported. In adults, S. bovis group strains cause bacteremia and endocarditis, and are associated with gastrointestinal malignancy. However, only a few studies have reported meningitis and septicemia in infants. Here, we describe a case of bacteremia and meningitis due to Streptococcus gallolyticus subsp. pasteurianus with a delayed CNS complication in an infant. A 28-day-old male infant was admitted to the hospital with a 1-day history of fever. Cultures of blood, cerebrospinal fluid, and urine showed the presence of S. bovis group strain-S. gallolyticus subsp. pasteurianus. He was discharged after 21 days of intravenous ampicillin and cefotaxime administration. Two weeks later, he was readmitted with a fever and short episodes of tonic-clonic movements. Brain magnetic resonance imaging showed marked bilateral frontal subdural effusion. He was discharged after 31 days of antibiotic therapy, and no neurological sequelae were observed at the 9-month follow-up. In conclusion, we present a rare case of neonatal S. gallolyticus subsp. pasteurianus infection causing urinary tract infection, septicemia, meningitis, and delayed CNS complications. This case emphasizes the need for physicians to be aware of S. bovis infection in infants.

Novel COL2A1 variant (c.619G>A, p.Gly207Arg) manifesting as a phenotype similar to progressive pseudorheumatoid dysplasia and spondyloepiphyseal dysplasia, Stanescu type.

Progressive pseudorheumatoid dysplasia (PPRD) is a rare, autosomal‐recessive condition characterized by mild spondyloepiphyseal dysplasia (SED) and severe, progressive, early‐onset arthritis due to WISP3 mutations. SED, Stanescu type, is a vaguely delineated autosomal‐dominant dysplasia of unknown genetic etiology. Here, we report three individuals from two unrelated families with radiological features similar to PPRD and SED, Stanescu type who share the same novel COL2A1 variant and were matched following discussion at an academic conference. In the first family, we performed whole‐exome sequencing on three family members, two of whom have a PPRD‐like phenotype, and identified a heterozygous variant (c.619G>A, p.Gly207Arg) in both affected individuals. Independently, targeted sequencing of the COL2A1 gene in an unrelated proband with a similar phenotype identified the same heterozygous variant. We suggest that the p.Gly207Arg variant causes a distinct type II collagenopathy with features of PPRD and SED, Stanescu type.

Comparative Evaluation of Three Homogenization Methods for Isolating Middle East Respiratory Syndrome Coronavirus Nucleic Acids From Sputum Samples for Real-Time Reverse Transcription PCR

Background Real-time reverse transcription PCR (rRT-PCR) of sputum samples is commonly used to diagnose Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Owing to the difficulty of extracting RNA from sputum containing mucus, sputum homogenization is desirable prior to nucleic acid isolation. We determined optimal homogenization methods for isolating viral nucleic acids from sputum. Methods We evaluated the following three sputum-homogenization methods: proteinase K and DNase I (PK-DNase) treatment, phosphate-buffered saline (PBS) treatment, and N-acetyl-L-cysteine and sodium citrate (NALC) treatment. Sputum samples were spiked with inactivated MERS-CoV culture isolates. RNA was extracted from pretreated, spiked samples using the easyMAG system (bioMérieux, France). Extracted RNAs were then subjected to rRT-PCR for MERS-CoV diagnosis (DiaPlex Q MERS-coronavirus, SolGent, Korea). Results While analyzing 15 spiked sputum samples prepared in technical duplicate, false-negative results were obtained with five (16.7%) and four samples (13.3%), respectively, by using the PBS and NALC methods. The range of threshold cycle (Ct) values observed when detecting upE in sputum samples was 31.1–35.4 with the PK-DNase method, 34.7–39.0 with the PBS method, and 33.9–38.6 with the NALC method. Compared with the control, which were prepared by adding a one-tenth volume of 1:1,000 diluted viral culture to PBS solution, the ranges of Ct values obtained by the PBS and NALC methods differed significantly from the mean control Ct of 33.2 (both P<0.0001). Conclusions The PK-DNase method is suitable for homogenizing sputum samples prior to RNA extraction.