Eun Hee Lee

High-resolution human papillomavirus genotyping by MALDI-TOF mass spectrometry

We describe a matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF) mass spectrometry (MS)-based assay for human papillomavirus (HPV) genotyping—the restriction fragment mass polymorphism (RFMP) assay, which is based on mass measurement of genotype-specific oligonucleotide fragments generated by TypeIIS restriction endonuclease cleavage after recognition sites have been introduced by PCR amplification. The use of a TypeIIS restriction enzyme makes the RFMP assay independent of sequence and applicable to a wide variety of HPV genotypes, because these enzymes have cleavage sites at a fixed distance from their recognition sites. After PCR amplification, samples are subjected to restriction enzyme digestion with FokI and BtsCI and desalting using Oasis purification plates, followed by analysis by MALDI-TOF MS. Overall, the protocol is simple, takes ∼4–4.5 h and can accurately detect and identify at least 74 different HPV genotypes.

Prevalence and Distribution of Human Papillomavirus Infection in Korean Women as Determined by Restriction Fragment Mass Polymorphism Assay

The development of a prophylactic vaccine that targets human papillomaviruses (HPV) 6, 11, 16, and 18 to prevent cervical cancer has increased interest in the ethnic and geographical distributions of HPV genotypes. We investigated HPV prevalence and type distribution by restriction fragment mass polymorphism (RFMP) testing a total of 60,775 specimens (aged 18-79 yr, median 44) taken from liquid-based cytology. Overall HPV positive rate of total patients was 34.2%. Among the positive patients, 87.7% was single type infections, and 12.3% was multiple HPV types. HPV-16 was the most prevalent genotype observed in 2,307 (26.0%), followed by type 52 in 2,269 (25.5%), type 58 in 1,090 (12.3%), type 18 in 633 (7.1%), type 56 in 436 (4.9%). The pattern of high risk-HPV positive rate according to age showed U-shape with a peak in HPV prevalence among women less than 30 yr of age, and a second peak among the older females aged 70 to 79 yr. The leading four high-risk HPV genotypes were HPV-16, HPV-52, HPV-58, and HPV-18 in descending order. In conclusion, this study provides the most representative prevalence and type-specific distribution of HPV among Korean women, and demonstrates that the epidemiology of HPV infection is different from that of other regions of the world.

Interferon-α Treatment of Chronic Hepatitis C in Children with Hemophilia

Background In children with hemophilia, hepatitis C virus (HCV) is the major cause of chronic liver disease. In this study, long-term efficacy of interferon-&agr; was studied to determine the factors that predict a sustained response to interferon therapy in young children with hemophilia who have chronic hepatitis C. Methods Seventeen Korean children with hemophilia and chronic hepatitis C were treated with 3.7 million units/m2 of interferon-&agr;2a three times weekly for 6 months. Liver biopsy, pretreatment serum HCV RNA quantitation with competitive reverse transcription assay, and HCV genotyping with reverse hybridization assay were performed. Results Hepatitis C virus genotypes 1a, 1b, and 2a were found in three (18%), five (29%), and six (35%) patients, respectively. Interferon-&agr; was well tolerated, and the frequency of bleeding did not increase. Of the 17 patients, 7 (41%) had a sustained response for 3 years after the end of therapy. Patients with a sustained response had lower pretreatment serum HCV RNA levels. One (13%) of eight patients with genotype 1 and five (83%) of six with genotype 2 had a sustained response (P < 0.05). Conclusions Interferon-&agr; treatment of chronic hepatitis C in children with hemophilia was safe and effective in producing sustained responses. The pretreatment serum HCV RNA level and viral genotype may be predictive factors for sustained response to interferon therapy.

Validation of QF–PCR in a Korean population

Quantitative fluorescence polymerase chain reaction (QF‐PCR) is a rapid and reliable method for screening common aneuploidies, but it is not an accustomed way of testing in Korea. Our objectives were to investigate QF‐PCR as a means for prenatal aneuploidy screening and to evaluate the short tandem repeat (STR) markers in a Korean population.

Detection of Isoniazid and Rifampicin Resistance by Sequencing of katG, inhA, and rpoB Genes in Korea

BACKGROUND In Korea, tuberculosis is resistant to isoniazid (INH) and/or rifampicin (RIF) in more than 10% of cases. To prevent the spread of resistant Mycobacterium tuberculosis strains, it is crucial to develop more rapid resistance detection methods. METHODS To determine the feasibility of using direct sequencing for detecting INH- and RIF-resistant strains, the katG gene, the regulatory region of the inhA gene, and the 81-bp hot-spot region of the rpoB gene from 95 culture isolates and 46 respiratory specimens were sequenced. Total 141 culture isolates were classified by conventional drug susceptibility testing (DST) as INH(R)/RIF(R) (N=30), INH(R)/RIF(S) (N=23), INH(S)/RIF(R) (N=15), and INH(S)/RIF(S) (N=73). RESULTS Compared with phenotypic DST, the overall sensitivity and specificity of sequencing were 83.0% (44/53) and 96.6% (85/88), respectively, for INH resistance, and 93.3% (42/45) and 100% (96/96), respectively, for RIF resistance. The rates were similar between culture isolates and respiratory specimens. Interestingly, three specimens with inhA -15C>T mutation were susceptible to INH by conventional DST. CONCLUSIONS Detection of mutations in the katG codon 315, the inhA regulatory region, and the hot-spot region of rpoB would be useful for rapid detection of INH and RIF resistance in Korea.

Detection and genotyping of human papillomavirus by five assays according to cytologic results

Five assays for the detection of human papillomavirus (HPV) with different assay principles were evaluated. A total of 230 cervical swab specimens were collected from subjects according to the cytologic results. All specimens were tested by the following assays: hybrid capture 2 (HC2), two real-time PCR assays (Abbott RealTime HR and AdvanSure RealTime), liquid beads microarray (GeneFinder) and peptide nucleic acid-based array (PANArray). The HPV DNA of 99 samples was sequenced to identify genotypes. Concordance rates between the results for the identification of 14 high risk HPV genotypes by any two of the evaluated assays, except for AdvanSure RealTime, ranged from 83.0% to 88.3%, and those for the identification of genotypes 16 and 18, except for HC2, were 93.0% and 96.1%, respectively. The results for the evaluation of high risk HPV genotypes by HC2 agreed with those of the other assays in 76.5-86.5% of cases. Identification of HPV genotype by GeneFinder and PANArray corresponded with that by direct sequencing in 88.9% and 84.8% of sequenced samples. This study demonstrated that HC2 and the two real-time PCR assays could be used for routine HPV screening, and the other genotyping assays can be applied for epidemiologic surveillance.

Effects of the Addition of Mosapride to Gastroesophageal Reflux Disease Patients on Proton Pump Inhibitor: A Prospective Randomized, Double-blind Study

Background/Aims Proton pump inhibitors (PPIs) which are the most effective agents for the treatment of gastroesophageal reflux disease (GERD), have been known to delay gastric emptying. Mosapride has been used as prokinetics by accelerating gastric emptying. We evaluated the efficacy of mosapride to prevent PPI-induced delayed gastric emptying in a prospective randomized, double-blind and placebo-controlled trial. Methods Thirty patients who were diagnosed as GERD and had normal gastric emptying were included in this study. PPI monotherapy group was treated with placebo drug in addition to pantoprazole and PPI plus mosapride group was treated with mosapride in addition to pantoprazole for 8 weeks. Gastric emptying scan and questionnaires about GERD and dyspeptic symptoms were assessed by scoring before and after treatment. To evaluate the changes of gastrointestinal endocrine hormones by PPI which are associated gastric acid secretion and gastric motility, fasting plasma gastrin and cholecystokinin were taken at weeks 0 and 8. Results Half gastric emptying time was increased (P = 0.023) in PPI monotherapy group, and there were no significant changes in PPI plus mosapride group. Plasma gastrin level increased in PPI monotherpay group (P = 0.028) and there were no significant changes in PPI plus mosapride group. Plasma cholecystokinin level was not changed after treatment in both groups. GERD symptoms were improved after treatment in both groups, and postprandial bloating and nausea were improved in PPI plus mosapride group. Conclusions Mosapride showed to be effective in preventing delayed gastric emptying and the increase in plasma gastrin level induced by PPI treatment, but did not show prominent clinical symptom improvements.

Mowat–Wilson syndrome detected by using high resolution microarray

Individuals with Mowat-Wilson syndrome (MWS; OMIM#235730) have characteristic facial features, a variety of congenital anomalies such as Hirschsprung disease, and intellectual disabilities caused by mutation or deletion of ZEB2 gene. This deletion or cytogenetic abnormality has been reported primarily from Europe, Australia and the United States, but not in Korea. Here we report a patient with characteristic facial features of MWS, developmental delay and spasticity. High resolution microarray analysis revealed 0.9 Mb deletion of 2q22.3 involving two genes: ZEB2 and GTDC1. This case shows the important role of high resolution microarray in patients with unexplained psychomotor retardation and/or facial dysmorphism. Knowledge about the most striking clinical signs and implementation of effective molecular tests like microarray could significantly increase the detection rate of new cases of MWS in Korea. This is the first reported case of MWS in Korea.

Comparison of clinical performances among Roche Cobas HPV, RFMP HPV PapilloTyper and Hybrid Capture 2 assays for detection of high-risk types of human papillomavirus

The cervical cancer screening guidelines suggest that early detection of HPV16 and HPV18 is helpful for identifying women with cervical intraepithelial neoplasia (CIN) grade two or higher. We comparatively evaluated three HPV DNA assays, Roche Cobas HPV, RFMP HPV PapilloTyper, and Hybrid Capture 2 (HC2). A total of 861 cervical swab samples from women over 30 years of age were classified into two groups, that is, high grade squamous intraepithelial lesion (HSIL) and non‐HSIL, according to cervical cytology results and analyzed by three assays. The results of direct sequencing or Linear array HPV genotyping test were considered true when the three assays presented discrepancies. The concordance rates between Roche Cobas HPV versus RFMP HPV PapilloTyper, RFMP HPV PapilloTyper versus HC2, and Roche Cobas versus HC2 were 94.5%, 94.3%, and 95.9%, respectively. For detection of HPV16 and HPV18, Roche Cobas HPV showed the concordance rates of 98.3% (κ = 0.73) and 99.4% (κ = 0.40) with the confirmation tests, respectively; and RFMP HPV PapilloTyper showed the concordance rates of 99.5% (κ = 0.92) and 100.0% (κ = 1.00), respectively. In conclusion, Roche Cobas HPV, RFMP HPV PapilloTyper, and HC2 showed high agreement rates. Roche Cobas HPV and RFMP HPV PapilloTyper are particularly useful, since both provide HPV specific genotypes, HPV16 and HPV18. J. Med. Virol. 87:1587–1593, 2015.

Frequency of FMR1 premutation carriers and rate of expansion to full mutation in a retrospective diagnostic FMR1 Korean sample

Detection of female premutation (PM) carriers of fragile X syndrome may be important in that a PM allele from the mother can expand to a full mutation (FM) when transmitted to the fetus. Although the PM carrier frequency might be different in varying populations, there is a little data on the Korean population. Furthermore, the risks of expansion to FM have not been studied in Korean PM carriers. In this retrospective study, we estimated the female PM carrier frequency and the risks of expansion to FM in Korean diagnostic samples collected for FMR1 gene testing. Of 10,241 pre‐conceptional or pregnant women, 13 PM [1 in 788; 95% confidence interval (CI), 1/1 250–1/455] and 75 intermediate allele carriers (1 in 137; 95% CI, 1/172–1/110) were identified. In 26 prenatal diagnoses cases, the PM allele was transmitted to the fetus in 13 pregnancies (50%), and five of these expanded to FM. All of the maternal alleles exceeding 70 repeats expanded to FM. In conclusion, the PM frequency in Korean diagnostic samples was lower than that reported in Western populations, while the risk for FM expansion in alleles exceeding 70 repeats might be higher than expected based upon previous reports.