Human Papilloma Virus Genotyping Assay using Restriction Fragment Mass Polymorphism Analysis, and Its Comparison with Sequencing and Hybrid Capture Assays / 대한진단검사의학회지

BACKGROUND: Infection with human papilloma virus (HPV) is the main cause of cervical cancer, and HPV genotyping is of increasing importance for determining clinical course and management of the disease based on the HPV genotypes. Here, we established a novel matrix-assisted laser desorption/ ionization time of flight mass spectrometry (MALDI-TOF MS) assay, termed restriction fragment mass polymorphism (RFMP) that is suitable for genotyping multiple HPV in an accurate and high-throughput manner. We evaluated the performance of the RFMP assay in HPV genotyping by comparing the results with those of direct or clonal sequencing and hybrid capture (HC) assays. METHODS: The study population consisted of 50 patients with histologically confirmed cervical lesions and a positive test for HPV DNA. HPV genotyping was performed with RFMP, sequencing, and HC assays. The assigned genotypes and risk groups were compared among the methods. RESULTS: Concordance rates in the genotype level between RFMP vs sequencing, sequencing vs HC, and HC vs RFMP were 98% (49/50), 88% (44/50), and 88% (44/50), respectivley. Especially, RFMP and sequencing were 100% concordant when assigned high-risk group was considered identical in 1 case of mixed genotypes identified only in RFMP. The observed discrepancy between HC and the other two methods is due to the assignment of six cases of low, intermediate, or unassigned risk genotypes as high-risk group in HC method. CONCLUSIONS: RFMP, sequencing, and HC assays were highly concordant with each other in HPV genotyping. Compared to sequencing assay, RFMP assay is found to be advantageous in detecting mixed genotype infections. The accuracy and amenability to high-throughput analysis should make the RFMP assay suitable for reliable screening of HPV genotypes in clinical laboratories.

Comparison of Efficacy of Human Papilloma Virus Genotyping Assays using Restriction Fragment Mass Polymorphism and DNA Chip Analysis in Patients with Abnormal Pap Smear and Uterine Cervical Cancer

BACKGROUND: High-risk human papilloma virus (HPV) infection is the primary cause of cervical cancer; there is a need for more sensitive and reliable methods for HPV genotyping to use as screening tools for early detection and intervention. METHODS: A novel MALDI-TOF MSbased assay, termed Restriction Fragment Mass Polymorphism (RFMP) was developed for multiple HPV genotyping. Its performance was compared with DNA chip technology. The study was based on 164 cases classified as normal (n=40), ASCUS (n=53) and invasive squamous cell carcinoma (SCC, n=71) by a PAP smear and/or cervical colposcopic biopsy. RESULTS: High-risk genotypes were detected in 7.5%, 47.2% and 97.2% in normal, ASCUS and SCC groups by RFMP, and in 20.0%, 41.5% and 90.1% using DNA chip technology, respectively. The results showed substantial concordance, with a kappa coefficient of 0.688, between the methods. Diagnostic sensitivity and specificity for cervical cancer were found to be 97.2% and 92.2% with RFMP and 90.1% and 80.0% using DNA chip microarrays. CONCLUSIONS: RFMP and DNA chip technologies were shown to be reliable methods for HPV genotyping with a high concordance. The improved sensitivity and specificity should make RFMP a viable option for the management of women with cervical neoplastic lesions.

Association between CCR5 Promoter Polymorphisms and Hepatitis B Virus Infection / 대한간학회지

BACKGROUND/AIMS: Immunogenetic factors may play a role in determining the susceptibility of an individual to viral infection. CCR5 promoter polymorphisms are known to be associated with HIV infection. However, there has been no report on the association between CCR5 promoter polymorphism and HBV infection. Therefore, we investigated the relationship between the CCR5 promoter polymorphism and HBV infection. METHODS: A total of 377 patients were classified into two groups according to their HBV infection status: (1)he spontaneous clearance group (SC); HBsAg (-), anti-HBc (+), anti-HBs (+) (2)he chronic HBsAg (+) carrier group (CC); HBsAg (+), anti-HBc (+), anti-HBs (-). CCR5 polymorphisms were detected by employing matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS)- based SNP scoring assay, termed Restriction Fragment Mass Polymorphism (RFMP), which exploits the differences in molecular masses between the common allele and rare allele bases of interest. RESULTS: We found that the genotype frequencies of CCR5 A59029G significantly differed between the SC group (n=138) and CC group (n=239) (P<0.05). The CCR5 59029A allelic genotype was associated with an increased risks of chronic infection rather than spontaneous clearance (P=0.002), and the presence of the CCR5 59029G allele was significantly associated with the spontaneous clearance of HBV (P=0.001). Strong linkage disequilibrium between the CCR5-59029 and the CCR5-59353 polymorphic variants was identified. None of the 377 subjects had the CCR5-32 bp deletion mutation. CONCLUSIONS: The CCR5 promoter polymorphisms at position 59029 might play a role in the clearance of HBV infection. This primary experimental evidence needs further studies to clarify the clinical usefulness of CCR5 promoter polymorphisms as a target for the screening or treatment of HBV infection.

Reappraisal of HBV Genotypes and Clinical Significance in Koreans Using MALDI-TOF Mass Spectrometry / 대한간학회지

BACKGROUND/AIMS: Recent studies have shown that the genotype of hepatitis B virus (HBV) may correlate with the disease natural history and treatment outcome. However, several of these studies used low sensitivity assays in a small number of patients, and this has precluded an accurate evaluation of Korean HBV genotypes. We analyzed Korean HBV genotypes in a large population by employing a new technology, restriction fragment mass polymorphism (RFMP) using MALDI-TOF mass spectrometry, in a sensitive and specific manner. METHODS: Between February 1995 and December 2003, a total of 475 patients with chronic HBV infection were enrolled. The assay is based on the mass measurement of oligonucleotides having genotypic variations of the S gene. Clinical features including the virologic status and disease progression were also evaluated. RESULTS: The median age of the total patients was 35.5 years. Out of 475 patients, there were 162 (34.1%) inactive carriers, 172 (36.2%) had chronic hepatitis, 77 (16.2%) had liver cirrhosis and 64 (13.5%) had hepatocellular carcinoma (HCC). There were 454 patients (95.6%) with genotype C, 4 patients (0.8%) with genotype A, 16 patients (3.4%) with the mixed A and C genotype [7 patients (1.4%) with AA], and 1 patient (0.2%) with B genotype. Comparing genotype A and C, genotype A patients were all inactive carriers without HCC, whereas genotype C patients included those with chronic hepatitis, liver cirrhosis and HCC. CONCLUSIONS: HBV genotype C is highly prevalent in Korea. Although it is a small percentage, genotype A also exists and it seems to take a more benign clinical course than genotype C. Further studies are necessitated to assess the relationship between HBV genotypes and the various aspects of the diseases' clinical course.