• Clinical and Experimental Pediatrics
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• v.53 no.3
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• pp.273-285
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• 2010

Completion of the human genome project has allowed a deeper understanding of molecular pathophysiology and has provided invaluable genomic information for the diagnosis of genetic disorders. Advent of new technologies has lead to an explosion in genetic testing. However, this overwhelming stream of genetic information often misleads physicians and patients into a misguided faith in the power of genetic testing. Moreover, genetic testing raises a number of ethical, legal, and social issues. Diagnostic genetic tests can be divided into three primary but overlapping categories: cytogenetic studies (including routine karyotyping, high-resolution karyotyping, and fluorescent in situ hybridization studies), biochemical tests, and DNA-based diagnostic tests. DNA-based testing has grown rapidly over the past decade and includes preandpostnatal testing for the diagnosis of genetic diseases, testing for carriers of genetic diseases, genetic testing for susceptibility to common non-genetic diseases, and screening for common genetic diseases in a particular population. Theoretically, once a gene's structure, function, and association with a disease are well established, the clinical application of genetic testing should be feasible. However, for routine applications in a clinical setting, such tests must satisfy a number of criteria. These criteria include an acceptable degree of clinical and analytical validity, support of a quality assurance program, possibility of modifying the course of the diagnosed disease with treatment, inclusion of pre-and postnatal genetic counseling, and determination of whether the proposed test satisfies cost-benefit criteria and should replace or complement traditional tests. In the near future, the application of genetic testing to common diseases is expected to expand and will likely be extended to include individual pharmacogenetic assessments.

• Journal of Microbiology and Biotechnology
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• v.10 no.5
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• pp.685-689
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• 2000

Due to the uncultivable nature of Mycobacterium leprae in vitro, the fast, easy, and accurate measurement of the antimicrobial drug susceptibility of this microbe has been difficult. Conventional methods for such testing are subjective, cumbersome, and expensive in some cases. Here, the utility of a reverse transcriptase-PCR (RT-PCR)-based assay for testing was examined and compared with a Buddmeyer-type radiorespirometric assay. The susceptibility of M. leprae to rifampin was determined by probing the presence of M.leprae-specific 18 kDa gene mRNA in M. leprae-infected IC-21 macrophage cells after drug treatment. The results showed that, as the refampin concentration was increased, the 360-bp cDNA products generated by the RT-PCR-based assay decreased in a dose-dependent manner as in the drug susceptibility observed in the Buddmeyer-type assay. The drug susceptibility testing of M. leprae by the RT-PCR based assay was found to be not only faster but also nearly $10^4$-fold more sensitive than the Buddmeyer-type assay. Moreover, it was also found that, unlike the RT-PCR based assay, the same testing by a DNA-PCR resulted in no differences in the 360-bp signal, regardless of the rifampin concentrations used. Accordingly, these results demonstrated that the drug susceptibility of M. leprae can be determined effectively by an RT-PCR-based assay, thereby providing a new, fast, and sensitive testing method.

• Journal of Genetic Medicine
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• v.4 no.2
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• pp.122-127
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• 2007

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.16
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• pp.6837-6842
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• 2014

Background: Northern Thailand is a region with a high cervical cancer incidence. Combined high-risk HPV (hrHPV) DNA testing and cytology (co-testing) has increasingly gained acceptance for cervical cancer screening. However, to our knowledge, data from a population-based screening using co-testing have not been available in this region. This study therefore aimed to evaluate the performance of cytology and hrHPV test in women in northern Thailand. Materials and Methods: Cervical samples were collected for hybrid capture 2 (HC2) testing and liquid-based cytology from women aged 30 to 60 years who were residents in 3 prefectures of Chiang Mai in northern Thailand between May and September 2011. Women with positive cytology were referred to colposcopy, while women with positive for HC2 only were followed for 2 years. Results: Of 2,752 women included in this study, 3.0% were positive in both tests, 4.1% for HC2 only, and 1.3% had positive cytology only. At baseline screening, positive HC2 was observed in 70.6% among cytology-positive women compared with 4.3% among cytology-negative women. The prevalence of positive HC2 or cytology peaked in the age group 35-39 years and was lowest in the age group 55-60 years. High-grade squamous intraepithelial lesion or worse lesions (HSIL+) were histologically detected in 23.5% of women with positive baseline cytology and in 9.8% of women with positive baseline HC2 only on follow-up. All women with histologic HSIL+ had positive baseline HC2. Conclusions: The hrHPV test is superior to cytology in the early detection of high-grade cervical epithelial lesions. In this study, the prevalence of histologic HSIL+ on follow-up of women with positive hrHPV test was rather high, and these women should be kept under careful surveillance. In northern Thailand, hrHPV testing has a potential to be used as a primary screening test for cervical cancer with cytology applied as a triage test.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.14
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• pp.5993-5999
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• 2015

Background: Molecular testing for human papillomavirus (HPV) is the most objective and reproducible of all cervical cancer screening tests and also less demanding in terms of training and quality assurance. However, there is an impending need for cost effective molecular HPV testing methods with sampling ease, easy storage measures and minimum turn around times suitable for a low resource setting. Objective : Our aim was to evaluate the feasibility of using a fast transfer analysis (FTA) mini elute cartridge for cervical sampling to identify high risk HPV by real time PCR and to compare molecular HPV testing and Pap cytology testing to predict histologically confirmed cervical precancer (CIN 2+ lesions) in a cervical cancer prevention program. Materials and Methods: This was conducted as a pilot study (n=200) on women sampled using FTA mini elute cartridges, genotyped by two different real time PCR assays, detecting 13 high risk HPV (HR HPV) species, including HPV16 along with its physical DNA status. Results obtained from each of the tests were compared and analysed using suitable statistical tests. Results: With FTA mini elute cartridge samples HR HPV positivity was seen in 48/200 (24%). Of these, presence of HPV 16 DNA was observed in 28/48 (58.3%) women. High risk HPV was positive in 20% (37/185) of women with benign cytology and 73.3% (11/15) of women with abnormal cytology findings. A very significant correlation (${\chi}^2=22.090$ ; p=0.000) was observed between cytology and HR HPV findings showing an increasing trend of HR HPV prevalence in 50% (1/2) of LSIL, 75% (3/4) of HSIL and 100% (3/3) of SCC. Of the CIN 2+ lesions identified by histopathology, 88.9% (8/9) had HR HPV. A significant association (${\chi}^2=11.223$ ; p=0.001) of HR HPV and histopathologically confirmed CIN 2+ lesions was found. Sensitivity of the two tests were comparable but specificity of Pap testing was better (90.7% vs 70.4%) to predict histopathologically diagnosed cervical precancers. Conclusions: The current study explored the feasibility of using a FTA mini elute cartridge for cervical sampling for the first time in India as a part of a community based cervical cancer prevention program. We suggest that FTA based sampling is suitable and feasible for real time based HPV testing. Molecular HR HPV testing can be more sensitive and useful to identify high risk women requiring Pap testing which is more specific to detect histologically confirmed cervical precancer.

• Clinical and Experimental Reproductive Medicine
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• v.45 no.3
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• pp.101-109
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• 2018

In an age when a small quantity of sperm can lead to pregnancy through in vitro fertilization or intracytoplasmic sperm injection, selecting healthy sperm is important. Sperm DNA fragmentation (SDF) is known to be higher in infertile men. Terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end labeling (TUNEL) and the alkaline comet test are SDF tests that directly measure DNA damage and have shown closer correlations with assisted reproduction results than indirect tools such as the sperm chromatin structure assay or the sperm chromatic dispersion test. It is difficult; however, to endorse a single test as the best test overall; instead, it is best to select a testing method based on each patient's clinical condition and goals. In a couple struggling with infertility, if the male partner has a high level of SDF, he should aim to decrease SDF through lifestyle modifications, antioxidant treatment, and ensuring an appropriate duration of abstinence, and physicians need to treat the underlying diseases of such patients. If sperm DNA damage continues despite the patient's and physician's efforts, other methods, such as micromanipulation-based sperm selection or testicular sperm extraction, should be used to select healthy sperm with nuclear DNA integrity.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.1
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• pp.511-514
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• 2013

Background: A small but significant proportion of cases with atypical squamous cells of undetermined significance (ASCUS) may harbour CIN 2-3, or even invasive carcinoma. Although immediate colposcopy, HPV-DNA testing or expectant management are three recommended options in ASCUS triage, a consensus does not currently exist on which one of these approaches is the most efficient. In this study, we aimed to compare the performance and cost of immediate colposcopy and colposcopy based on the human papillomavirus (HPV) testing for detecting histologically confirmed high-grade cervical intraepithelial neoplasia (CIN) in women with ASCUS. Materials and Methods: Records of 594 women with an index Papanicolaou smear showing ASCUS were retrospectively analyzed. Women in the immediate colposcopy arm were referred directly to colposcopy (immediate colposcopy group, n=255) and those in the HPV triage arm were proceeded to colposcopy if the high-risk HPV (hrHPV) test was positive (HPV triage group, n=339). High grade CIN (CIN2+) detection rate and treatment costs were compared between the groups. Results: The detected rate of CIN2+ was higher in the HPV triage group compared to immediate colposcopy group (8% vs. 1.6%, p=0.011). In the HPV triage group, the total cost, cost per patient, and the cost for detecting one case of high grade CIN were higher than the immediate colposcopy group (p<0.001). Conclusions: In women with ASCUS cytology, HPV DNA testing followed by colposcopy is more costly than immediate colposcopy, but this approach is associated with a higher rate of CIN2+ detection. This findings suggest that HPV DNA testing combined with cervical cytology could reduce the referral rate to colposcopy.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.9
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• pp.4409-4413
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• 2016

Background: Cervical cancer is the second most common of malignancy found in Thai women. Human papillomavirus (HPV) infection is a major cause. The objective of the present study was to evaluate the prevalence of HPV infection and association with abnormal cervical cytology in Thai women. Materials and Methods: This study was conducted at the Gynecologic Clinic, Thammasat University, Pathum Thani, Thailand. A total of 2,144 cases who underwent annual cervical cancer screening by co-testing (liquid based cytology and HPV testing, DNA versus mRNA) during the priod from July 2013 to June 2016 were recruited in this study. Results: Prevalence of positive high risk (HR) HPV DNA and mRNA test were 19.7 and 8.4%, respectively with a statistically significant difference. Majority of cases of abnormal cytology in this study were atypical squamous cells of undetermined significance (ASC-US). In patients with ASC-US, positive HR HPV DNA was greater than in the mRNA group (10.1 and 4.5%, p<0.001). Nonetheless, there was no significant difference in participants with cervical intraepithelial neoplasia (CIN). HPV mRNA test had slightly lower sensitivity but higher negative predictive value (NPV) than the DNA test to detect abnormal cytology during cervical cancer screening (p<0.001). Both HPV test (DNA and mRNA) had equally efficacy to detect high grade precancerous lesion or higher (CIN 2+). Conclusions: Prevalence of HR HPV DNA and mRNA were 19.7 and 8.4 percent, respectively. NPV of HPV mRNA was higher than DNA test. Both tests had equal efficacy to detect CIN 2+ with sensitivity and specificity of 63% vs 55.7% and 83% vs 92%, respectively.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.12
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• pp.1822-1830
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• 2002

The microsatellites are the short tandem repeats of 1 to 6 bp long monomer sequences that are repeated several times. These short tandem repeats are considered to be generated by the slipped strand mispairing. Based on the unique capability of alternating purine-pyrimidine residues to form Z-DNA, the possible role of the microsatellites in gene regulation has been proposed. The microsatellites are highly polymorphic, follow Mendelian inheritance and are evenly distributed throughout the genomes of eukaryotes. They are easy to isolate and the polymerase chain reaction based typing of the alleles can be readily automated. These properties make them the preferred markers for comparison of the genetic structure of the closely related breeds/populations; very high-resolution genetic mapping and parentage testing etc. The microsatellites have rapidly replaced the restriction fragment length polymorphism (RFLP) and the random amplified polymorphic DNA (RAPD) in most applications in the population genetics studies in most species, including the various farm animals viz. cattle, buffalo, goat, sheep and pigs etc. More and more reports are now available describing the use of microsatellites in pigs ranging from measurement of genetic variation between breeds/populations, developing high resolution genetic maps to identifying and mapping genes of biological and economic importance.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.17
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• pp.7935-7941
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• 2015

The aim of this study was to implement massive parallel sequencing (MPS) technology in clinical genetics testing. We developed and tested an amplicon-based method for resequencing the BRCA1 and BRCA2 genes on an Illumina MiSeq to identify disease-causing mutations in patients with hereditary breast or ovarian cancer (HBOC). The coding regions of BRCA1 and BRCA2 were resequenced in 96 HBOC patient DNA samples obtained from different sample types: peripheral blood leukocytes, whole blood drops dried on paper, and buccal wash epithelia. A total of 16 random DNA samples were characterized using standard Sanger sequencing and applied to optimize the variant calling process and evaluate the accuracy of the MPS-method. The best bioinformatics workflow included the filtration of variants using GATK with the following cut-offs: variant frequency >14%, coverage ($>25{\times}$) and presence in both the forward and reverse reads. The MPS method had 100% sensitivity and 94.4% specificity. Similar accuracy levels were achieved for DNA obtained from the different sample types. The workflow presented herein requires low amounts of DNA samples (170 ng) and is cost-effective due to the elimination of DNA and PCR product normalization steps.