DNA Methylation Differences in Peripheral Blood of Patients with Anaphylaxis / 法医学杂志

Objective To study the DNA methylation of nucleated cells in peripheral blood of patients died from anaphylactic shock caused by cephalosporin drugs and to provide a new research direction and basis for the forensic diagnosis of shock caused by drug hypersensitiveness. Methods Methylation microarray was used to detect DNA methylation of nucleated cells in peripheral blood of patients died from anaphylactic shock caused by cephalosporin drugs and normal subjects. Sequencing data and chip data were analyzed for differences in DNA methylation using R language methylkit, ChAMP package. Random forest algorithm was used to evaluate the importance of the DNA methylation differential sites. Results Differential sites of DNA methylation highly associated with anaphylaxis caused by cephalosporin drugs were obtained at loci such as ETS1, PRR23B and GNAS. Conclusion Cephalosporin allergy is associated with DNA methylation, and DNA methylation may be a new strategy for forensic identification of anaphylactic shock and death.

The current status and future prospects of DNA computing / 生物工程学报

As the demand for high-performance computing continues to grow, traditional computing models are facing unprecedented challenges. Among the many emerging computing technologies, DNA computing has attracted much attention due to its low energy consumption and parallelism. The DNA circuit, which is the basis for DNA computing, is an important technology for the regulation and processing of the molecular information. This review highlights the basic principles of DNA computing, summarizes the latest research progress, and concludes with a discussion of the challenges of DNA computing. Such integrated molecular computing systems are expected to be widely used in the fields of aerospace, information security and defense system.

Rapid detection of deformed wing virus in honeybee using ultra-rapid qPCR and a DNA-chip

Deep analysis of methylation profile in congenital microtia and verification of the differential genes / 中华整形外科杂志

Objectives@#To explore the differences in signal pathway and gene expression related to the pathogenesis of congenital microtia by the in-depth analysis of DNA methylation profiling of auricular chondrocytes from congenital microtia patients.@*Methods@#Genome wide methylation profile of congenital microtia was obtained by MeDIP chip technology, and analyzed by Gene ontology (GO) and Pathway analysis. The gene expression levels of Wnt1 and Wnt11 were evaluated by Real-time PCR in the auricular cartilage from the healthy side and affected side of the congenital microtia patients , and healthy controls.@*Results@#The GO and Pathway assay showed that Wnt signal pathway was enriched in differential methylated levels. The Wnt1 and Wnt11 genes were with higher methylation in the promoter region and CpG islands in healthy control group than that in microtia group, in addition the methylation level in the affected side auricular cartilage was lower than that in the healthy side. There was no difference in Wnt1 and Wnt11 gene expression in microtia patients and healthy controls. The higher Wnt11 gene expression was detected in the affected side residual cartilage tissues than in the healthy side cartilage tissues of the same congenital microtia patient.@*Conclusions@#The over expression of Wnt11 during embryonic development might be associated with the pathogenesis of congenital microtia. The mechanism of the difference in methylation levles of Wnt11 affecting pathogenesis of congenital microtia needs further research.

Comparison of Four Human Papillomavirus Genotyping Methods: Next-generation Sequencing, INNO-LiPA, Electrochemical DNA Chip, and Nested-PCR

BACKGROUND: Human papillomavirus (HPV) infection causes cervical cancer, thus necessitating early detection by screening. Rapid and accurate HPV genotyping is crucial both for the assessment of patients with HPV infection and for surveillance studies. METHODS: Fifty-eight cervicovaginal samples were tested for HPV genotypes using four methods in parallel: nested-PCR followed by conventional sequencing, INNO-LiPA, electrochemical DNA chip, and next-generation sequencing (NGS). RESULTS: Seven HPV genotypes (16, 18, 31, 33, 45, 56, and 58) were identified by all four methods. Nineteen HPV genotypes were detected by NGS, but not by nested-PCR, INNO-LiPA, or electrochemical DNA chip. CONCLUSIONS: Although NGS is relatively expensive and complex, it may serve as a sensitive HPV genotyping method. Because of its highly sensitive detection of multiple HPV genotypes, NGS may serve as an alternative for diagnostic HPV genotyping in certain situations.

Clinical Significance of an HPV DNA Chip Test with Emphasis on HPV-16 and/or HPV-18 Detection in Korean Gynecological Patients

BACKGROUND: Human papillomavirus (HPV) is a major risk factor for cervical cancer. METHODS: We evaluated the clinical significance of the HPV DNA chip genotyping assay (MyHPV chip, Mygene Co.) compared with the Hybrid Capture 2 (HC2) chemiluminescent nucleic acid hybridization kit (Digene Corp.) in 867 patients. RESULTS: The concordance rate between the MyHPV chip and HC2 was 79.4% (kappa coefficient, κ = 0.55). The sensitivity and specificity of both HPV tests were very similar (approximately 85% and 50%, respectively). The addition of HPV result (either MyHPV chip or HC2) to cytology improved the sensitivity (95%, each) but reduced the specificity (approximately 30%, each) compared with the HPV test or cytology alone. Based on the MyHPV chip results, the odds ratio (OR) for ≥ high-grade squamous intraepithelial lesions (HSILs) was 9.9 in the HPV-16/18 (+) group and 3.7 in the non-16/18 high-risk (HR)-HPV (+) group. Based on the HC2 results, the OR for ≥ HSILs was 5.9 in the HR-HPV (+) group. When considering only patients with cytological diagnoses of “negative for intraepithelial lesion or malignancy” and “atypical squamous cell or atypical glandular cell,” based on the MyHPV chip results, the ORs for ≥ HSILs were 6.8 and 11.7, respectively, in the HPV-16/18 (+) group. CONCLUSIONS: The sensitivity and specificity of the MyHPV chip test are similar to the HC2. Detecting HPV-16/18 with an HPV DNA chip test, which is commonly used in many Asian countries, is useful in assessing the risk of high-grade cervical lesions.

Clinical Usefulness of a DNA Microarray-based Assay for the Diagnosis of Sexually Transmitted Infections

BACKGROUND: Many molecular diagnostic methods have been developed to detect sexually transmitted infections (STI). The STDetect Chip (LabGenomics, Korea) which is a DNA microarray-based tool, newly developed for STI diagnosis in vitro, and the real-time PCR-based Anyplex STI-7 (Seegene, Korea) in clinical use were evaluated using ATCC DNA and clinical samples to determine the clinical usefulness of the STDetect Chip. METHODS: The two methods were compared for consistency, sensitivity, and specificity for 6 pathogens in 300 prospectively selected clinical samples. Analytical sensitivity for ATCC Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma hominis and Trichomonas vaginalis DNA and the effect of mixing bacterial DNA were studied. RESULTS: The consistency of the two methods for clinical samples was superior at more than 0.92 kappa value. The sensitivity and specificity of the STDetect Chip compared with Anyplex STI-7 were 90.5-98.8%, and 95.6-99.6%, respectively. With similar analytical performance for ATCC DNA, the STDetect Chip detected 10(-5) ng/µL of N. gonorrhoeae, 10(-4) ng/µL of C. trachomatis, 10(-6) ng/µL of M. hominis, and 10(-3) ng/µL of T. vaginalis. For the mixture of three bacterial DNAs, less sensitive detection level was observed for T. vaginalis. CONCLUSIONS: The STDetect Chip showed good agreement with the Anyplex STI-7 test and it is considered clinically useful for detecting sexually transmitted pathogens.

The Application of DNA Chip Technology to Identify Herbal Medicines: an Example from the Family Umbelliferae

Comparative molecular analysis has been frequently adopted for the authentication of herbal medicines as well as the identification of botanical origins. Roots and rhizomes of the family Umbelliferae have been used as traditional herbal medicines to relieve various symptoms such as inflammation, neuralgia and paralysis in countries of East Asia. Since most herbal medicines of the Umbelliferae roots or rhizomes are generally supplied in the form of dried slices, morphological examination does not often provide sufficient evidence to identify the botanical origin. Using species-specific probes developed by the comparative analysis of nrDNA ITS sequences, a DNA chip was developed to identify herbal medicines for 13 species in the Umbelliferae. The developed DNA Chip proves its potential as a rapid, sensitive and effective tool for authenticating herbal medicines in future.

Focal epithelial hyperplasia arising after delivery of metal-ceramic fixed dental prosthesis

Focal epithelial hyperplasia (FEH) is a human papillomavirus (HPV)-induced alteration of the oral mucosa that presents with a clinically distinct appearance. While other HPV-infected lesions such as squamous papilloma, verruca vulgaris, and condyloma acuminatum involve the skin, oral mucosa, and genital mucosa, FEH occurs only in the oral mucosa. The affected oral mucosa exhibits multiple papules and nodules with each papule/nodule being flat-topped or sessile. The affected region resembles the normal color of oral mucosa rather than appearing as a white color since the epithelial surface is not hyperkeratinized. Almost all cases present with multiple sites of occurrence. This rare, benign epithelial proliferation is related to low-risk HPV, especially HPV-13 and -32, and is not transformed into carcinoma. We report a case of FEH that arose on the attached gingiva of an East Asian male adult related to prosthesis without detection of any HPV subtype in HPV DNA chip and sequencing.

Prevalence of Human Papillomavirus Infection in the Korean Oral Cancer Patients

Genetic Relationship in Bone Samples Using SNP-Based Human Identification DNA Chip / 대한법의학회지

DNA profiling with sets of short tandem repeat (STR) markers is the most popular method for identifying human DNA in forensics. Identification by STR typing might fail when DNA is degraded or is present in low amounts, such as in disaster victim identification (DVI) samples. In such cases, more information might be obtained by using additional markers such as single nucleotide polymorphisms (SNPs). Multiplex PCR and microarray are convenient techniques to analyze SNP markers. We used an AccuID(TM) Chip, SNP-based DNA chip manufactured by DNA Link Corporation, to confirm genetic relationship between two human bone samples that had been buried for more than 50 years and blood samples from the alleged descendants of the sources of the bone fragments. The chip combines an Affymetrix resequencing array with a multiplex PCR technology and can genotype hundreds of SNP markers in a single experiment. Genotyping the two bone samples yielded 90.5 and 77 SNP markers. The commonly genotyped markers (61 and 47 SNP loci) in each bone-family pair provided high paternity indices to support the genetic relationships in both cases.

Comparative Evaluation of the HPV28 Detection and HPV DNA Chip Test for Detecting and Genotyping Human Papillomaviruses

BACKGROUND: The HPV28 Detection test (Seegene) is a real-time polymerase chain reaction assay that is designed for testing a total of 28 human papillomavirus (HPV) genotypes and estimating the approximate HPV viral load. The aim of this study was to evaluate the clinical applicability of the HPV28 Detection test with regard to the prevalence of HPV infection and distribution of HPV genotypes by using the HPV28 Detection and HPV DNA Chip tests (Biomedlab). METHODS: HPV DNA Chip and HPV28 Detection tests were performed for 500 cervical swab specimens. HPV genotype results were confirmed by sequencing analysis of the specimens that showed discordant results in the 2 test methods. RESULTS: The positive rate of HPV detection determined by using HPV28 Detection and HPV DNA Chip tests were 43.8% and 40.6%, respectively. The sequencing results in 64 discordant specimens that showed single HPV infection in the 2 test methods were in complete agreement with the test results obtained with the HPV28 Detection test. The genotyping results of the HPV28 Detection test were 100% concordant in repeated experiments with HPV-infected specimens that have 12 different HPV genotypes, i.e., types 16, 31, 33, 39, 42, 51, 52, 53, 58, 66, 68, and 70. The HPV28 Detection test was 100-fold more sensitive than the HPV DNA Chip test with serially diluted HPV DNAs. CONCLUSIONS: The HPV28 Detection test can be applied in the clinical field as an HPV genotyping test can accurately identify various HPV genotypes with high specificity and low detection limit.

Gene expression profile analysis of xylitol-sensitive and xylitol-resistant Streptococcus mutans in 0.5% glucose containing TYE media using DNA chip / 대한구강보건학회지

OBJECTIVES: Streptococcus mutans (S. mutans) is the major causative bacteria in dental caries. Xylitol is an effective anticarious natural sugar substitute by inhibiting the virulence of S. mutans. However, long-term xylitol consumption leads to the emergence of the xylitol-resistant S. mutans (XR). The aim of this study is to analyze the difference of gene expression profile of xylitol-sensitive S. mutans (XS) and XR in 0.5% glucose containing TYE media, using a DNA chip. METHODS: S. mutans KCTC3065 was maintained in 0.5% glucose and 1% xylitol containing TYE media, during 30 days at 37degrees C 10% CO2 to form XR. The same procedures without xylitol were repeated for the formation of XS. Both XS and XR were cultured in 0.5% glucose with or without 1% xylitol containing TYE media overnight and total RNA was extracted. RNA from XS was labeled with Cy-3 dye as control, and XR were labeled with Cy-5 as references. DNA chip was hybridized for 18-20 h at 42degrees C. RESULTS: A total of 277 genes of DNA chip data were significantly increased or decreased in XR. There is a total of 174 XR up-regulated genes in 0.5% glucose and 1% xylitol containing TYE media, and a total of 103 down-regulated genes. For compare with results of DNA chip, 11 in up-regulated genes and 10 in down-regulated were verified by RT-PCR. The most abundant increased genes in XR were related to cell envelope, cellular processes, DNA metabolism, transcription, and protein folding and stabilization. The decreased genes in XR were related to amino acid biosynthesis, toxin production and resistance, energy metabolism, ribosomal proteins synthesis, and signal transduction. CONCLUSIONS: These results indicate that the difference of gene expression profile of XS and XR may be in existence. In particular, results of this study for XR up-regulated genes have a lot of similarities with the already published xylitol-related researches and other functional studies.

Cytomorphologic Features According to HPV DNA Type in Histologically Proven Cases of the Uterine Cervix

BACKGROUND: This study investigated whether human papillomavirus (HPV) genotype is related to koilocytic changes in cervical cytology and histology, and what factors cause discrepancies among cytology, HPV DNA chip tests, and biopsies. METHODS: We examined 174 of 949 cases histologically confirmed by both cytology and HPV DNA chip testing. We analyzed koilocytic changes in cytology and biopsies according to HPV genotype. RESULTS: HPV-16 significantly coincided with nuclear size variation and hyperchromasia, although the cytomorphologic features correlated with other HPV genotypes were not statistically significant. By analyzing 68 cases in which there were discrepancies between the HPV DNA chip test and histological results, we confirmed that artifacts or glycogen acanthosis resulted in the over-diagnoses of four HPV-negative cases with normal cytology. Four diagnostic errors and four sampling errors were present in eight HPV-positive cases. The degree of nuclear size variation significantly influenced the cytologically under-diagnosed cases (p=0.006). CONCLUSIONS: Other than HPV-16, HPV genotype exhibited no cytological or histological differences. The discrepancy between the results of HPV DNA chip test and histology was created by glycogen acanthosis, immature squamous metaplasia, artifacts, and sampling errors.

A Clustering Tool Using Particle Swarm Optimization for DNA Chip Data

DNA chips are becoming increasingly popular as a convenient way to perform vast amounts of experiments related to genes on a single chip. And the importance of analyzing the data that is provided by such DNA chips is becoming significant. A very important analysis on DNA chip data would be clustering genes to identify gene groups which have similar properties such as cancer. Clustering data for DNA chips usually deal with a large search space and has a very fuzzy characteristic. The Particle Swarm Optimization algorithm which was recently proposed is a very good candidate to solve such problems. In this paper, we propose a clustering mechanism that is based on the Particle Swarm Optimization algorithm. Our experiments show that the PSO-based clustering algorithm developed is efficient in terms of execution time for clustering DNA chip data, and thus be used to extract valuable information such as cancer related genes from DNA chip data with high cluster accuracy and in a timely manner.

Implementation of a Particle Swarm Optimization-based Classification Algorithm for Analyzing DNA Chip Data

DNA chips are used for experiments on genes and provide useful information that could be further analyzed. Using the data extracted from the DNA chips to find useful patterns or information has become a very important issue. In this paper, we explain the application developed for classifying DNA chip data using a classification method based on the Particle Swarm Optimization (PSO) algorithm. Considering that DNA chip data is extremely large and has a fuzzy characteristic, an algorithm that imitates the ecosystem such as the PSO algorithm is suitable to be used for analyzing such data. The application enables researchers to customize the PSO algorithm parameters and see detail results of the classification rules.

Variation analysis of early gene expression profiles of lung in rats with endotoxic shock / 中华创伤杂志

Objective To observe the difference of gene expression profiles of lung in rats before and after endotoxic shock (ES). Methods A total of 20 male Wistar rats were randomly divided into control group and lipopolysaceharide (LPS) group ( 10 rats per group). The LPS rat model was made by injecting LPS into tail vein. Six hours after ES, partial pressure of oxygen in the arterial blood ( PaO2 )was measured. Gene expression profiles of the lung in each group were detected by rats oligo gene chip Affymetrix RAT 230A. The expression level of five genes was verified via semi-quantitative RT-PCR. The data were analyzed in combination with type of differential gene and character of ES. Results Compared with control group, PaO2 in LPS group was decreased more significantly (P ＜0.05). Among 15 650 probes detected, 158 genes showed differential expression in ES group in comparison with control group. The expression level of 117 genes was up-regulated while that of 34 genes down-regulated significantly. According to their biological function, differentially expressed genes were classified as inflammation genes, material transporter genes, transcription regulator genes, signal transduction genes, stress response genes, metabolic genes, apoptosis genes and cell adhesion genes. The results of Semi-quantitative RT-PCR of five genes were consistent with those of the microarray examination. Conclusion The expression of many genes of the lung may change in ES rats, especially the inflammatory genes.

Hepatic gene expression of rats subjected to hemorrhagic shock / 中华急诊医学杂志

Objective To analyze the differential gene expression profiling of liver in rats subjected to hemorrhagic shock(HS) and sham hemorrhage shock(SHAM) by gene chip technology, thus to evaluate the possible molecular pathogenesis of HS. Method 20 male Wistar rats were randomly divided into a SHAM group and a HS group, with 10 rats in each group. Hepatic gene expression profiles were detected by oligonucleotide microarrays of 5705 mouse genes in two groups for three times. Genes with ratio(R) > 2 were identified as up-regulated and R < 0.5 were identified as down-regulated. Biological function of differentially expressed genes was analyzed and 9 genes were selected to undergo semi-quantitative RT-PCR. Results Among the total 5705 probes detected,86 genes showed differential expression in HS group comparison with SHAM group. The expression levels of 72 genes were up-regulated while those of 14 genes were down-regulated significantly. Differentially expressed genes were classified according to their biological function: transport genes, transcription regulator genes, signaling genes, response to stress genes, metabolic genes, development genes and cell adhesion genes. Conclusions cDNA microarray is an efficient and high-throughout method to survey gene expression profiles in HS.The variation of those gene expressions might be a potential pathogenic mechanism for HS that may offer a novel target for further study of therapeutic strategies of HS.

The Usefulness of the HPV DNA Microchip Test for Women with ASC-US

BACKGROUND: This study was performed to ascertain the usefulness of the human papillomavirus (HPV) DNA microchip test for the screening and management of women with atypical squamous cells of undetermined significance (ASC-US). METHODS: The subject group consisted of 534 patients, and all of whom were diagnosed as ASC-US according to a Papanicolaou smear, and they all underwent concomitant HPV DNA microchip test. RESULTS: The occurrence rates of overall squamous lesions and high risk lesion (cervical intraepithelial neoplasia grade 2 and grade 3, and invasive carcinoma) of the HPV-positive ASC-US patients were significantly higher than those of the HPV-negative ASC-US patients. High risk lesion was detected more frequently among the older patients and the patients with HPV 56, 33 or 70. On the follow-up HPV DNA microchip test, only 1 of 11 (9.1%) HPV type-switched women developed squamous lesion compared with 8 of 13 (61.6%) HPV type-persistent women who developed squamous lesion. CONCLUSIONS: The HPV DNA microchip test is useful for the management of ASC-US patients. HPV-positive ASC-US patients should undergo a HPV DNA microchip test periodically. If the same genotype of HPV is persistent on the follow-up test, more increased surveillance is needed.

Construction of a DNA Chip for Screening of Genetic Hearing Loss

OBJECTIVES: Hearing loss is the most common sensory disorder in humans and genetic causes are estimated to cause more than 50% of all incidents of congenital hearing loss. To develop an efficient method for a genetic diagnosis of hearing loss, we have developed and validated a genetic hearing loss DNA chip that allows the simultaneous analysis of 7 different mutations in the GJB2, SLC26A4, and the mtDNA 12S rRNA genes in Koreans. METHODS: A genotyping microarray, based on the allele-specific primer extension (ASPE) method, was used and preliminary validation was examined from the five patients and five controls that were already known their genotypes by DNA sequencing analysis. RESULTS: The cutoff Genotyping index (GI) of genotyping for each mutation was set up and validated to discriminate among the genotypes. The result of the DNA chip assay was identical to those of previous results. CONCLUSION: We successfully designed the genetic hearing loss DNA chip for the first time in Korea and it would be useful for a clinical genetic diagnosis of hearing loss. Further consideration will be needed in order to examine the accuracy of this DNA chip with much larger patient sample numbers.