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Genotyping
Kinds of Genotyping Terms modified by Genotyping Selected AbstractsGenetic and expression analysis of all non-synonymous single nucleotide polymorphisms in the human deoxyribonuclease I-like 1 and 2 genesELECTROPHORESIS, Issue 12 2010Misuzu Ueki Abstract Members of the human DNase I family, DNase I-like 1 and 2 (DNases 1L1 and 1L2), with physiological role(s) other than those of DNase I, possess three and one non-synonymous SNPs in the genes, respectively. However, only limited population data are available, and the effect of these SNPs on the catalytic activity of the enzyme remains unknown. Genotyping of all the non-synonymous SNPs was performed in three ethnic groups including six different populations using the PCR-RFLP method newly developed. Asian and African groups including Japanese, Koreans, Ghanaians and Ovambos were typed as a single genotype at each SNP, but polymorphism at only SNP V122I in DNase 1L1 was found in Caucasian groups including Germans and Turks; thus a Caucasian-specific allele was identified. The DNase 1L1 and 1L2 genes show relatively low genetic diversity with regard to these non-synonymous SNPs. The level of activity derived from the V122I, Q170H and D227A substituted DNase 1L1 corresponding to SNPs was similar to that of the wild-type, whereas replacement of the Asp residue at position 197 in the DNase 1L2 protein with Ala, corresponding to SNP D197A, reduced its activity greatly. Thus, SNP V122I in DNase 1L1 exhibiting polymorphism exerts no effect on the catalytic activity, and furthermore SNP D197A in DNase 1L2, affecting its catalytic activity, shows no polymorphism. These findings permit us to postulate that the non-synonymous SNPs identified in the DNase 1L1 and 1L2 genes may exert no influence on the activity levels of DNases 1L1 and 1L2 in human populations. [source] Strain persistence of invasive Candida albicans in chronic hyperplastic candidosis that underwent malignant changeGERODONTOLOGY, Issue 2 2001DW Williams Abstract Objectives: The aim of this study was to assess persistence and tissue invasion of Candida albicans strains isolated from a 65 year-old patient with chronic hyperplastic candidosis (CHC), that subsequently developed into squamous cell carcinoma (SCC). Materials and Methods: C. albicans (n=7) were recovered from the oral cavity of the patient over seven years. Confirmation of CHC and SCC in this patient was achieved by histopathological examination of incisional biopsy tissue. DNA fingerprinting was performed on the seven isolates from the CHC patient together with a further eight isolates from patients with normal oral mucosa (n=2), chronic atrophic candidosis (n=1), SCC (n=1) and CHC (n=4). Genotyping involved the use of inter-repeat PCR using the eukaryotic repeat primer 1251. Characterisation of the tissue invasive abilities of the isolates was achieved by infecting a commercially available reconstituted human oral epithelium (RHE; SkinEthic, Nice, France). After 24 h. C. albicans tissue invasion was assessed by histopathological examination. Results: DNA fingerprinting demonstrated strain persistence of C. albicans in the CHC patient over a seven year period despite provision of systemic antifungal therapy. The strain of C. albicans isolated from this patient was categorised as a high invader within the RHE compared to other isolates. Conclusions: Candidal strain persistence was evident in a patient with CHC over seven years. This persistence may be due to incomplete eradication from the oral cavity following antifungal therapy or subsequent recolonisation from other body sites or separate exogenous sources. The demonstration of enhanced in vitro tissue invasion by this particular strain may, in part, explain the progression to carcinoma. [source] Pyrosequencing for detection of mutations in the connexin 26 (GJB2) and mitochondrial 12S RNA (MTRNR1) genes associated with hereditary hearing loss,HUMAN MUTATION, Issue 4 2002Alessandro Ferraris Abstract Hereditary hearing loss (HHL) is one of the most common congenital disorders and is highly heterogeneous. Mutations in the connexin 26 (CX26) gene (GJB2) account for about 20% of all cases of childhood deafness, and approach 50% in documented recessive cases of non-syndromic hearing loss. In addition, a single mitochondrial DNA mutation, mt1555A>G, in the 12S rRNA gene (MTRNR1), is associated with familial cases of progressive deafness. Effective screening of populations for HHL necessitates rapid assessment of several of these potential mutation sites. Pyrosequencing links a DNA synthesis protocol for determining sequence to an enzyme cascade that generates light whenever pyrophosphate is released during primer strand elongation. We assessed the ability of Pyrosequencing to detect common mutations causing HHL. Detection of the most common CX26 mutations in individuals of Caucasian (35delG), Ashkenazi (167delT), and Asian (235delC, V37I) descent was confirmed by Pyrosequencing. A total of 41 different mutations in the CX26 gene and the mitochondrial mt1555A>G mutation were confirmed. Genotyping of up to six different adjacent mutations was achieved, including simultaneous detection of 35delG and 167delT. Accurate and reproducible results were achieved taking advantage of assay flexibility and experimental conditions easily optimized for a high degree of standardization and cost-effectiveness. The standardized sample preparation steps, including target amplification by PCR and preparation of single-stranded template combined with automated sequence reaction and automated genotype scoring, positions this approach as a potentially high throughput platform for SNP/mutation genotyping in a clinical laboratory setting. Hum Mutat 20:312,320, 2002. © 2002 Wiley-Liss, Inc. [source] Role of the NFKB1 ,94ins/delATTG promoter polymorphism in IBD and potential interactions with polymorphisms in the CARD15/NOD2, IKBL, and IL-1RN genesINFLAMMATORY BOWEL DISEASES, Issue 7 2006Jürgen Glas MD Abstract Background: Recently, an association of the NFKB1 polymorphism ,94ins/delATTG with ulcerative colitis (UC) has been reported. This 4-bp insertion/deletion polymorphism is localized in the promoter region of the NFKB1 gene and appears to be functionally relevant. The aim of the present study was to confirm the association of the ,94ins/delATTG (W/D) NFKB1 promoter polymorphism with UC in a population of German origin and to test for a potential association with Crohn's disease (CD). Furthermore, potential interactions of the ,94ins/delATTG polymorphism with the IKBL and the IL-1RN genes should be determined. Materials and Methods: The study population comprised 630 patients with CD, 365 patients with UC, and 974 healthy controls. Genotyping was performed using polymerase chain reaction and restriction fragment length polymorphism analysis. For statistical evaluation, the chi-square test and the Fisher exact test were used. Results: No significant association of the W/D NFKB1 polymorphism with CD or UC was detected. In addition, no significant interactions between the ,94ins/delATTG NFKB1 polymorphism and polymorphisms within the IKBL and the IL-1RN genes, respectively, were found in CD or UC. Also, no significant interactions of the NFKB1 polymorphism with mutations of the CARD15/NOD2 gene and with clinical phenotypes were detected in CD. Moreover, no associations of the NFKB1 polymorphism were found in UC depending on disease localization. Conclusions: The present study could not confirm the reported association of the ,94ins/delATTG NFKB1 polymorphism with UC and also found no evidence for a role of this polymorphism in CD. The results do not give evidence for a role of this NFKB1 polymorphism in the pathogenesis of UC and CD. [source] A population- and family-based study of Canadian families reveals association of HLA DRB1*0103 with colonic involvement in inflammatory bowel diseaseINFLAMMATORY BOWEL DISEASES, Issue 1 2003Dr. Mark S. Silverberg Abstract The aim of this study was to identify major histocompatibility complex alleles associated with the development and clinical features of inflammatory bowel disease (IBD). Genotyping at the human leukocyte antigen (HLA) DRB1 and DQB1 loci was performed on individuals from 118 Caucasian IBD sibling pair families and on 216 healthy controls. Both population- and family-based association tests were used to analyze data obtained on the entire study population and on clinical subgroups stratified by diagnosis, ethnicity, and disease distribution. HLA DRB1*0103 was significantly associated with IBD (OR = 6.0, p = 0.0001) in a case,control analysis of non-Jewish IBD-affected individuals. This association was apparent among both Crohn's disease (OR = 5.23, p = 0.0007) and ulcerative colitis (OR = 7.9, p = 0.0001) patients and was confirmed in the non-Jewish IBD population by results of family-based association analysis using the transmission disequilibrium test. HLA DQB1*0501 was also associated with IBD (OR = 1.64, p = 0.02) in the non-Jewish population, but statistically significant association of this allele with disease was not detected for Crohn's disease and ulcerative colitis separately. No significant associations were identified among the Jewish patients. In the non-Jewish IBD families, IBD was as strongly associated with the DRB1*0103 DQB1*0501 haplotype as with the DRB1*0103 allele alone. The carrier frequency of the DRB1*0103 allele was found to be 10-fold higher in Crohn's disease patients with pure colonic involvement than in healthy controls (38.5% vs. 3.2%; p = 0.0002). These data demonstrate the association of the HLA DRB1*0103 allele with both Crohn's disease and ulcerative colitis and with large intestine,restricted disease in non-Jewish IBD patients and therefore identify HLA DRB1*0103 as a potentially important contributor to disease susceptibility and to expression of colonic involvement in IBD. [source] GBV-C/hepatitis G virus infection and non-Hodgkin lymphoma: a case control studyINTERNATIONAL JOURNAL OF CANCER, Issue 12 2010Mel Krajden Abstract We investigated whether there was an association between GBV-C viremia and the development of non-Hodgkin lymphoma (NHL) in 553 NHL cases and 438 controls from British Columbia, Canada. Cases were aged 20,79, diagnosed between March 2000 and February 2004, and resident in Greater Vancouver or Victoria. Cases and controls were tested for GBV-C RNA by RT-PCR and positive samples were genotyped. Overall, GBV-C RNA was detected in 4.5% of NHL cases vs. 1.8% of controls [adjusted odds ratio (OR) = 2.72, 95% confidence interval (CI) = 1.22,6.69]. The association between GBV-C RNA detection and NHL remained even after individuals with a history of prior transfusion, injection drug use and hepatitis C virus sero-positivity were excluded. GBV-C viremia showed the strongest association with diffuse large B cell lymphoma (adjusted OR = 5.18, 95% CI = 2.06,13.71). Genotyping was performed on 29/33 GBV-C RNA positive individuals; genotypes 2a (n = 22); 2b (n = 5) and 3 (n = 2) were identified, consistent with the distribution of genotypes found in North America. This is the largest case-control study to date associating GBV-C viremia and NHL risk. As GBV-C is known to be transmitted through blood products this may have important implications for blood safety. [source] Single nucleotide polymorphisms in the XPG gene: Determination of role in DNA repair and breast cancer riskINTERNATIONAL JOURNAL OF CANCER, Issue 5 2003Rajiv Kumar Abstract In this study we determined the effect of single nucleotide polymorphisms in the XPG gene on DNA repair and breast cancer susceptibility. Ninety individuals, with previously studied DNA repair rate at 24 hr of 2 types of UV-specific cyclobutane pyrimidines dimers (CPDs) in skin were genotyped for XPG polymorphism at codon 1104 (exon 15 G>C; Asp > His). The repair rate of TT=C dimer was similar in both wild-type GG homozygotes and GC heterozygotes, whereas, for TT=T, dimer repair was non-significantly (Student's t -test, p = 0.34) lower in GC heterozygotes than wild-type GG homozygotes. Genotyping of 220 breast cancer cases and 308 controls for the same single nucleotide polymorphism in exon 15 of the XPG gene exhibited marginally significant increased frequency of the variant allele (,2 3.84, p = 0.05; OR 1.33, 95% CI 1.0,1.8) in cases (C-allele 0.29) compared to controls (C-allele 0.24). Combined heterozygote and variant homozygote genotype frequency was also higher in cases than controls (,2 4.79, p = 0.03; OR 1.50, 95%CI 1.04,2.16). © 2002 Wiley-Liss, Inc. [source] Methylenetetrahydrofolate reductase gene and risk of Alzheimer's disease in KoreansINTERNATIONAL JOURNAL OF GERIATRIC PSYCHIATRY, Issue 5 2008Jae-Min Kim Abstract Background The association between methylenetetrahydrofolate reductase (MTHFR) c.677C,>,T (A222V) polymorphism and Alzheimer's disease (AD) is controversial. The objectives of the study were to investigate the association between MTHFR c.677C,>,T polymorphism and AD in Korean elders and to the extent to which it is modified by the major components of one-carbon metabolism and apolipoprotein E (APOE) genotype. Methods Seven hundred and thirty-two community residents aged 65 or over were clinically assessed for AD. Genotyping was performed for MTHFR c.677C,>,T and APOE; serum levels of folate, vitamin B12, and homocysteine were assayed. Age, gender and education were included as covariates. Results A trend of association between TT genotype of MTHFR c.677C,>,T and AD was found [adjusted OR (95% CI): 1.73 (0.80,3.74)]. The association was significant in the presence of below-median vitamin B12 level [3.66 (1.14,11.71)] and in APOE e4 non-carriers [2.97 (1.00,8.55)] with significant interaction terms, and bordered on significance in the presence of above-median homocysteine level [2.73 (0.94,7.90)]. Conclusions These findings suggest gene-environment and gene-gene interactions on the risk of AD in Koreans. Copyright © 2007 John Wiley & Sons, Ltd. [source] No relationship observed between human p53 codon-72 genotype and HPV-associated cervical cancer in a population group with a low arginine-72 allele frequencyINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 3 2007V. A. Govan Summary Infection with high-risk human papillomavirus (HR-HPV) is a necessary but not a sufficient event in the development of cervical cancer, as most infections regress without intervention. Thus, genetic host factors and cellular immune responses could be potential modifiers for the risk of developing cervical cancer. In particular, p53 is considered as the most critical tumour suppressor gene and is involved in regulating cell division. The polymorphism on p53, which encodes either a proline or an arginine amino acid residue at codon 72, has been reported as a possible risk factor for cervical disease. This polymorphism has been shown to differentially affect the efficiency of degradation of p53 protein mediated by HR-HPV E6 oncoprotein. Women with histologically proven cancer of the cervix (n = 111) and hospital-based controls (n = 143) were included in this study. The patients and controls were from the Western Cape Province in South Africa. Genotyping of the p53 polymorphism was conducted using polymerase chain reaction and restriction fragment-length polymorphism method. The distributions of the allelic frequencies were stratified in both patients and controls into two South African ethnic population groups. In this study, we observed no association between the distribution of p53 polymorphism and susceptibility to cervical cancer in the Western Cape Province populations (P = 0.466). However, the frequency of the Pro/Pro residue at codon 72 was increased in the South African population when compared to Caucasians, Indians and Portuguese population groups. Notably, as the distribution of the Pro/Pro at codon 72 of p53 gene was significantly different (P < 0.05) between the control groups of South Africa and other population groups. This result suggests that ethnic disparity may influence the levels of p53 produced. [source] Association between ICAM-1 Gly-Arg polymorphism and renal parenchymal scarring following childhood urinary tract infectionINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 1 2006R. A. Gbadegesin Summary Renal parenchymal scarring (RPS) following urinary tract infection (UTI) is an important cause of renal morbidity in children. Studies have shown that the intensity of the inflammatory response following infection is related to the risk of RPS. However, genetic variability in this response has not been studied. Adhesion molecules play a crucial role in leucocyte recruitment following infection, and polymorphisms have been reported in the genes for key cell adhesion molecules. We have investigated the possibility that children who develop RPS following UTI may exhibit altered genotype or allele frequencies for polymorphisms of the intercellular adhesion molecule-1 (ICAM-1) (exons 4 and 6), E-selectin (exons 2 and 4), platelet endothelial cell adhesion molecule-1 (PECAM-1) (exon 3) and CD11b (3,UTR) genes, which may predict outcome of UTI. DNA was isolated from 99 children shown to have developed RPS, 43 children with no evidence of scarring (NS) following UTI and 170 healthy controls. Genotyping was performed by restriction fragment length polymorphism (RFLP) analysis. When the RPS group was compared with the NS group, there was a significant reduction in the frequency of the ICAM-1 exon 4 A allele (10.6 vs. 21.3%, respectively, ,2= 6.01, P= 0.014). There was no significant difference in either allele or genotype frequency for any of the other polymorphisms studied. These data suggest that the A allele of the ICAM-1 exon 4 polymorphism may protect against the risk of RPS following UTI and may participate in the regulation of the inflammatory response following UTI. [source] Isolation and identification of Acanthamoeba species related to amoebic encephalitis and nonpathogenic free-living amoeba species from the rice fieldJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2010S.-Y. Liang Abstract Aims:, Isolation and characterization of the clinically relevant amphizoic amoebas in vegetated farmlands, which may present a risk to farmers' health. Methods and Results:,Acanthamoeba species was isolated and characterized via morphological and molecular means in the rice field where the patient was exposed to rice paddy water which most probably was the point of infection. An Acanthamoeba sp. abundant in the rice field was identified. Genotyping showed the strain to be genotype T4, which was identical to the amoebic parasite found in patient's cerebrospinal fluid. During the course of the study, three nonpathogenic free-living amoeba species were also isolated and characterized for the first time in Taiwan. Conclusions:, This study successfully located a possible source of granulomatous amoebic encephalitis in a patient and provided the first evidence that Acanthamoeba genotype T4 may be a potential pathogen in Taiwan. Significance and Impact of the Study:, The integration of field survey, clinical data and morphological and genetic examination represents a sound strategy for investigation of the possible role of free-living amoebae in causing human diseases. Future work should include investigating the potential contributory role of other nonpathogenic free-living protozoa in disease of livestock or even human. [source] Genotyping of thermotolerant Campylobacter from poultry slaughterhouse by amplified fragment length polymorphismJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2007G. Johnsen Abstract Aim:, To examine the occurrence, diversity and transmission of Campylobacter in a poultry slaughterhouse. Methods and Results:, During a 4-week period, a slaughterhouse was sampled alternately during slaughtering and the following mornings post-disinfection. Samples were taken from poultry at six stages in the slaughter process and from 25 environmental sites. For positive broiler flocks slaughtered on one occasion, 92% and 48% of the environmental sites were positive during slaughter and post-disinfection, respectively. For positive laying hen flocks slaughtered on three occasions, 8,56% and 12,20% of the environmental sites were positive during slaughter and post-disinfection, respectively. Genetic fingerprinting by amplified fragment length polymorphism (AFLP) of the 109 isolates obtained resulted in 28 different AFLP clones. Five AFLP clones were present for more than 1 week. Conclusions:, Slaughtering of Campylobacter -positive broilers resulted in extensive contamination of the slaughterhouse, including the air. A high proportion of the laying hen flocks were Campylobacter positive, but these caused less environmental contamination than the broilers. This, together with the freezing of all layer carcasses, results in a lower public health risk from laying hens, when compared with broilers. Significance and Impact of the Study:, When slaughtering Campylobacter -positive broilers, the implementation of preventive measures is important to reduce contamination of negative carcasses and to protect the workers against infection. [source] Genotyping of Campylobacter spp. from retail meats by pulsed-field gel electrophoresis and ribotypingJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2006B. Ge Abstract Aims:, To determine the genetic relatedness of Campylobacter spp. from retail meat products, and compare the discriminatory power of pulsed-field gel electrophoresis (PFGE) and automatic ribotyping. Methods and Results:, A total of 378 Campylobacter isolates recovered from 159 raw meats (130 chicken, 25 turkey, three pork and one beef) sampled from 50 retail grocery stores of four supermarket chains in the Maryland suburban area from August 1999 to July 2000 were analysed by PFGE with SmaI, 120 isolates of which were also characterized by ribotyping with PstI using RiboPrinter® system. A total of 148 unique PFGE patterns were identified, 91 of which were present in multiple Campylobacter isolates and 24 in multiple meat samples. Nineteen Campylobacter clones with identical PFGE patterns recurred frequently (up to nine times) throughout the sampling period. Comparing ribotyping with PFGE, we identified 44 PFGE patterns and 22 RiboGroups among the 120 isolates tested. Multiple PFGE patterns within one RiboGroup were commonly observed, as well as multiple RiboGroups within one PFGE pattern. Conclusions:, Although Campylobacter present in retail meats were genetically diverse, certain clones persisted in poultry meats. PFGE had a greater discriminatory power than ribotyping, and the two methods were complementary in genotyping Campylobacter. Significance and Impact of the Study:, Genomic DNA fingerprinting of Campylobacter confirmed diverse and recurrent Campylobacter clones in the retail meats, which provides additional data for a better understanding of the epidemiological aspect of Campylobacter infection. [source] Genotyping of Campylobacter jejuni strains from Danish broiler chickens by restriction fragment length polymorphism of the LPS gene clusterJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2005K.N. Knudsen Abstract Aims:, To apply and evaluate LG (LPS genes) genotyping, which is a genotyping method based on a cluster of genes involved in the synthesis of surface lipopolysaccharides (LPS) in Campylobacter species, for typing of Campylobacter jejuni isolates obtained from Danish broiler chickens. Furthermore, the LG genotyping method was used to study the genetic stability of four C. jejuni strains after gastrointestinal passage through experimentally infected chickens. Methods and Results:, In the present study, the LG genotyping method was modified with respect to the restriction enzymes used. To validate the method, 63 Penner serotype reference strains and 107 C. jejuni chicken isolates, representing the most common Penner serotypes of C. jejuni in Danish poultry, were selected for typing. The method was successfully used for typing all isolates and the LG genotype profiles were reproducible. There were no changes in the LG genotype of the C. jejuni strains obtained after experimental passage through chickens. Conclusions:, All C. jejuni strains obtained from broiler chickens were typeable by the LG genotyping method. Application of the RsaI restriction enzyme improved the method in terms of ease and consistency of analyses and increase of discriminatory power. Significance and Impact of the Study:, The LG genotyping method is a valuable tool for typing C. jejuni isolates obtained from poultry. However, the association between Penner serotyping based on passive haemagglutination of heat-stable antigens and LG genotyping was low when applied to poultry isolates. This is in contrast to previous studies on isolates of human origin that reported a high correlation between results obtained by the two typing methods (Shi et al. 2002). [source] Genotyping of samples lacking expected antibodies in ABO blood groupJOURNAL OF CLINICAL LABORATORY ANALYSIS, Issue 6 2007Zhi-Hui Deng Abstract We report nine donations with ABO inconsistency in reverse typing caused by partly or entirely missing antibodies. A and B antigens and antibodies were examined by serological blood typing, and ABO deoxyribonucleic acid (DNA) analyses were performed by sequence-specific priming and sequencing. A B101 allele was demonstrable in a case with O phenotype. The molecular mechanisms in deficiency of natural ABO antibody could be partly clarified. The ABO genotyping technique is an accurate method for determining the blood samples involved in ABO grouping discrepancies and is a valuable complement to serology for correct determination of donor blood status. The mechanisms involved in the absence of potent natural antibodies directed against A and B antigen lacking on an individual's own red cell membranes remain to be further investigated. J. Clin. Lab. Anal. 21:363,366, 2007. © 2007 Wiley-Liss, Inc. [source] Genotypic characterization of Porphyromonas gingivalis isolated from subgingival plaque and blood sample in positive bacteremia subjects with periodontitisJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 9 2008P. Juliana Pérez-Chaparro Abstract Aim: The objective of this study was to investigate clonal relationship among Porphyromonas gingivalis isolated from subgingival plaque and blood samples in positive transient bacteremia subjects with periodontitis. Material and Methods: Unrelated patients with general chronic periodontitis or general aggressive periodontitis requiring scaling and root planing (SRP) were included in the study. Genotyping of each isolate was performed using pulsed field gel electrophoresis technique. Genetic relatedness of strains isolated within an individual or between different patients was determined by dendogram analysis. Results: Following SRP, from 16 patients, seven patients showed positive P. gingivalis bacteremia and nine were negative. Thirty-two strains were isolated from subgingival plaque and blood samples before and during induced transient bacteremia. The majority of the patients harboured one clonal type. Two patients showed different clones in plaque and blood samples suggesting that more than one clone can be found in subgingival plaque. P. gingivalis isolates from periodontitis patients after transient bacteremia following SRP, revealed a high heterogeneity among isolates. Conclusion: In 6/16 subjects the same P. gingivalis isolate was found in the blood and in oral cavity. P. gingivalis heterogeneity suggests no association of a unique clonal type with transient bacteremia. [source] No correlation of five gene polymorphisms with periodontal conditions in a Greek populationJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 11 2006D. Sakellari Abstract Background: Various studies have examined possible correlations between a number of cytokine gene polymorphisms and periodontal disease in populations of different origins. The present study sought the correlation between four single-nucleotide polymorphisms (IL1A+3954, IL1B+4845, TNFA,308, COL1A1 Sp1), a variable number of tandem repeats polymorphism (IL1RN intron 2) and periodontal conditions in subjects of Greek origin. Methods: One hundred and ninety-two healthy subjects, stratified as non-periodontitis and periodontitis (chronic and aggressive) cases, participated in the present study. Genotyping was performed by polymerase chain reaction-based techniques using the primers and conditions described in the literature. The frequencies of genotypes between study groups were compared using Genepop v3.3 genetic software and Instat statistical package. Results: No differences were observed among the groups concerning the distributions of genotypes under investigation. Conclusions: Carriage rates of the polymorphisms under investigation in systemically healthy subjects of Greek origin are well within the range reported for Caucasians but these polymorphisms cannot discriminate between non-periodontitis and periodontitis (chronic or aggressive) cases. [source] CTLA-4 gene promoter and exon 1 polymorphisms in Iranian patients with gastric and colorectal cancersJOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 12 2007Abolghasem Hadinia Abstract Background and Aim:, Cytotoxic T-lymphocyte antigen-4 (CTLA-4) is a potent immunoregulatory molecule that suppresses antitumor response by down-regulating T-cell activation. Effects of several polymorphisms in CTLA-4 on CTLA-4 expression and function have been previously documented. The aim of this study was to investigate the putative effect of CTLA-4 polymorphisms on susceptibility to gastric and colorectal cancers in an Iranian population. Methods:, A total of 155 patients (109 with colorectal cancer and 46 with gastric cancer) and 190 age- and sex-matched healthy controls were evaluated. Genotyping of ,1722T/C, ,1661A/G, and +49A/G were performed by PCR restriction fragment length polymorphism methods and of ,318C/T by a PCR amplification refractory mutation system technique. Results:, No statistically significant differences were found in the genotype distribution and allele frequencies among patients and controls. Haplotype analysis demonstrated that the TACG haplotype (,1722T, ,1661A, ,318C, +49G) frequency was significant increased in patients with colorectal cancer (P = 0.009) and gastric cancer (P = 0.006) in comparison to the control group. In contrast, the TACA haplotype frequency was significantly decreased in patients with colorectal cancer (P = 0.02) and not significantly decreased in patients with gastric cancer (P = 0.13) compared to the control group. Conclusion:, A positive association between CTLA-4 TACG haplotype and gastric and colorectal cancers was found in an Iranian population. A protective role for TACA haplotype is postulated. [source] Seroprevalence of Kaposi's sarcoma-associated herpesvirus and risk factors in Xinjiang, China,JOURNAL OF MEDICAL VIROLOGY, Issue 8 2009Bishi Fu Abstract Xinjiang, China is an endemic area for Kaposi's sarcoma (KS) but the seroprevalence of Kaposi's sarcoma-associated herpesvirus (KSHV) and risk factors remain undefined. In this study, antibodies to one KSHV latent protein (ORF73) and two KSHV lytic proteins (ORF65 and ORF-K8.1) were examined in 2,228 subjects from the general population and 37 subjects infected with HIV-1 in Xinjiang, and 560 subjects from the general population in Hubei, a low KS incidence region. The serostatus of a serum sample was defined based on positive results in any one of the three serologic assays. The seroprevalence of KSHV in the general population was higher in Xinjiang than in Hubei (19.2% vs. 9.5%; odds ratios [OR], 2.28; 95% confidence interval [CI], 1.68,3.08; P,<,0.001). Among the ethnic groups in Xinjiang, 68 (15.8%) Han, 182 (20.7%) Uygur, 140 (19.9%) Hazakh, 9 (33.3%) Xibo, and 29 (16.8%) Hui were KSHV-seropositive, respectively. Compared to the Han, the latter groups had an increase in the risk of KSHV of 62.2%, 63.8%, 180.1%, and 30.2% (P,=,0.003, 0.004, 0.018, and 0.286, respectively). Subjects aged <20, 20,50, and >50 had a seroprevalence of KSHV of 11.8%, 17.9%, and 24.6%, respectively. Compared to subjects aged <20, the latter groups had an increase in the risk of KSHV of 63.3% and 144.5% (P,=,0.009 and <0.001, respectively). Subjects infected with HIV-1 in Xinjiang had a seroprevalence of KSHV of 43.2%, and a 220% increase in the risk of KSHV compared to the general population (P,<,0.001). Similar results were obtained when the seroprevalence of KSHV was analyzed with any single or two of the three serologic assays alone. Genotyping identified three unique sequences clustered in the A clade. This study indicates that Xinjiang has a high seroprevalence of KSHV. Geographic location, ethnicity, age and HIV-1 infection are risk factors. Serologic and genotyping results suggest the introduction of KSHV into Xinjiang by specific ethnic groups. J. Med. Virol. 81:1422,1431, 2009. © 2009 Wiley-Liss, Inc. [source] Hepatitis B virus genotypes in children and adolescents in Japan: Before and after immunization for the prevention of mother to infant transmission of hepatitis B virusJOURNAL OF MEDICAL VIROLOGY, Issue 6 2007Ayano Inui Abstract The genotype distribution of hepatitis B virus (HBV) was investigated in 118 children in Japan. One hundred and sixteen children (98%) had chronic HBV infection, and the remainder had acute hepatitis. Genotyping of HBV was determined by PCR and sequencing analysis in the S gene. Genotype C (86%) was the most frequent, followed by genotype B (9%), D (2.5%), and A (1.0%). Transmission routes of HBV to children were from mothers in 91 patients (77%), fathers in 8 (6.5%), mother or father in 1 (1%), family members other than the parents in 5 (4%), and unknown in 13 (11.5%). The relationship between routes of HBV transmission and HBV genotypes was studied. Eighty-eight (97%) of 91 children of mother-to-infant transmission were genotype C, while 13 (49%) of 27 children of the routes other than the mother to infant transmission were genotype C. The number of children with genotype C who were infected from their mothers was significantly higher than those with genotype B, D, or A (P,<,0.01). In conclusion, HBV genotypes influence not only clinical characteristics but also the mechanisms of inter-personal HBV transmission. J. Med. Virol. 79: 670,675, 2007. © 2007 Wiley-Liss, Inc. [source] Distinct patterns of evolution between respiratory syncytial virus subgroups A and B From New Zealand isolates collected over thirty-seven years,JOURNAL OF MEDICAL VIROLOGY, Issue 10 2006James W. Matheson Abstract Respiratory syncytial virus (RSV) is the most important cause of viral lower respiratory tract infections in infants and children worldwide. In New Zealand, infants with RSV disease are hospitalized at a higher rate than other industrialized countries, without a proportionate increase in known risk factors. The molecular epidemiology of RSV in New Zealand has never been described. Therefore, we analyzed viral attachment glycoprotein (G) gene sequences from 106 RSV subgroup A isolates collected in New Zealand between 1967 and 2003, and 38 subgroup B viruses collected between 1984 and 2004. Subgroup A and B sequences were aligned separately, and compared to sequences of viruses isolated from other countries during a similar period. Genotyping and clustering analyses showed RSV in New Zealand is similar and temporally related to viruses found in other countries. By quantifying temporal clustering, we found subgroup B viruses clustered more strongly than subgroup A viruses. RSV B sequences displayed more variability in stop codon usage and predicted protein length, and had a higher degree of predicted O-glycosylation site changes than RSV A. The mutation rate calculated for the RSV B G gene was significantly higher than for RSV A. Together, these data reveal that RSV subgroups exhibit different patterns of evolution, with subgroup B viruses evolving faster than A. J. Med. Virol. 78:1354,1364, 2006. © 2006 Wiley-Liss, Inc. [source] Genotyping of the JC virus in urine samples of healthy Korean individualsJOURNAL OF MEDICAL VIROLOGY, Issue 2 2004Byung-Hoon Jeong Abstract A human polyomavirus, JC virus (JCV) is ubiquitous in humans and infects children asymptomatically. It persists in renal tissue and is excreted progeny in urine. DNAs from urine samples of 100 healthy Korean individuals were screened for the presence of JCV by polymerase chain reaction (PCR). Twenty of the samples were positive for JCV. JCV DNA was found in one individual (4%) in the 1,19-year group, two individuals (9%) in the 20,39-year group, ten individuals (38%) in the 40,59-year group, seven individuals (28%) in the over 60-year group. The prevalence of JC viral DNA was the highest in the 40,59-year-old Korean population. To investigate genotypes of JCV in Korea, the genotypes were determined by DNA sequence analysis of the regulatory region (333 bp) and the VT-intergenic region (656 bp) of DNA from the 20 JCV isolates. We have identified three distinctive JCV strains in the regulatory region and ten distinctive JCV strains in the VT-intergenic region of DNA from the 20 isolates. Based on restriction fragment length polymorphism (RFLP) analysis and phylogenetic analysis of the VT-intergenic region of JCV, two distinct subtypes, CY and type 2A (MY), were found to be prevalent in this Korean population. CY and type 2A of JCV were identified in 13 individuals (65%) and four individuals (20%), respectively. Interestingly, type 1, which was distributed mostly in Europe, was found in 3 (15%) isolates from healthy Korean individuals. J. Med. Virol. 72:281,289, 2004. © 2004 Wiley-Liss, Inc. [source] ACE and MTHFR gene polymorphisms in unexplained recurrent pregnancy lossJOURNAL OF OBSTETRICS AND GYNAECOLOGY RESEARCH (ELECTRONIC), Issue 3 2008Venkatesan Vettriselvi Abstract Aim:, To assess the association between polymorphisms in angiotensin converting enzyme and methylene tetrahydrofolate reductase genes and recurrent pregnancy loss by a case-control study in South Indian women. Methods:, DNA was extracted from peripheral blood leukocytes of 104 women with Recurrent Pregnancy Loss (RPL) and 120 controls. Genotyping of ACE Insertion Deletion and MTHFR C677T polymorphism were carried out by PCR and PCR-RFLP, respectively. Results:, No statistically significant difference was observed in the distribution of genotypes between cases and controls for ACE and MTHFR polymorphisms. Further, the combination of MTHFR and ACE genotypes failed to reveal an association. Conclusion:, In conclusion, the present study reveals lack of association of MTHFR C677T and ACE I/D polymorphisms in RPL in South Indian women. However, we cannot exclude the possibility that other polymorphisms of ACE and MTHFR genes could be associated with the disease and might be clinically useful as a marker to assess risk for RPL. [source] Should we be ,pushing meds'?JOURNAL OF PSYCHIATRIC & MENTAL HEALTH NURSING, Issue 5 2008The implications of pharmacogenomics Medication continues to be the most widely prescribed treatment in the NHS for mental health problems. It has been known for many years that individuals differ in the way they respond to a given pharmaceutical therapy, and one reason for this lies in the genetic variation between individuals. This paper recognizes the impact that pharmacogenomics and pharmacogenetics are having in the field of mental health. Variants in genes that code for the drug metabolizing enzymes in the liver have been found to influence the way in which these enzymes handle psychotropic medication. Individuals can be classified as poor, moderate or extensive metabolizers when standard regimes are used, and this can lead to huge differences in therapeutic effect and toxicity. There are now genotyping tests available which provide information on the individual's ability to metabolize psychotropic medication. One author provides an account of the effects of medication on her son's physical and psychological well-being. Genotyping provided evidence for his poor metabolism of psychotropic medication, and his life is now changing as he is being very gradually weaned off this medication. This emerging field of work has implications for the way in which practitioners consider medication adherence. [source] Searching for Responders to Acamprosate and Naltrexone in Alcoholism Treatment: Rationale and Design of the Predict StudyALCOHOLISM, Issue 4 2009Karl Mann Background:, Alcoholism represents a major public health issue and treating alcohol dependent patients remains an imminent challenge. Evidence based psychotherapies and pharmacotherapies are available. However, when administered to heterogeneous populations of patients effect sizes are only modest. We present the rationale and design of a double-blind randomized trial comparing acamprosate, naltrexone, and placebo. Additionally we subtype patients on the basis of biological and psychometric measures and explore their treatment response to both acamprosate and naltrexone. According to our initial hypothesis, the "relief drinker/craver" is an endophenotype associated with glutamatergic dysfunction who responds to acamprosate. The "reward drinker/craver" is mainly associated with alterations in the dopaminergic and opioidergic system and responds to naltrexone. Methods:, The study is planned for 430 patients (2:2:1 for both drugs and placebo) over 12 weeks of medication. All receive manualized counselling to improve compliance (Medical Management) which is extended to 6 months. Subtyping is primarily done using the acoustic startle reflex, functional magnetic resonance imaging, positron emission tomography (in a subset of patients), and the Inventory of Drinking Situations. Relapsers will be re-randomized into a second study where additional psychotherapy (Cognitive Behavioral Intervention) is used in a stepped care approach. Genotyping and additional analyses such as health economy are being done as well. The study follows the assessment methods, treatments, and medications used in the U.S. based COMBINE study, which will allow for a direct comparison between this U.S. study trial and a study performed in Europe. [source] Alcohol and Colorectal Cancer: The Role of Alcohol Dehydrogenase 1C PolymorphismALCOHOLISM, Issue 3 2009Nils Homann Background:, Chronic alcohol consumption is a risk factor for colorectal cancer. Animal experiments as well as genetic linkage studies in Japanese individuals with inactive acetaldehyde dehydrogenase leading to elevated acetaldehyde concentrations following ethanol ingestion support the hypothesis that acetaldehyde may be responsible for this carcinogenic effect of alcohol. In Caucasians, a polymorphism of alcohol dehydrogenase 1C (ADH1C) exists resulting in different acetaldehyde concentrations following ethanol oxidation. Methods:, To evaluate whether the association between alcohol consumption and colorectal tumor development is modified by ADH1C polymorphism, we recruited 173 individuals with colorectal tumors diagnosed by colonoscopy and 788 control individuals without colorectal tumors. Genotyping was performed using genomic DNA extracted from whole blood followed by polymerase chain reaction. Results:, Genotype ADH1C*1/1 was more frequent in patients with alcohol-associated colorectal neoplasia compared to patients without cancers in the multivariate model controlling for age, gender, and alcohol intake (odds ratio = 1.674, 95% confidence interval = 1.110,2.524, 2-sided p from Wald test = 0.0139). In addition, the joint test of the genetic effect and interaction between ADH1C genotype and alcohol intake (2-sided p = 0.0007) indicated that the difference in ADH1C*1 polymorphisms between controls and colorectal neoplasia is strongly influenced by the alcohol consumption and that only individuals drinking more than 30 g ethanol per day with the genotype ADH1C*1/1 had an increased risk for colorectal tumors. Conclusions:, These data identify ADH1C homozygosity as a genetic risk marker for colorectal tumors in individuals consuming more than 30 g alcohol per day and emphasize the role of acetaldehyde as a carcinogenic agent in alcohol-related colorectal carcinogenesis. [source] The association between MIF-173 G>C polymorphism and prostate cancer in southern ChineseJOURNAL OF SURGICAL ONCOLOGY, Issue 2 2009G.X. Ding MD Abstract Background and Objectives Accumulating epidemiological and molecular evidence suggests that inflammation is an important component in the etiology of PCa. Macrophage migration inhibitory factor (MIF) plays an important role in the pro- and anti-inflammatory response to infection. This study is aimed at investigating the potential association between MIF-173 G>C polymorphism, Gleason score, clinical stage, and prostate-specific antigen (PSA) value with respect to PCa incidence among the Han nationality in Southern China. Methods Genotyping was performed by using tetraprimer polymerase chain reaction (PCR) on 259 PCa patients and 301 cancer-free controls. Results We found that the MIF-173*C variant allele was significantly associated with an increased risk of PCa [adjusted odd ratio (OR),=,2.99, 95% confident interval (CI): 1.94,4.60] and higher Gleason scores from the PCa subjects (adjusted OR,=,10.72, 95% CI: 5.35,21.49). In addition, we noted that the MIF ,173*C variant allele was related to higher clinical stages and PSA values in PCa patients (adjusted OR,=,15.68, 95% CI: 7.40,33.23; adjusted OR,=,4.37, 95% CI: 2.41,7.92, respectively). Conclusion Our data suggest that MIF-173 polymorphisms may be associated with a higher incidence of prostate cancer compared to controls, and appears to be associated with higher Gleason scores, higher clinical stages, and PSA values in those with prostate cancer. J. Surg. Oncol. 2009;100:106,110. © 2009 Wiley-Liss, Inc. [source] Genetic Determinants of Alcohol Addiction and Metabolism: A Survey in ItalyALCOHOLISM, Issue 2 2001Roberta Pastorelli Background: Although multiple genes are involved in alcoholism and can contribute differently to the risk of dependence and liver damage, no studies have investigated susceptibility to addiction in combination with susceptibility to liver damage due to differences in ethanol metabolism. Methods: We evaluated the role of three polymorphic genes related to alcohol metabolism (CYP2E1) and, possibly, dependence (DRD2 and SLC6A4 promoter) in a series of 60 alcoholics admitted to a specialized referral center in Florence, Italy. Eighteen had a diagnosis of liver cirrhosis. A control series of 64 blood donors were identified at the same hospital. Genotyping was done by polymerase chain reaction-restriction fragment length polymorphism methods. Results: No difference was found in the frequency of the CYP2E 1 Rsa I c2 allele (2.5% among alcoholics and 4.7% among controls) and the Dra I C allele (6.7% and 10.1%). Similarly, no difference was found in the frequency of the DRD2 A1 allele (15.8% and 13.3%) and the B1 allele (10.8% and 8.6%). The proportion of controls with a combined B1 genotype (B1/B1 or B1/B2) was significantly associated with smoking (p= 0.03). The distribution of the S and L allele of the SLC6A4 gene was similar in the two groups, with 15% and 14%, respectively, homozygous S/S carriers. A significant association, however, emerged in the group of alcoholics, with a five times higher risk for S/S carriers of developing cirrhosis (p < 0.05). This association with liver persisted even after exclusion of the subgrouped of 10 hepatitis C virus positive alcoholics. Conclusions: Overall, our results provided no evidence of an increased susceptibility to develop alcoholism that was associated with the three genotypes investigated, either alone or in combination. An increased risk of developing liver cirrhosis for S/S homozygous carriers among alcohol-dependent patients was observed for the first time. [source] CMTX: heterozygosity for a GJB1/CX32 mutation in a XXY male results in a mild phenotypeJOURNAL OF THE PERIPHERAL NERVOUS SYSTEM, Issue 2 2004M Milani Mutations in the GJB1/Cx32 gene (Xq13.1) cause the most common X-linked form of CMT (CMTX1) and are the most frequent cause of CMT disease after the CMT1A duplication. The disorder is characterized by a moderate-to-severe neuropathy in affected males and mild-to-no symptoms in carrier females. We report here a CMT1A-negative family in which 4 females and 2 males were affected, exhibiting different disease severity. Molecular analysis of the GJB1/Cx32 gene uncovered a nonsense mutation (Arg22stop) in exon 2. The mutation, which had been previously described by others and observed by us in numerous other families, occurred in heterozygous form in the 4 females. However, while one of the two male patients was severely affected and shown to be hemizygous, as expected, the other was mildly affected and found to carry the mutation in heterozygous form. Genotyping at the SRY (Yp11.3) and DMD (Xp21) loci suggested the occurrence of the XXY genotype associated with Klinefelter syndrome. Microsatellite analysis indicated that the nondysjunctional error was of paternal origin, as it is usually observed in about half the cases. The patient had no children. At clinical examination, he exhibited a very mild neurologic phenotype and showed signs of hypogonadism (mild gynecomastia and small testes) as well as moderate cognitive impairment. Electrophysiologic, cytogenetic and endocrinologic investigations are in progress in order to define the unusual phenotype in this patient. [source] TRACING THE ORIGIN OF MULTI-DRUG RESISTANT (MDR) ESCHERICHIA COLI INFECTIONS FROM URINARY CATHETERS IN ICU CANINE PATIENTSJOURNAL OF VETERINARY EMERGENCY AND CRITICAL CARE, Issue S1 2004J Ogeer-Gyles Introduction: Urinary tract infections (UTIs) in dogs with urinary catheters in intensive care units (ICUs) are frequent. Historically, multi-drug resistant (MDR) Escherichia coli account for about 10% of the UTIs. The objectives of this study were to determine the frequency of E. coli infections and of MDR E. coli in dogs with UTIs in our ICU, and to assess whether the MDR E. coli were community-acquired or nosocomial in origin. Methods: Over a 1-year period, rectal swabs were taken from all dogs in the ICU on the day of admission (D0) and on days 3 (D3), 6 (D6), 9 (D9) and 12 (D12). Urine was collected on these days from dogs with an indwelling urinary catheter (n=190). Rectal swabs and urine were routinely cultured. E. coli isolates were identified by biochemical tests. Using NCCLS guidelines, antibiotic susceptibility testing was done by disk diffusion method on fecal and urinary E. coli isolates. Twelve antimicrobial agents were used: nalidixic acid, enrofloxacin, cephalothin, cefoxitin, cefotaxime, ceftiofur, trimethoprim-sulfa, chloramphenicol, gentamicin, tetracycline, ampicillin, and amoxicillin/clavulanate. Pulsed-field gel electrophoresis (PFGE) was used to compare MDR E. coli UTI strains with fecal E. coli strains from the same patient and with MDR fecal E. coli from patients that were adjacent to, or housed in the same cages. Results: E. coli was cultured from 12 (48%) of 25 UTIs. Two of the E. coli were MDR. For one dog, PFGE showed no similarities among fecal E. coli and the urinary MDR E. coli isolates from the patient or between these isolates and fecal E. coli from a dog housed in the same kennel on the previous day. The MDR E. coli UTI was likely acquired prior to admission to the ICU, as it was present on D0. For the other dog, PFGE showed genetic similarity but not complete identity between the D3 MDR E. coli urinary isolate and the D3, D6, D9 fecal MDR isolates. This suggests that the UTI originated with the fecal E. coli. Using selective plates, fecal MDR E. coli were not found on D0. Selection of the MDR strain in the intestine by the use of antibiotics occurred while the dog was in the ICU and possibly led to the UTI. Conclusions: Multi-drug resistant E. coli accounted for 2 of 12 E. coli UTIs in dogs in the ICU over a 1-year period. Genotyping showed that one of the two MDR E. coli infections could possibly be of nosocomial origin. [source] | |||||||||||||||||||||||||||||||||||||