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Common Genotypes (common + genotype)
Selected AbstractsFolate metabolism genes, vegetable intake and renal cancer risk in central EuropeINTERNATIONAL JOURNAL OF CANCER, Issue 8 2008Lee E. Moore Abstract In a multicenter case-control study of renal cell carcinoma (RCC) conducted in central and eastern Europe, we reported a strong inverse association with high vegetable intake and RCC risk. The odds ratio (OR) for high compared to the lowest tertile of vegetable intake was OR = 0.67; (95% confidence interval (CI): 0.53,0.83; p -trend < 0.001). We hypothesized that variation in key folate metabolism genes may modify this association. Common variation in 5 folate metabolism genes (CBS: Ex9+33C > T (rs234706), Ex13 +41C > T (rs1801181), Ex18 ,391 G > A (rs12613); MTHFR: A222V Ex5+79C > T (rs1801133), Ex8,62A > C (rs1801131); MTR: Ex26 20A > G (rs1805087), MTRR: Ex5+136 T > C (rs161870), and TYMS:IVS2,405 C > T (rs502396), Ex8+157 C > T (rs699517), Ex8+227 A > G (rs2790)) were analyzed among 1,097 RCC cases and 1,555 controls genotyped in this study. Having at least 1 variant T allele of MTHFR A222V was associated with higher RCC risk compared to those with 2 common (CC) alleles (OR = 1.44; 95% CI: 1.17,1.77; p = 0.001). After stratification by tertile of vegetable intake, the higher risk associated with the variant genotype was only observed in the low and medium tertiles (p -trend = 0.001), but not among those in the highest tertile (p -interaction = 0.22). The association remained robust after calculation of the false discovery rate (FDR = 0.05). Of the 3 TYMS SNPs examined, only the TYMS IVS2 ,405 C (rs502396) variant was associated with a significantly lower risk compared to the common genotype (OR = 0.73; 95% CI: 0.57,0.93). Vegetable intake modified the association between all 3 TYMS SNPs and RCC risk (p -interaction < 0.04 for all). In summary, these findings suggest that common variation in MTHFR and TYMS genes may be associated with RCC risk, particularly when vegetable intake is low. © 2007 Wiley-Liss, Inc. [source] Human papillomavirus genotypes and their association with cervical neoplasia in a cohort of Western Australian womenJOURNAL OF MEDICAL VIROLOGY, Issue 1 2005Brian Brestovac Abstract Human papillomavirus (HPV) is known to be the cause of almost all cervical cancers. The genotypes have been classified into high and low risk types according to their oncogenic potential. However, data for many of the genotypes are limited and some (HPV-26, 53, and 66) have no agreed status. A study was undertaken to determine the HPV genotype distribution in women of Western Australia and the association with cervical neoplasia. Liquid based cervical samples from a cohort of 282 Western Australian women were tested for HPV DNA by PCR followed by DNA sequencing to determine HPV genotypes. HPV-53 and HPV-16 were the most common genotypes found in this population. In addition 86 archived liquid based cervical samples from women with cervical intraepithelial neoplasia grades 1,3 (CIN 1,3) were tested for HPV DNA. Also 32 archived paraffin biopsy samples from women with squamous cell carcinoma were also tested. HPV-16 was the most common genotype found in these samples. Of the cohort of Western Australian women tested, 27% were found to contain HPV and approximately half of these contained known high-risk HPV genotypes, but only 30% of these were types 16 or 18. The data from this study indicate that HPV-53 is not oncogenic based on an R value and odds ratio (OR) of zero. The data also suggest that HPV-73 may be oncogenic, while HPV-66 is unlikely to be. Two high-risk HPV genotypes that are associated with the Asian region (HPV-52 and HPV-58) were found in Western Australian women suggesting a possible epidemiological link between women in these countries. J. Med. Virol. 76:106,110, 2005. © 2005 Wiley-Liss, Inc. [source] Audioprofiling identifies TECTA and GJB2 -related deafness segregating in a single extended pedigreeCLINICAL GENETICS, Issue 2 2007NC Meyer An audioprofile displays phenotypic data from several audiograms on a single graph that share a common genotype. In this report, we describe the application of audioprofiling to a large family in which a genome-wide screen failed to identify a deafness locus. Analysis of audiograms by audioprofiling suggested that two persons with hearing impairment had a different deafness genotype. On this basis, we reassigned affectation status and identified a p.Cys1837Arg autosomal dominant mutation in ,-tectorin segregating in all family members except two persons, who segregated autosomal recessive deafness caused by p.Val37Ile and p.Leu90Pro mutations in Connexin 26. One nuclear family in the extended pedigree segregates both dominant and recessive non-syndromic hearing loss. [source] Human papillomavirus genotypes and their association with cervical neoplasia in a cohort of Western Australian womenJOURNAL OF MEDICAL VIROLOGY, Issue 1 2005Brian Brestovac Abstract Human papillomavirus (HPV) is known to be the cause of almost all cervical cancers. The genotypes have been classified into high and low risk types according to their oncogenic potential. However, data for many of the genotypes are limited and some (HPV-26, 53, and 66) have no agreed status. A study was undertaken to determine the HPV genotype distribution in women of Western Australia and the association with cervical neoplasia. Liquid based cervical samples from a cohort of 282 Western Australian women were tested for HPV DNA by PCR followed by DNA sequencing to determine HPV genotypes. HPV-53 and HPV-16 were the most common genotypes found in this population. In addition 86 archived liquid based cervical samples from women with cervical intraepithelial neoplasia grades 1,3 (CIN 1,3) were tested for HPV DNA. Also 32 archived paraffin biopsy samples from women with squamous cell carcinoma were also tested. HPV-16 was the most common genotype found in these samples. Of the cohort of Western Australian women tested, 27% were found to contain HPV and approximately half of these contained known high-risk HPV genotypes, but only 30% of these were types 16 or 18. The data from this study indicate that HPV-53 is not oncogenic based on an R value and odds ratio (OR) of zero. The data also suggest that HPV-73 may be oncogenic, while HPV-66 is unlikely to be. Two high-risk HPV genotypes that are associated with the Asian region (HPV-52 and HPV-58) were found in Western Australian women suggesting a possible epidemiological link between women in these countries. J. Med. Virol. 76:106,110, 2005. © 2005 Wiley-Liss, Inc. [source] Major histocompatibility complex variability in the clonal Amazon molly, Poecilia formosa: is copy number less important than genotype?MOLECULAR ECOLOGY, Issue 6 2009K. P. LAMPERT Abstract The evolution of sex is still a major unsolved puzzle in biology. One of the most promising theoretical models to answer this question is the Red Queen hypothesis. The Red Queen hypothesis proposes a fast adaptation of pathogens to common genotypes and therefore a negative frequency-dependent selection against common genotypes. Clonal organisms should be especially endangered when co-occurring with closely related sexual species. In this context, major histocompatibility (MHC) genes have been discussed to be auspicious candidates that could provide the genetic basis on which selection for immune competence could act. In this study, we investigated MHC variability in a clonal teleost fish: the Amazon molly, Poecilia formosa. The Amazon molly is an ideal candidate to test the Red Queen hypothesis as it is a clonal species but co-occurs with a closely related sexual species and should therefore be especially susceptible to pathogen infection. We found that allele numbers did in general not differ between sexual and clonal ,species' but that genotypic variability is reduced in the clonally reproducing fish, especially in the polyploids. We conclude that in clonal organisms, genotype frequency might be more important for immune competence than MHC allele number. Amazon mollies and their co-occurring parental species clearly fulfil a prerequisite of the Red Queen hypothesis and should therefore provide an ideal system to experimentally test this basic principle probably underlying the evolution of sex. [source] Occurrence and distribution of Raspberry bushy dwarf virus in commercial Rubus plantations in England and WalesPLANT PATHOLOGY, Issue 6 2001D. J. Barbara Serological surveys for Raspberry bushy dwarf virus (RBDV) made between 1995 and 1997 and covering ,,10% of the commercial farms growing Rubus (red raspberry and hybrid berries) in England and Wales showed that this virus was present on approximately one-quarter of all farms and in approximately one-sixth of all plots tested. RBDV was found in all of the four main raspberry cultivars being grown at that time (Autumn Bliss, Glen Moy, Glen Prosen and Leo), in Loganberry and in Tayberry. Fifteen RBDV genotypes (including two that appeared to be mixed) were identified using RT-PCR/RFLPs, but the majority of genotypes were found only rarely. Of the RBDV isolates tested, two genotypes each comprised 12·5% and another 46·4%. None of the three most common genotypes was associated solely with single Rubus cultivars and vice versa. It is suggested that two separate outbreaks of RBDV are occurring in England and Wales. One outbreak comprises the most frequent genotype combined with one of the moderately frequent genotypes; this outbreak is largely confined to the main growing areas and is either spreading between farms or coming from multiple local sources. Circumstantial evidence suggests that these isolates (and hence this first outbreak) are of the RB pathotype. The second outbreak consists of the other moderately frequent genotype and those genotypes which are less common. These genotypes appear to be more scattered across England and Wales and seem more likely to be coming from local sources and not to be spreading naturally between commercial farms. [source] Current concepts on human papillomavirus infections in childrenAPMIS, Issue 6-7 2010STINA SYRJÄNEN Syrjänen S. Current concepts on human papillomavirus infections in children. APMIS 2010; 118: 494,509. Current evidence is strong enough to conclude that human papillomavirus (HPV) can be transmitted both sexually and non-sexually. The debate on HPV infections in children still continues but it is more focused on HPV prevalence than on transmission modes. HPV DNA detection in amniotic fluid, foetal membranes, cord blood and placental trophoblastic cells all suggest HPV infection in utero, i.e. prenatal transmission. Based on recent meta-analysis, vertical transmission occurs in approximately 20% of cases. Most of the mucosal HPV infections in infants are incident, persistent infections in oral and genital mucosa being found in less than 10% and 2% respectively. The mother seems to be the main transmitter of HPV to her newborn, but subsequent HPV infections are acquired horizontally via saliva or other contacts. Bimodal peak prevalence is seen for skin warts, oral papillomas and recurrent respiratory papillomatosis (RRP) in younger and older age groups, suggesting similar epidemiology. Of the clinical HPV diseases, juvenile-onset-RRP and genital condylomata are problematic; the former because of its life-threatening potential and the latter because of possible sexual abuse. HPV6 and 11 are the most common genotypes in both the lesions. Early in life, infections by the high-risk HPV genotypes may also remain persistent for a considerable period, and should be of considerable importance for HPV vaccination strategies. [source] Development of a laboratory project to determine human ABO genotypes,Limitations lead to further student explorationsBIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 6 2009Theresa A. Salerno Abstract A multiplex allele-specific PCR analysis was developed to identify six "common" genotypes: AA, AO, BB, BO, OO, and AB. This project included a pre-laboratory exercise that provided active learning experiences and developed critical thinking skills. This laboratory resulted in many successful analyses, which were verified by student knowledge of their phenotypes. However, the design was found to be deficient for the analysis of variants. The limitations in the original allied-health multiplex design were verified through a student designed problem-based laboratory project in an advanced level biochemistry class. Variants were further analyzed in an undergraduate research project using SSCP analyses. The topic of ABO genotyping provides several opportunities for student-centered explorations. [source] The adaptive role of Phosphoglucomutase and other allozymes in a marine snail across the vertical rocky-shore gradientBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2009JUAN GALINDO Natural selection can play an important role in the maintenance of genetic polymorphisms, despite ongoing gene flow. In the present study, we use previously analysed allozymic loci and perform an FST outlier-based analysis to detect the signatures of divergent selection between sympatric ecotypes of the marine snail Littorina saxatilis at different localities. The results obtained show that different allozyme polymorphisms are affected (directly or indirectly) by selection at distinct geographical regions. The Phosmogluco mutase-2 locus was the best candidate for adaptation and further biochemical analyses were performed. The kinetic properties of the three more common genotypes of Pgm-2 were studied. The results obtained are concordant with two alternative hypotheses: (1) natural selection is acting directly on this locus or, more probably, (2) selection is affecting a genomic region tightly linked to the enzyme locus. In both cases, the known existence of a parallel and partially independent origin of these ecotypes would explain why different candidate loci were detected in different localities. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 225,233. [source] | |||||||||||||