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Polymorphism Frequencies (polymorphism + frequency)
Selected AbstractsGenetic diversity contribution to errors in short oligonucleotide microarray analysisPLANT BIOTECHNOLOGY JOURNAL, Issue 5 2006Matias Kirst Summary DNA arrays based on short oligonucleotide (, 25-mer) probes are being developed for many species, and are being applied to quantify transcript abundance variation in species with high genetic diversity. To define the parameters necessary to design short oligo arrays for maize (Zea mays L.), a species with particularly high nucleotide (single nucleotide polymorphism, SNP) and insertion-deletion (indel) polymorphism frequencies, we analysed gene expression estimates generated for four maize inbred lines using a custom Affymetrix DNA array, and identified biases associated with high levels of polymorphism between lines. Statistically significant interactions between probes and maize inbreds were detected, affecting five or more probes (out of 30 probes per transcript) in the majority of cases. SNPs and indels were identified by re-sequencing; they are the primary source of probe-by-line interactions, affecting probeset level estimates and reducing the power of detecting transcript level variation between maize inbreds. This analysis identified 36 196 probes in 5118 probesets containing markers that may be used for genotyping in natural and segregating populations for association gene analysis and genetic mapping. [source] ORIGINAL ARTICLE: Genetic Predisposition to Idiopathic Recurrent Spontaneous Abortion: Contribution of Genetic Variations in IGF-2 and H19 Imprinted GenesAMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY, Issue 2 2008a Ostoji Problem, Recurrent spontaneous abortion (RSA) is a common clinical problem with a complex etiology of genetic and non-genetic causes, which remains to be fully determined. IGF-2 stimulates trophoblast invasion, proliferation and maturation of placenta, while H19 RNA suppresses growth. As genomic imprinting plays a critical role in the development of placenta and embryo, our aim was to evaluate the possible role of variations in IGF-2 and H19 imprinted genes as factors of predisposition for RSA. Method of study, A case,control study was conducted to determine the association between IGF-2 and H19 gene polymorphisms and the susceptibility to RSA in 113 couples with RSA and 226 controls. PCR/RFLP were performed to analyze IGF-2 ApaI and H19 HhaI polymorphisms. Results, We found a statistically significant difference in the genotype frequency distribution of IGF-2 ApaI polymorphism between males from couples with RSA and healthy males (,2(2) = 45.12; P < 0.0001). There were no differences in the genotype and allele distribution of H19 polymorphism frequencies, or for the IGF-2 ApaI polymorphism between female groups. Conclusion, The presence of IGF-2 ApaI polymorphism in partners of RSA women could affect IGF-2 level of expression in placenta and embryo and represent a risk factor for RSA susceptibility. [source] Parkin gene variations in late-onset Parkinson's disease: comparison between Norwegian and German cohortsACTA NEUROLOGICA SCANDINAVICA, Issue 1 2006A. M. Schlitter Objectives ,, Mutations in the Parkin gene can cause autosomal recessive early-onset Parkinson's disease (PD). Recently, Parkin mutations were also suggested to play a role in the commoner late-onset forms of PD. Methods ,, We compared a German cohort of PD patients (95) with a Norwegian cohort of PD patients (96). Both cohorts have predominant late-onset form of PD. Mutation and polymorphism frequencies were compared via single-strand conformation polymorphism and sequence analyses. Results ,, Three heterozygous missense mutations (Arg256Cys, Arg402Cys and Thr240Met) were found in late-onset PD patients in the German patient cohort (1.6%). A missense mutation (Arg402Cys) was also found in one of 149 healthy control subjects (0.3%). Only one heterozygous missense mutation (Arg256Cys) was identified in a Norwegian patient suffering from late-onset PD (0.5%). The frequencies of four known single nucleotide polymorphisms significantly differ between the two distant European populations. Conclusion ,, The results support the hypothesis that heterozygous mutations in the Parkin gene may act as susceptibility alleles for late-onset forms of PD in rare cases. [source] Urokinase gene 3,-UTR T/C polymorphism is associated with oral cancerJOURNAL OF CLINICAL LABORATORY ANALYSIS, Issue 5 2004Ming-Hsui Tsai Abstract Urokinase is thought to be involved in the formation of oral cancer, although there is a lack of genetic evidence. Our aim was to study single nucleotide polymorphisms in order to investigate the possibility. A total of 130 oral cancer patients and 105 controls were studied. Polymerase chain reaction (PCR) based restriction analysis was used to identify the C/T polymorphism of the urokinase gene, which is located on the 3,-untranslated region (3,-UTR) of chromosome 10. There was a significant difference in the distribution of the urokinase gene 3,-UTR C/T polymorphism frequency between cancer patients and the normal control group (P<0.05). The "T" allele was prominent in the cancer group. The odds ratio for the risk of the "T" allele in cancer patients was 2.71 (95% CI=1.325,5.562). The cancer patients were further categorized according to gender and whether or not they were habitual smokers or betel nut chewers. These clinical parameters were then compared with tumor cell differentiation and tumor progression. No significant differences were found. Therefore, the urokinase gene 3,-UTR "T" allele is associated with oral cancer and may play a role in oral cancer formation. However, we did not find the relationship between tumor progression and this polymorphism. J. Clin. Lab. Anal. 18:276,279, 2004. © 2004 Wiley-Liss, Inc. [source] Angiotensin-converting enzyme gene insertion/deletion polymorphism frequency in normotensive children with a positive family history of essential hypertensionJOURNAL OF PAEDIATRICS AND CHILD HEALTH, Issue 12 2009Lale Camci Aim: To evaluate the possible relationship between blood pressure (BP) and angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism in normotensive children with a positive family history of essential hypertension (EHT). Material and Methods: Three hundred seventy-six randomly selected normotensive schoolchildren (147 boys, 229 girls) between the ages of seven and 17 years were enrolled. Children were subdivided into a ,first-degree relative group' and a ,second-degree relative group' according to the presence of EHT in parents or grandparents, respectively. BP was measured twice from the right arm and the systolic BP, diastolic BP and mean BP were recorded. ACE gene I/D polymorphism was performed from all studied children and frequency od DD, ID and ID allele were analysed in each study group. Results: Allelic frequencies of the DD genotype of the ACE gene were higher in children with a positive history in the first- (36.2%) and second-degree (38.3%) relatives for EHT than the controls (30.7%) (P < 0.05 for both). Children with a positive family history of EHT and a DD genotype, had significantly higher SBP, DBP and MBP levels (P < 0.05) than the children with ID or II genotypes. Conclusion: We found that the ACE gene DD genotype was common and that BP levels were higher in Turkish children with a positive family history of EHT and DD genotype. Because the presence of DD allele might be the one of the potential contributor of EHT pathogenesis, further studies needed in large cohort for long term follow-up for EHT in children with DD allele. [source] p.Q223R leptin receptor polymorphism associated with obesity in Brazilian multiethnic subjectsAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 4 2006Stenio Fernando Pimentel Duarte Several genes play a major role in obese phenotypes, and studies suggest that genetic variations among individuals, as well as their lifestyles, may bring about different body compositions. Among these genes, LEP, which codifies leptin, and the LEPR gene encoding its receptor were extensively studied for variants that could explain the obese phenotype. The LEPR p.Q223R gene polymorphism was analyzed in a sample of obese and nonobese individuals from Brazil to evaluate the role of this polymorphism in the obese phenotype in the population. Two hundred obese patients (60 males, 140 females, body mass index (BMI) >30 kg/m2) were screened, together with 150 lean or normal healthy individuals (63 males, 87 females, BMI <24 kg/m2). Genomic DNA was extracted and amplified by polymerase chain reaction (PCR). PCR products were digested with the restriction of endonuclease MspI, and separated by electrophoresis through an 8% polyacrilamide gel stained with silver nitrate. There was a significant difference in LEPR p.Q223R polymorphism frequency when comparing obese and lean subjects, with an odds ratio of 1.92 and a 95% confidence interval of 1.15,3.22 (P = 0.013). There is a strong association of the LEPR p.Q223R gene polymorphism with obesity in Brazil. Am. J. Hum. Biol. 18:448,453, 2006. © 2006 Wiley-Liss, Inc. [source] | |||||||||||||