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Allele-specific Polymerase Chain Reaction (allele-specific + polymerase_chain_reaction)
Selected AbstractsThe analysis of JAK2 and MPL mutations and JAK2 single nucleotide polymorphisms in MPN patients by MassARRAY assayINTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY, Issue 4 2010S.-J. ZHANG Summary Recent studies have shown that JAK2 V617F, MPL W515L/K and JAK2 exon 12 mutations underlie the major molecular pathogenesis of myeloproliferative disorders (MPN). Allele-Specific Polymerase Chain Reaction (AS-PCR), direct sequencing and MassARRAY assay were used to ascertain the real prevalence of these mutations and the influence of genetic susceptibility in Chinese MPN patients. The positive rate of JAK2 V617F in polycythaemia vera (PV), essential thrombocythaemia (ET) and primary myelofibrosis (PMF) was 82.0%, 36.6% and 51.1% respectively. One ET patient and two PMF patients harboured the MPL W515L mutation and three PV patients harboured JAK2 exon 12 mutations. All of these patients were confirmed as JAK2 V617F negative. Clinical data demonstrated that PV patients with JAK2 exon 12 mutations were younger, had higher haemoglobin levels and white blood cell counts than PV patients with JAK2 V617F. In addition, through analysis of 4 polymorphic loci of JAK2 gene, no significant difference of distribution frequency was found among PV, ET and PMF patients. Distribution frequency of haplotype also was not significantly different among PV, ET and PMF patients. We conclude that JAK2 V617F is a major molecular pathogenesis in Chinese MPN patients. MPL W515L mutation and JAK2 exon 12 mutations can also be found in JAK2 V617F negative MPN patients. [source] A study of a single variant allele (rs1426654) of the pigmentation-related gene SLC24A5 in Greek subjectsEXPERIMENTAL DERMATOLOGY, Issue 2 2009Gerasimos Dimisianos Abstract:, The SLC24A5 gene, the human orthologue of the zebrafish golden gene, has been shown to play a key role in human pigmentation. In this study, we investigate the prevalence of the variant allele rs1426654 in a selected sample of Greek subjects. Allele-specific polymerase chain reaction was performed in peripheral blood samples from 158 attendants of a dermatology outpatient service. The results were correlated with pigmentary traits and MC1R genotype. The vast majority of subjects (99%) were homozygous for the Thr111 allele. Only two subjects from the control group (1.26%) were heterozygous for the alanine and threonine allele. Both of these Thr111/Ala111 heterozygotes carried a single polymorphism of MC1R (one with the V92M variant and another with the V60L variant). Following reports of the rs1426654 polymorphism reaching fixation in the European population, our study of Greek subjects showed a prevalence of the Thr111 allele, even among subjects with darker skin pigmentation or phototype. [source] Thiopurine S -methyltransferase (TPMT) genetic polymorphisms in Mexican newbornsJOURNAL OF CLINICAL PHARMACY & THERAPEUTICS, Issue 6 2009A. González-del Angel MD Abstract Background:, Thiopurine S -methyltransferase (TPMT) is involved in the toxicity and therapeutic efficacy of thiopurine drugs, and its gene exhibits genetic polymorphisms that differ across diverse populations. Four TPMT polymorphisms (TPMT*2, *3A, *3B and *3C) account for 80,95% of alleles that cause reduced enzyme activity. To date, only a single study in the Mexican population involving 108 individuals has been performed, but the regional and ethnic origin of this population was not described. Accordingly, information about the TPMT polymorphism in the Mexican population is limited. Objective:, To determine the TPMT allele and genotype frequencies in a sample of newborns from Mexico City. Methods:, Three hundred and sixty DNA samples from unrelated, anonymous individuals were obtained from dried blood spots collected on filter paper as part of the Newborn Screening National Program. Allele-specific polymerase chain reaction for the TPMT*2 allele and PCR restriction fragment length polymorphism for TPMT*3A, TPMT*3B, TPMT*3C alleles were used to determine the respective allelic and genotypic frequencies. Results and Discussion:, Of 720 TPMT alleles analysed, 49 (6·81%) were deficiency alleles. The most common deficiency allele was TPMT*3A (5·69%), followed by TPMT*3C (0·56%), TPMT*3B (0·28%) and TPMT*2 (0·28%). Fourty-five newborns were heterozygous for one mutant allele (12·5%) and two showed a genotype with two deficiency alleles (0·56%). Despite its unique ethnic composition, our Mexican population exhibited variant allele frequencies that were similar to some Caucasian populations. Conclusion:, Our data suggest that approximately 1 in 180 persons born in Mexico City might have low or undetectable TPMT enzyme activity, a frequency that, overall, is somewhat higher than that reported for Caucasian populations generally (1 in 300). [source] HLA-B27 typing: Evaluation of an allele-specific PCR melting assay and two flow cytometric antigen assaysCYTOMETRY, Issue 1 2005Michael T. Seipp Abstract Background Human leukocyte antigen B27 (HLA-B27) is a major histocompatibility complex class 1 molecule that is strongly associated with the disease ankylosing spondylitis. Testing for HLA-B27 is of diagnostic value because 90% of patients with ankylosing spondylitis have the B27 antigen. Two commonly used HLA-B27 flow cytometric assays are commercially available. Methods An allele-specific polymerase chain reaction (PCR) melting assay for HLA-B27 was compared with two available antigen assays on 371 clinical samples. The accuracy of the assays was measured by receiver operating characteristic analysis using the PCR method and sequencing as the reference standard. Results When PCR results were compared with those of the antigen assays, complete concordance was observed except for five discrepant results that were resolved by sequence analysis. Using DNA sequencing as the gold standard, the sensitivity and specificity of PCR were 99.6 and 100.0, those of the best single antigen assay were 98.2 and 97.6, and those of a reflex combination of both antigen assays were 98.8 and 97.6. Conclusions The allele-specific PCR melting assay for HLA-B27 genotyping is easy to perform and has better sensitivity and specificity than antigen assays. The performance of the two flow cytometric antigen assays depends on the antibody used and the positive cutoff values assigned. © 2004 Wiley-Liss, Inc. [source] Promoter polymorphism of IL-18 gene in pulmonary tuberculosis in South Indian populationINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 5 2007M. Harishankar Summary Interleukin-18 (IL-18) plays a vital role in both innate and acquired immunity. We analysed polymorphisms at ,607(C/A) and ,137(G/A) in the promoter region of IL-18 gene by allele-specific polymerase chain reaction in normal healthy subjects (n = 173) and patients with pulmonary tuberculosis (n = 165). Allele, genotype and haplotype frequencies did not differ significantly between normal healthy subjects and patients. The results suggest that the IL-18 gene promoter polymorphisms are not associated with susceptibility or resistance to pulmonary tuberculosis in south Indian population of Dravidian descent. [source] Parkinson's disease due to the R1441G mutation in Dardarin: A founder effect in the basquesMOVEMENT DISORDERS, Issue 11 2006Javier Simón-Sánchez BSc Abstract The recent discovery of mutations in Dardarin (LRRK2) have been related to the appearance of Parkinson's disease in several families. Notably, one single mutation in this gene (R1441G) not only appeared in familial, but also in apparently sporadic Parkinson disease (PD) patients of Basque descent. A clinical population was ascertained, and subjects were classified into Basque and non-Basque descent according to their known ancestry. The R1441G mutation was assayed using an allele-specific polymerase chain reaction, and several single nucleotide polymorphisms surrounding this mutation were analyzed by direct sequencing. In addition to 22 members of the original Basque families where R1441G was identified, we observed 17 carriers of the mutation who were apparently related through a common ancestor. From a clinical perspective, the disease observed in mutation carriers is indistinguishable from that in noncarriers. The R1441G mutation causes a form of Parkinson's disease that is equivalent to that observed in idiopathic Parkinson's disease. This mutation appears in 16.4% and 4.0% of familial and sporadic PD in this Basque population, respectively. © 2006 Movement Disorder Society [source] Association of the IL4R single-nucleotide polymorphism I50V with rapidly erosive rheumatoid arthritisARTHRITIS & RHEUMATISM, Issue 5 2006Iryna Prots Objective To examine whether single-nucleotide polymorphisms (SNPs) of the interleukin-4 receptor gene IL4R influence susceptibility to, or radiographic progression in, rheumatoid arthritis (RA). Methods The contribution of 2 SNPs (I50V and Q551R) in the coding region of IL4R to RA susceptibility was analyzed by allele-specific polymerase chain reaction in a case,control study of 471 RA patients and 371 healthy controls. Patients with available radiographs of the hands and feet obtained 2 years after disease onset (n = 302) were stratified retrospectively according to radiologic outcome into an erosive and a nonerosive group to evaluate the association between IL4R SNPs and disease progression. Results No differences in the genotype and allele frequencies of the I50V or Q551R SNPs were identified between the RA patients and healthy controls. In contrast, significant differences in the distribution of I50V IL4R SNP genotypes between patients with erosive and nonerosive disease were observed (,2 = 15.68, P = 0.0004). Bone erosions at 2 years after disease onset were present in 68.1% of patients homozygous for the V50 allele compared with 37.0% of patients homozygous for the I50 allele (odds ratio 3.86, P < 0.0001). This association was independent of individual factors previously associated with severe disease, such as rheumatoid factor or the HLA,DR shared epitope. On a cellular level, the V50 allele conferred significantly reduced responsiveness to interleukin-4, providing a possible mechanism for the association of the I50V IL4R polymorphism with early erosions in RA. Conclusion Our data identify the I50V IL4R SNP as a novel genetic marker in RA, showing high predictive value for early joint destruction. [source] No allelic association between harm avoidance and the debrisoquine 4-hydroxylase geneACTA NEUROPSYCHIATRICA, Issue 5 2002Adriaan H Veefkind Background: Several reports suggest that variance in personality traits is inherited, but little is known about the genes responsible. It has been suggested that there is a relationship between personality characteristics and the gene responsible for the activity of the enzyme debrisoquine 4-hydroxylase (CYP2D6). Objective: To examine the proportion of poor metabolizers in a group of personality disordered patients. Methods: Blood samples were obtained from 23 patients with a high or very high score on the dimension ,harm avoidance' of the Temperament and Character Inventory (TCI). The samples were genotyped for the null alleles CYP2D6*3 and*4 by performing an allele-specific polymerase chain reaction. Results: The frequencies of genotypes in the sample were very similar to the frequencies found in a general white population. Conclusions: The investigation produced no support for the idea that the CYP2D6 gene is related to personality by means of variations in the temperament dimension of harm avoidance. [source] | ||||||||||