Search results for " Polymorphism."
showing 10 items of 1006 documents
Rapid microarray-based typing of forensic SNPs
2006
The single base extension-tag array (SBE-Tag Array) method is carried out on glass slides and combines the specificity of minisequencing for SNP typing with the high throughput capacity of microarrays. Following multiplex PCR, a single tube SBE reaction is carried out, and the fluorescent labelled extension products are hybridized to the complementary DNA sequence tag (cTag) immobilized on a glass slide for locus-specific laser scan analysis. The aim is to prove and optimise the conventional microarray reaction on accuracy and efficiency for forensic applications. © 2005 Elsevier B.V. All rights reserved.
Analyzing Illumina Gene Expression Microarray Data from Different Tissues: Methodological Aspects of Data Analysis in the MetaXpress Consortium
2012
Microarray profiling of gene expression is widely applied in molecular biology and functional genomics. Experimental and technical variations make meta-analysis of different studies challenging. In a total of 3358 samples, all from German population-based cohorts, we investigated the effect of data preprocessing and the variability due to sample processing in whole blood cell and blood monocyte gene expression data, measured on the Illumina HumanHT-12 v3 BeadChip array. Gene expression signal intensities were similar after applying the log(2) or the variance-stabilizing transformation. In all cohorts, the first principal component (PC) explained more than 95% of the total variation. Technic…
Mutations in the rpoB and katG Genes Leading to Drug Resistance in Mycobacterium tuberculosis in Latvia
2002
ABSTRACT To characterize the genetic basis of drug resistance in Mycobacterium tuberculosis in Latvia, mutations involved in rifampin ( rpoB gene) and isoniazid ( katG gene) resistance in DNA from 19 drug-susceptible and 51 multidrug-resistant M. tuberculosis complex isolates were analyzed. The most frequent rpoB gene mutations found by the Line Probe assay were the S531L (14 of 34 isolates), D516V (7 of 34), H526D (4 of 34), and D516Y plus P535S (4 of 34) mutations. Direct sequencing of seven isolates with unclear results from Line Probe assay showed the presence of the L533P mutation and the Q510H plus H526Y (1 of 34) and D516V plus P535S (4 of 34) double mutations, neither of which has b…
Genomic Changes of Chagas Disease Vector, South America
2004
We analyzed the main karyologic changes that have occurred during the dispersion of Triatoma infestans, the main vector of Chagas disease. We identified two allopatric groups, named Andean and non-Andean. The Andean specimens present C-heterochromatic blocks in most of their 22 chromosomes, whereas non-Andean specimens have only 4-7 autosomes with C-banding. These heterochromatin differences are the likely cause of a striking DNA content variation (approximately 30%) between Andean and non-Andean insects. Our study, together with previous historical and genetic data, suggests that T. infestans was originally a sylvatic species, with large quantities of DNA and heterochromatin, inhabiting th…
Epidemiological investigations and molecular characterization of ‘candidatus phytoplasma solani’ in grapevines, weeds, vectors and putative vectors i…
2020
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Comparative evaluation of three different genotyping methods for investigation of nosocomial outbreaks of Legionnaires' disease in hospitals.
2000
ABSTRACT The increased incidence of nosocomial Legionnaires' disease in two hospitals prompted investigation of possible environmental sources. In the search for an effective DNA-typing technique for use in hospital epidemiology, the performance and convenience of three methods— Sfi I macrorestriction analysis (MRA), amplified fragment length polymorphism (AFLP), and arbitrarily primed PCR (AP-PCR)—were compared. Twenty-nine outbreak-associated and eight nonassociated strains of Legionella pneumophila with 13 MRA types and subtypes were investigated. These strains comprised isolates from bronchoalveolar lavages, from environmental, patient-related sources, and type strains. All three typing…
Helicobacter pylori: clonal population structure and restricted transmission within families revealed by molecular typing.
2000
ABSTRACT Helicobacter pylori infects up to 50% of the human population worldwide. The infection occurs predominantly in childhood and persists for decades or a lifetime. H. pylori is believed to be transmitted from person to person. However, tremendous genetic diversity has been reported for these bacteria. In order to gain insight into the epidemiological basis of this phenomenon, we performed molecular typing of H. pylori isolates from different families. Fifty-nine H. pylori isolates from 27 members of nine families were characterized by using restriction fragment length polymorphism analysis of five PCR-amplified genes, by pulsed-field gel electrophoresis (PFGE) of chromosomal DNA, and …
Polymorphisms within the TNFSF4 and mapkapk2 loci influence the risk of developing invasive aspergillosis: A two-stage case control study in the cont…
2020
Here, we assessed whether 36 single nucleotide polymorphisms (SNPs) within the TNFSF4 and MAPKAPK2 loci influence the risk of developing invasive aspergillosis (IA). We conducted a twostage case control study including 911 high-risk patients diagnosed with hematological malignancies that were ascertained through the aspBIOmics consortium. The meta-analysis of the discovery and replication populations revealed that carriers of the TNFSF4rs7526628T/T genotype had a significantly increased risk of developing IA (p = 0.00022). We also found that carriers of the TNFSF4rs7526628T allele showed decreased serum levels of TNFSF14 protein (p = 0.0027), and that their macrophages had a decreased fungi…
Identifying four Trypanosoma cruzi I isolate haplotypes from different geographic regions in Colombia
2007
Abstract Trypanosoma cruzi has been classified into the groups T. cruzi I and T. cruzi II. The latter is subdivided into five smaller lineages based on multilocus enzyme electrophoresis and random amplified polymorphic DNA, designated as IIa-IIe, which shows correspondence with rRNA/mini-exon lineages. Twelve previously characterised T. cruzi isolates from different hosts, including humans, Didelphis marsupialis, and triatomines were analysed to establish genetic variability in T. cruzi group T. cruzi I isolates from different geographical regions of Colombia. DNA samples were sequenced based on the mini-exon gene intergenic region. Sequences were analysed using Clustal W, Staden 1.5 and ME…
Whole-genome sequencing of Mycobacterium tuberculosis directly from clinical samples for high-resolution genomic epidemiology and drug resistance sur…
2020
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