The Experts below are selected from a list of 131856 Experts worldwide ranked by ideXlab platform
Kåre Bondeson - One of the best experts on this subject based on the ideXlab platform.
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2008. Simultaneous detection of Chlamydophila pneumoniae and Mycoplasma pneumoniae by use of molecular beacons in a duplex real-time
2016Co-Authors: Karolina Gullsby, Martin Storm, Kåre BondesonAbstract:A real-time PCR was designed for detection of Chlamydophila pneumoniae and Mycoplasma pneumoniae such that each pathogen could be detected in a single tube and differentiated using molecular beacons marked with different fluorochromes. This duplex PCR, targeting the P1 adhesion gene for M. pneumoniae and the ompA gene for C. pneumoniae, was compared with two conventional PCR assays targeting the 16S rRNA gene and the ompA gene. A total of 120 clinical throat and nasopharyngeal swab samples were tested. DNA extraction was performed using an alkali denaturation/neutralization method, and real-time amplification, detection, and data analysis were performed using a Rotor-Gene 2000 real-time rotary analyzer (Corbett Life Science, Sydney, Australia). Using conventional PCR as a Reference in an analysis of 120 samples, 13 of 14 samples positive for C. pneumoniae were detected by the novel real-time PCR. In an analysis of M. pneumoniae, 22 samples were positive in the conventional PCR and the novel assay detected 24 positive samples. When using the conven-tional PCR as a Reference, Sensitivity and specificity were 93 % and 100%, respectively, for C. pneumoniae and 100 % and 98%, respectively, for M. pneumoniae. With an overall agreement of 98.8%, this suggests that performance of the new duplex real-time PCR is comparable to that of conventional PCR. Chlamydophila pneumoniae and Mycoplasma pneumoniae are important and common causes of community-acquired pneumonia, where these pathogens are the etiological agent i
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simultaneous detection of chlamydophila pneumoniae and mycoplasma pneumoniae by use of molecular beacons in a duplex real time pcr
Journal of Clinical Microbiology, 2008Co-Authors: Karolina Gullsby, Martin Storm, Kåre BondesonAbstract:A real-time PCR was designed for detection of Chlamydophila pneumoniae and Mycoplasma pneumoniae such that each pathogen could be detected in a single tube and differentiated using molecular beacons marked with different fluorochromes. This duplex PCR, targeting the P1 adhesion gene for M. pneumoniae and the ompA gene for C. pneumoniae, was compared with two conventional PCR assays targeting the 16S rRNA gene and the ompA gene. A total of 120 clinical throat and nasopharyngeal swab samples were tested. DNA extraction was performed using an alkali denaturation/neutralization method, and real-time amplification, detection, and data analysis were performed using a Rotor-Gene 2000 real-time rotary analyzer (Corbett Life Science, Sydney, Australia). Using conventional PCR as a Reference in an analysis of 120 samples, 13 of 14 samples positive for C. pneumoniae were detected by the novel real-time PCR. In an analysis of M. pneumoniae, 22 samples were positive in the conventional PCR and the novel assay detected 24 positive samples. When using the conventional PCR as a Reference, Sensitivity and specificity were 93% and 100%, respectively, for C. pneumoniae and 100% and 98%, respectively, for M. pneumoniae. With an overall agreement of 98.8%, this suggests that performance of the new duplex real-time PCR is comparable to that of conventional PCR.
Hubert Pausch - One of the best experts on this subject based on the ideXlab platform.
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Accurate sequence variant genotyping in cattle using variation-aware genome graphs
Genetics Selection Evolution, 2019Co-Authors: Danang Crysnanto, Christine Wurmser, Hubert PauschAbstract:AbstractBackgroundGenotyping of sequence variants typically involves, as a first step, the alignment of sequencing reads to a linear Reference genome. Because a linear Reference genome represents only a small fraction of all the DNA sequence variation within a species, Reference allele bias may occur at highly polymorphic or divergent regions of the genome. Graph-based methods facilitate the comparison of sequencing reads to a variation-aware genome graph, which incorporates a collection of non-redundant DNA sequences that segregate within a species. We compared the accuracy and Sensitivity of graph-based sequence variant genotyping using the Graphtyper software to two widely-used methods, i.e., GATK and SAMtools, which rely on linear Reference genomes using whole-genome sequencing data from 49 Original Braunvieh cattle.ResultsWe discovered 21,140,196, 20,262,913, and 20,668,459 polymorphic sites using GATK, Graphtyper, and SAMtools, respectively. Comparisons between sequence variant genotypes and microarray-derived genotypes showed that Graphtyper outperformed both GATK and SAMtools in terms of genotype concordance, non-Reference Sensitivity, and non-Reference discrepancy. The sequence variant genotypes that were obtained using Graphtyper had the smallest number of Mendelian inconsistencies between sequence-derived single nucleotide polymorphisms and indels in nine sire-son pairs. Genotype phasing and imputation using the Beagle software improved the quality of the sequence variant genotypes for all the tools evaluated, particularly for animals that were sequenced at low coverage. Following imputation, the concordance between sequence- and microarray-derived genotypes was almost identical for the three methods evaluated, i.e., 99.32, 99.46, and 99.24% for GATK, Graphtyper, and SAMtools, respectively. Variant filtration based on commonly used criteria improved genotype concordance slightly but it also decreased Sensitivity. Graphtyper required considerably more computing resources than SAMtools but less than GATK.ConclusionsSequence variant genotyping using Graphtyper is accurate, sensitive and computationally feasible in cattle. Graph-based methods enable sequence variant genotyping from variation-aware Reference genomes that may incorporate cohort-specific sequence variants, which is not possible with the current implementation of state-of-the-art methods that rely on linear Reference genomes.
Stefan Acosta - One of the best experts on this subject based on the ideXlab platform.
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validation of computed tomography angiography using mean arterial pressure gradient as a Reference in stented superior mesenteric artery
Abdominal Radiology, 2020Co-Authors: Niklas Lundin, Leena Lehti, Olle Ekberg, Stefan AcostaAbstract:The aim of this prospective study was to validate the diagnostic performance of computed tomography angiography (CTA) in endoprosthesis stenosis in the superior mesenteric artery (SMA) using mean arterial pressure (MAP) gradients during angiography as a Reference method. Twenty-nine patients with mesenteric atherosclerotic disease underwent 45 paired measurements of endoprosthesis stenosis in the SMA with CTA and MAP gradients between March 2009 and July 2015. The grade of endoprosthesis stenosis in the SMA at CTA using the TeraRecon Aquarius workstation was correlated with MAP gradients. Grade of endoprosthesis stenosis in the SMA (r = 0.37, p = 0.013) correlated with MAP gradients. The intraclass correlations between the first and second CTA rater was 0.76 (95% CI 0.56–0.87) for estimation of grade of endoprosthesis stenosis in the SMA. The area under the receiver operating characteristics curve was 0.79 for diagnosis of significant endoprosthesis stenosis in the SMA at CTA for different threshold values using MAP gradient of ≥ 10 mmHg as Reference. Sensitivity, specificity and positive predictive value for endoprosthesis stenosis in the SMA ≥ 50% at CTA were 52.4% (95% CI 31.0–73.7), 87.5% (95% CI 74.3–100.0) and 78.6 (95% CI 57.1–1.00), respectively. Grading endoprosthesis stenosis in the SMA with CTA performed fair when using trans-stenotic MAP gradient as Reference. Software development towards reduction of endoprosthesis artefacts may result in more accurate CTA assessment of the narrowest part.
Karolina Gullsby - One of the best experts on this subject based on the ideXlab platform.
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2008. Simultaneous detection of Chlamydophila pneumoniae and Mycoplasma pneumoniae by use of molecular beacons in a duplex real-time
2016Co-Authors: Karolina Gullsby, Martin Storm, Kåre BondesonAbstract:A real-time PCR was designed for detection of Chlamydophila pneumoniae and Mycoplasma pneumoniae such that each pathogen could be detected in a single tube and differentiated using molecular beacons marked with different fluorochromes. This duplex PCR, targeting the P1 adhesion gene for M. pneumoniae and the ompA gene for C. pneumoniae, was compared with two conventional PCR assays targeting the 16S rRNA gene and the ompA gene. A total of 120 clinical throat and nasopharyngeal swab samples were tested. DNA extraction was performed using an alkali denaturation/neutralization method, and real-time amplification, detection, and data analysis were performed using a Rotor-Gene 2000 real-time rotary analyzer (Corbett Life Science, Sydney, Australia). Using conventional PCR as a Reference in an analysis of 120 samples, 13 of 14 samples positive for C. pneumoniae were detected by the novel real-time PCR. In an analysis of M. pneumoniae, 22 samples were positive in the conventional PCR and the novel assay detected 24 positive samples. When using the conven-tional PCR as a Reference, Sensitivity and specificity were 93 % and 100%, respectively, for C. pneumoniae and 100 % and 98%, respectively, for M. pneumoniae. With an overall agreement of 98.8%, this suggests that performance of the new duplex real-time PCR is comparable to that of conventional PCR. Chlamydophila pneumoniae and Mycoplasma pneumoniae are important and common causes of community-acquired pneumonia, where these pathogens are the etiological agent i
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simultaneous detection of chlamydophila pneumoniae and mycoplasma pneumoniae by use of molecular beacons in a duplex real time pcr
Journal of Clinical Microbiology, 2008Co-Authors: Karolina Gullsby, Martin Storm, Kåre BondesonAbstract:A real-time PCR was designed for detection of Chlamydophila pneumoniae and Mycoplasma pneumoniae such that each pathogen could be detected in a single tube and differentiated using molecular beacons marked with different fluorochromes. This duplex PCR, targeting the P1 adhesion gene for M. pneumoniae and the ompA gene for C. pneumoniae, was compared with two conventional PCR assays targeting the 16S rRNA gene and the ompA gene. A total of 120 clinical throat and nasopharyngeal swab samples were tested. DNA extraction was performed using an alkali denaturation/neutralization method, and real-time amplification, detection, and data analysis were performed using a Rotor-Gene 2000 real-time rotary analyzer (Corbett Life Science, Sydney, Australia). Using conventional PCR as a Reference in an analysis of 120 samples, 13 of 14 samples positive for C. pneumoniae were detected by the novel real-time PCR. In an analysis of M. pneumoniae, 22 samples were positive in the conventional PCR and the novel assay detected 24 positive samples. When using the conventional PCR as a Reference, Sensitivity and specificity were 93% and 100%, respectively, for C. pneumoniae and 100% and 98%, respectively, for M. pneumoniae. With an overall agreement of 98.8%, this suggests that performance of the new duplex real-time PCR is comparable to that of conventional PCR.
Danang Crysnanto - One of the best experts on this subject based on the ideXlab platform.
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Accurate sequence variant genotyping in cattle using variation-aware genome graphs
Genetics Selection Evolution, 2019Co-Authors: Danang Crysnanto, Christine Wurmser, Hubert PauschAbstract:AbstractBackgroundGenotyping of sequence variants typically involves, as a first step, the alignment of sequencing reads to a linear Reference genome. Because a linear Reference genome represents only a small fraction of all the DNA sequence variation within a species, Reference allele bias may occur at highly polymorphic or divergent regions of the genome. Graph-based methods facilitate the comparison of sequencing reads to a variation-aware genome graph, which incorporates a collection of non-redundant DNA sequences that segregate within a species. We compared the accuracy and Sensitivity of graph-based sequence variant genotyping using the Graphtyper software to two widely-used methods, i.e., GATK and SAMtools, which rely on linear Reference genomes using whole-genome sequencing data from 49 Original Braunvieh cattle.ResultsWe discovered 21,140,196, 20,262,913, and 20,668,459 polymorphic sites using GATK, Graphtyper, and SAMtools, respectively. Comparisons between sequence variant genotypes and microarray-derived genotypes showed that Graphtyper outperformed both GATK and SAMtools in terms of genotype concordance, non-Reference Sensitivity, and non-Reference discrepancy. The sequence variant genotypes that were obtained using Graphtyper had the smallest number of Mendelian inconsistencies between sequence-derived single nucleotide polymorphisms and indels in nine sire-son pairs. Genotype phasing and imputation using the Beagle software improved the quality of the sequence variant genotypes for all the tools evaluated, particularly for animals that were sequenced at low coverage. Following imputation, the concordance between sequence- and microarray-derived genotypes was almost identical for the three methods evaluated, i.e., 99.32, 99.46, and 99.24% for GATK, Graphtyper, and SAMtools, respectively. Variant filtration based on commonly used criteria improved genotype concordance slightly but it also decreased Sensitivity. Graphtyper required considerably more computing resources than SAMtools but less than GATK.ConclusionsSequence variant genotyping using Graphtyper is accurate, sensitive and computationally feasible in cattle. Graph-based methods enable sequence variant genotyping from variation-aware Reference genomes that may incorporate cohort-specific sequence variants, which is not possible with the current implementation of state-of-the-art methods that rely on linear Reference genomes.