Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Sequencing quality”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 541 records · Page 30Linked to original sources
PubMed2006

Dynamic pulmonary perfusion and flow quantification with MR imaging, 3.0T vs. 1.5T: initial results.

PURPOSE: To prospectively evaluate the technical feasibility and relative performance of pulmonary time-resolved MR angiography (MRA) and pulmonary artery (PA) flow quantification at 3.0T vs. 1.5T. MATERIALS AND METHODS: Time-resolved contrast-enhanced (CE) MRA of the pulmonary circulation, and flow quantification of the main PA (MPA) were performed in 14 consecutive adult healthy volunteers at both 1.5 and 3.0 Tesla with nearly identical sequence parameters. Image quality, signal-to-noise ratio (SNR), and quantitative indices of pulmonary perfusion, flow, and velocity were evaluated and compared at both field strengths. RESULTS: Time-resolved pulmonary MRA, perfusion, and flow quantification were successfully performed at both magnetic fields. The results of pulmonary perfusion and flow indices were comparable at both magnetic fields, with no statistically significant difference. The SNR values for vascular structures were higher at 3.0T vs. 1.5T (P = 0.001). The SNR values and the definition scores for parenchymal enhancement were significantly lower (P = 0.008 and 0.001, respectively) at 3.0T. CONCLUSION: Time-resolved pulmonary MRA, perfusion, and flow quantification at 3.0T was feasible, with comparable results to 1.5T. The lower parenchymal enhancement at 3.0T is believed to reflect increased susceptibility effects at higher magnetic fields. Further work is needed to fully exploit the potential of pulmonary perfusion imaging at 3.0T and to address the current limitations.

Adult↗
PubMed2006

Imaging living mice using a 1-T compact MRI system.

PURPOSE: To determine the feasibility of imaging living mice with a 1-T compact MRI system and investigate appropriate imaging techniques for use in routine animal experiments. MATERIALS AND METHODS: An MRI system consisting of a 1-T permanent magnet and compact console was used. Images of the entire trunks of living mice were obtained on the system using a T1-weighted three-dimensional fast low-angle shot (3D FLASH) sequence, and image quality was evaluated in relation to imaging techniques. RESULTS: Restraint of respiratory motion improved the image quality. Decreasing the slice thickness reduced artificial inhomogeneity in signal intensity (SI). Substantial effects of TR and FA on image quality were also demonstrated. With the determined techniques, images covering the entire trunk with a voxel size of 0.26x0.26x0.52 mm were acquired in an acquisition time of five minutes 28 seconds and a total experiment time of <20 minutes, and various organs and subcutaneous tumors were clearly visualized. CONCLUSION: The compact MRI system provides images of living mice with acceptable quality in a reasonable time. Considering its convenience, it appears to be suitable for use in routine mouse experiments.

Animals↗
PubMed1990

Switched array coils.

Switched array coils (SACs) are a useful tool in local coil imaging since they allow in a user-friendly manner one to make the best choice in the trade-off between field of view and signal-to-noise ratio. This is done by selecting the current path within a conductor array equipped with suitable switches. Since the switching can be controlled by the system, this allows changing of the coil dimensions within multislice sequences. Thus image quality can be improved due to smaller coil dimensions for a given slice and a larger area can be covered by electronically shifting this sensitive area. The principle can be applied to surface--as well as volume--coil designs.

Electronics, Medical↗
PubMed1999

Classification of Arabidopsis thaliana gene sequences: clustering of coding sequences into two groups according to codon usage improves gene prediction.

While genomic sequences are accumulating, finding the location of the genes remains a major issue that can be solved only for about a half of them by homology searches. Prediction methods are thus required, but unfortunately are not fully satisfying. Most prediction methods implicitly assume a unique model for genes. This is an oversimplification as demonstrated by the possibility to group coding sequences into several classes in Escherichia coli and other genomes. As no classification existed for Arabidopsis thaliana, we classified genes according to the statistical features of their coding sequences. A clustering algorithm using a codon usage model was developed and applied to coding sequences from A. thaliana, E. coli, and a mixture of both. By using it, Arabidopsis sequences were clustered into two classes. The CU1 and CU2 classes differed essentially by the choice of pyrimidine bases at the codon silent sites: CU2 genes often use C whereas CU1 genes prefer T. This classification discriminated the Arabidopsis genes according to their expressiveness, highly expressed genes being clustered in CU2 and genes expected to have a lower expression, such as the regulatory genes, in CU1. The algorithm separated the sequences of the Escherichia-Arabidopsis mixed data set into five classes according to the species, except for one class. This mixed class contained 89 % Arabidopsis genes from CU1 and 11 % E. coli genes, mostly horizontally transferred. Interestingly, most genes encoding organelle-targeted proteins, except the photosynthetic and photoassimilatory ones, were clustered in CU1. By tailoring the GeneMark CDS prediction algorithm to the observed coding sequence classes, its quality of prediction was greatly improved. Similar improvement can be expected with other prediction systems.

Algorithms↗
PubMed2001

HMSC: simultaneously detected heteronuclear shift correlation through multiple and single bonds.

A new 2D pulse sequence HMSC (heteronuclear multiple-bond and single-bond coupling connectivities) for the simultaneous detection of long-range and one-bond heteronuclear connectivities is proposed which allows the two types of responses to be separated and the corresponding (n)J(CH) and (1)J(CH) connectivity maps to be calculated. (n)J(CH) coherences are selectively labeled in the course of the pulse sequence, the correspondingly acquired data are separately stored, and a simple add/subtract procedure is applied to disentangle and edit (n)J(CH) and (1)J(CH) responses prior to final data processing. Unlike standard methods, which are designed to measure one single type of heteronuclear spin-spin interactions and to efficiently suppress the other, both (n)J(CH) and (1)J(CH) are measured simultaneously in a single experiment with the HMSC pulse sequence. Compared to the common strategy with two standard experiments applied one after the other, e.g., HMBC and HMQC, valuable measuring time may be saved with this single experiment approach. The efficiency of the new pulse sequence and the quality of the corresponding spectra are demonstrated using strychnine. Features such as sensitivity, lineshapes, and the suppression of (1)J(CH) residual peaks in the final (n)J(CH) subspectra are investigated and compared with the corresponding results obtained with standard methods. The attractive and unique single experiment approach, its high efficiency, and its easy experimental setup together with straightforward data processing make HMSC a valuable experimental alternative for the today's more time-consuming "two-step" practice and makes it suitable for standard routine applications.

Journal Article↗
PubMed2025

Guidelines to Analyze ChIP-Seq Data: Journey Through QC and Analysis Considerations.

ChIP-Seq is used to study DNA-protein interactions, unraveling chromatin states and gene regulatory properties of transcription factors. ChIP-Seq involves immunoprecipitation followed by sequencing using Next-Generation sequencing approaches. The ENCODE consortium provides extensive guidelines for ChIP-Seq analysis. Meanwhile, appropriate QC metrics and knowledge to interpret outcomes are essential for a good ChIP-Seq experiment. This chapter outlines the various QC metrics and analytical tools for ChIP-Seq analysis to provide a better understanding of the results.

Chromatin Immunoprecipitation Sequencing↗
PubMed1992

A reformulation of quality of life for medical science.

Current quality of life measuring tools are suited for economic decision making, not to investigate causal processes which lead to patients making evaluations of their lives. An alternative approach is presented based on research into positive versus negative life-satisfaction. Quality of life is a causal sequence of psychological states where perceived symptoms cause problems and the problems and symptoms cause evaluations, and where the causal sequence is a complex interaction between morbidity and psychological factors. Different types of medical intervention affect different stages in the causal sequence and so different types of quality of life instrument are needed for different kinds of medical research.

Adaptation, Psychological↗
PubMed2006

Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes.

The high-quality rice genome sequence is serving as a reference for comparative genome analysis in crop plants, especially cereals. However, early comparisons with bread wheat showed complex patterns of conserved synteny (gene content) and colinearity (gene order). Here, we show the presence of ancient duplicated segments in the progenitor of wheat, which were first identified in the rice genome. We also show that single-copy (SC) rice genes, those representing unique matches with wheat expressed sequence tag (EST) unigene contigs in the whole rice genome, show more than twice the proportion of genes mapping to syntenic wheat chromosome as compared to the multicopy (MC) or duplicated rice genes. While 58.7% of the 1,244 mapped SC rice genes were located in single syntenic wheat chromosome groups, the remaining 41.3% were distributed randomly to the other six non-syntenic wheat groups. This could only be explained by a background dispersal of genes in the genome through transposition or other unknown mechanism. The breakdown of rice-wheat synteny due to such transpositions was much greater near the wheat centromeres. Furthermore, the SC rice genes revealed a conserved primordial gene order that gives clues to the origin of rice and wheat chromosomes from a common ancestor through polyploidy, aneuploidy, centromeric fusions, and translocations. Apart from the bin-mapped wheat EST contigs, we also compared 56,298 predicted rice genes with 39,813 wheat EST contigs assembled from 409,765 EST sequences and identified 7,241 SC rice gene homologs of wheat. Based on the conserved colinearity of 1,063 mapped SC rice genes across the bins of individual wheat chromosomes, we predicted the wheat bin location of 6,178 unmapped SC rice gene homologs and validated the location of 213 of these in the telomeric bins of 21 wheat chromosomes with 35.4% initial success. This opens up the possibility of directed mapping of a large number of conserved SC rice gene homologs in wheat. Overall, only 46.4% of these SC genes code for proteins with known functional domains; the remaining 53.6% have unknown function, and hence, represent an important, but yet, under explored category of genes.

Gene Deletion↗
PubMed2007

Reconstruction of the ancestral ferungulate karyotype by electronic chromosome painting (E-painting).

By comparing high-coverage and high-quality whole genome sequence assemblies it is now possible to reconstruct putative ancestral progenitor karyotypes, here called protokaryotypes. For this study we used the recently described electronic chromosome painting technique (E-painting) to reconstruct the karyotype of the 85 million-year-old (MYA) ferungulate ancestor. This model is primarily based on dog (Canis familiaris) and cattle (Bos taurus) genome data and is highly consistent with comparative gene mapping and chromosome painting data. The protokaryotype bears 23 autosomal chromosome pairs and the sex chromosomes and preserves most of the chromosomal associations described previously for the boreo-eutherian protokaryotype. The model indicates that five interchromosomal rearrangements occurred during the transition from the boreo-eutherian to the ferungulate ancestor. From there on 66 further interchromosomal rearrangements took place in the lineage leading to cattle and 61 further interchromosomal rearrangements in the lineage to dog.

Animals↗
PubMed1992

Evaluation of the MPN, Anderson-Baird-Parker, Petrifilm E. coli and Fluorocult ECD method for enumeration of Escherichia coli in foods of animal origin.

Commercially available beta-D-glucuronidase (GUR) based methods, Petrifilm E. coli (PEC) and Fluorocult ECD (FECD), and ISO standard MPN and Anderson-Baird-Parker (ABP) procedures were evaluated for routine enumeration of E. coli in naturally contaminated foods of animal origin. The methods concerned were classifiable in a sequence of best qualities for: production, MPN > ABP = PEC = FECD; costs, FECD > ABP = PEC > MPN; time per measurement, ABP = PEC = FECD > MPN; practical use, PEC > FECD > ABP > MPN; detection at low contamination, MPN > ABP = PEC > FECD. The ABP and PEC method appeared useful for routine counting of E. coli in raw meat, poultry and meat products, whereas the MPN procedure turned out to be more sensitive, however, impractical and considerably more expensive. The FECD method was inexpensive although suitable for the enumeration of E. coli at higher contamination level (> 50 cfu/g). The indole and MUG indicators both applied to demonstrate E. coli with the ABP or FECD method proved to be equal in specificity.

Colony Count, Microbial↗
PubMed1997

Small (< 1.5 cm) angiomyolipomas of the kidney: characterization by the combined use of in-phase and fat-attenuated MR techniques.

The purpose of this study was to evaluate the ability of in-phase spoiled gradient echo combined with chemically selective fat suppression or out-of-phase spoiled gradient echo MR images to characterize small renal masses as angiomyolipomas. Eleven patients with a total of 35 small (< 1.5 cm) angiomyolipomas underwent MR examination at 1.5T. Eight patients had solitary and three patients had multiple angiomyolipomas. One of the patients with multiple angiomyolipomas had tuberous sclerosis and the number of angiomyolipomas were quantified as 20. MR examinations included in-phase spoiled gradient echo (all patients), chemically selective fat suppressed spin echo (six patients), chemically selective fat suppressed spoiled gradient echo (three patients), selective water excitation spoiled gradient echo (one patient) and out-of-phase spoiled gradient echo (seven patients). Angiomyolipomas were minimally (4 lesions) or moderately (31 lesions) high in signal intensity relative to renal cortex on in-phase spoiled gradient echo images. On out-of-phase spoiled gradient echo images, demonstration of signal void fat-water phase cancellation was present in all eight lesions in the seven patients who were imaged with this sequence. Small lesion size rendered the entire angiomyolipoma signal void in seven of these eight lesions due to phase cancellation artifact. Signal void phase cancellation of lesion border or signal void of the entire angiomyolipoma resulted in high lesion conspicuity in all lesions. Mild loss of signal intensity was observed in 7 lesions and moderate loss of signal intensity noted in 25 lesions on chemically selective fat suppressed images. On chemically selective fat-suppressed images, seven lesions were difficult to identify due to limited signal differences between medium intensity cortex and low intensity angiomyolipomas (six lesions in two patients) and moderate breathing artifact (one lesion in one patient). Characterization of small renal masses as angiomyolipomas may be reliably performed using the combination of in-phase and fat-attenuating MR sequences. Consistent image quality and high conspicuity of fat-water phase cancellation interfaces renders out-of-phase imaging a reliable fat attenuating method to demonstrate the presence of fat in small angiomyolipomas. Breath-hold fat-suppressed spoiled gradient echo is also effective; however, this technique demonstrates less signal loss in fatty lesions and is subject to problems with inhomogeneity of fat suppression.

Adult↗
PubMed2002

High-throughput approaches to study salivary proteins and genes from vectors of disease.

Blood-feeding arthropods have in their saliva a variety of molecules that affect the vertebrate host's hemostatic, inflammatory, and immune systems. The saliva of blood feeders also helps to facilitate infection of the pathogens they carry to the host, making vector saliva an attractive target to control pathogen transmission. The isolation and identification of salivary molecules from vectors of disease has been slow and difficult. Emerging technologies and new approaches in the fields of molecular biology and protein chemistry are facilitating this work. Massive sequencing of high quality, full-length cDNA libraries, coupled with proteomics and functional genomic approaches has led to the discovery of novel proteins, transcription products (genes), and biologic activities from the salivary glands of blood-feeding arthropods. This review focuses on the biologic activities identified in the saliva of various vectors of disease using classic biochemical and molecular biology approaches and new types of molecules and activities identified with high-throughput strategies.

Animals↗
PubMed2004

Bovine genomics update: making a cow jump over the moon.

Recent research in bovine genetics has focused on characterization of the biological differences underlying phenotypic variation for qualitative and quantitative traits of economic value in existing cattle populations. The much-anticipated benefits of DNA-based tools to routinely guide selection decisions for more efficient genetic gain and widened profit margins have not been fully met since the origin of this premise over two decades ago. However, the impending release of a high-quality draft genome sequence in 2005 should mark a turning point in these efforts. The following discussion summarizes how the bovine genetics research community has positioned itself to fully utilize a genome sequence resource and frames how genome sequence information can not only be applied to better implement marker-assisted selection, but also address rising consumer concerns relative to animal well-being and food safety.

Animals↗
PubMed2003

A novel technique for the examination of skin biopsies by laser capture microdissection.

BACKGROUND: Skin is an inherently heterogeneous tissue, thus the procurement of pure cell populations is critical for the accurate correlation of a molecular profile to a particular cell type or histological location. Laser Capture Microdissection (LCM) permits the efficient procurement of cells and mapping of genetic changes from histologically prepared samples. METHODS: This paper describes a robust LCM protocol established in our laboratory for the extraction of high quality DNA which sequenced from 100% of microdissected samples without the need for cloning. The unique properties of skin, in particular its strong intercellular adhesive forces, have dictated a significant modification to the normal procedure of tissue preparation to ensure reliable cell procurement. RESULTS: Using the methods outlined below we were able to precisely map the pattern of genomic mutations in our target gene of interest in normal skin, actinic keratosis and squamous cell carcinoma. CONCLUSIONS: The capability to select pure cell populations from the skin will revolutionise our ability to understand the processes involved in cutaneous tumourigenesis.

Biopsy↗
PubMed2006

Assessment of left ventricular outflow tract geometry in non-stenotic and stenotic aortic valves by cardiovascular magnetic resonance.

PURPOSE: To assess the geometry and area of the left ventricular outflow tract (LVOT) in non-stenotic and stenotic aortic valves and to determine the aortic valve area (AVA) in non-stenotic valves by magnetic resonance imaging (MRI) using a modified continuity equation. METHODS: Twenty patients (10 male, mean age 54.8 +/- 15 years) without known aortic valve disease and 10 patients (7 male, mean age 65.1 +/- 14 years) with moderate to severe aortic stenosis were included in this study. MRI was performed using a 1.5 T scanner (Philips Intera CV). AVA was assessed by planimetry on high quality SSFP cine sequences and used as reference standard. LVOT area was defined by calculating a circular area using the LVOT diameter from the 3 chamber view (3CV) and by planimetry. Peak flow velocity was assessed in the LVOT and the proximal aorta. AVA was calculated by a modified Gorlin equation, the continuity equation and a modified continuity equation using the planimetric LVOT area. RESULTS: Planimetric AVA ranged from 2.9 to 6.4 cm2 in patients with non-stenotic and from 0.3 to 1.3 cm2 with stenotic valves, LVOT area from 3.4 to 6.1 cm2 and from 2.6 to 6.5 cm2, respectively. The LVOT area based on the LVOT diameter derived from the 3CV was significantly underestimated in comparison to planimetry in non-stenotic and stenotic aortic valves (3.3 +/- 0.7 vs. 4.7 +/- 1.0 cm2, p < 0.0001; mean difference 1.1 +/- 0.12 cm2, CI 0.86-1.36 and 3.7 +/- 1.2 vs. 4.7 +/- 1.5 cm2, p < 0.05; mean difference 1.0 +/- 1.0 cm2, CI 0.24-1.71). The Gorlin formula showed a poor agreement with planimetry, whereas continuity equation and the modified continuity equation revealed a very good agreement. Planimetry of the LVOT displayed an elliptic shape of the LVOT in all patients with the minimum diameter perpendicular to the 3CV, which was the reason for the above mentioned underestimation. CONCLUSION: The LVOT area calculated from the 3CV-LVOT diameter underestimates the LVOT area compared to planimetry due to an elliptic shape of the LVOT in patients with non-stenotic as well as with stenotic aortic valves. The modified Gorlin equation proved to be less useful to assess AVA in non-stenotic valves, whereas the continuity equation and a modified continuity equation displayed a very good agreement with planimetric area measurements.

Aged↗
PubMed1997

Iterative reconstruction of PET images using a high-overrelaxation single-projection algorithm.

An iterative image reconstruction procedure is described which is able to calculate high-precision images within eight iterative steps. High initial overrelaxation parameters are used which drop down towards about one during continuing iteration. The parameters are determined pragmatically, postulating-maximum gain of image quality during a sequence of iterative steps. Results with simulated and measured data show that parameters derived from one data set may be widely used for other data sets. The acceleration of iterative reconstruction achieved by the estimation of optimum overrelaxation parameters is important for large data sets, especially for fully 3D reconstruction.

Algorithms↗
PubMed1998

Automated protein sequence database classification. II. Delineation Of domain boundaries from sequence similarities.

MOTIVATION: Decomposing each protein into modular domains is a basic prerequisite to classify accurately structural units in biological molecules. Boundaries between domains are indicated by two similar amino acid sequence segments located within the same protein (repeats) or within homologous proteins at notably different distances from their respective N- or C-termini. RESULTS: We have developed an automated method that combines such positional constraints derived from various detected pairwise sequence similarities to delineate the modular organization of proteins. The procedure has been applied to a non-redundant data set of 26 990 proteins whose sequences were taken from the PIR and SWISS-PROT databanks and shared <60% sequence identity amongst pairs. The resultant clustering, delineation and multiple alignment of 24 380 sequence fragments yielded a new database of 4364 domain families. Comparison of the domain collection with that of PRODOM indicates a clear improvement in the number and size of domain families, domain boundaries and multiple sequence alignments. The accuracy and sensitivity of the method are illustrated by results obtained for ankyrin-like repeats and EGF-like modules. AVAILABILITY: The resulting database, called DOMO, is available through the database search routine SRS at Infobiogen (http://www.infobiogen.fr/srs5/), EBI (http://srs.ebi.ac.uk:5000/) and EMBL (http://www.embl-heidelberg.de/srs5/) World Wide Web sites. CONTACT: gracy@infobiogen.fr

Algorithms↗
PubMed2003

A divide-and-conquer approach to fragment assembly.

MOTIVATION: One of the major problems in DNA sequencing is assembling the fragments obtained by shotgun sequencing. Most existing fragment assembly techniques follow the overlap-layout-consensus approach. This framework requires extensive computation in each phase and becomes inefficient with increasing number of fragments. RESULTS: We propose a new algorithm which solves the overlap, layout, and consensus phases simultaneously. The fragments are clustered with respect to their Average Mutual Information (AMI) profiles using the k-means algorithm. This removes the unnecessary burden of considering the collection of fragments as a whole. Instead, the orientation and overlap detection are solved efficiently, within the clusters. The algorithm has successfully reconstructed both artificial and real data. AVAILABILITY: Available on request from the authors.

Algorithms↗