scholarly journals Integrating detection of copy neutral chromosomal losses in a clinical setting in leukemia and lymphoma by means of allelic imbalance and read depth ratio comparison

2019 ◽  
Author(s):  
Marcus C. Hansen ◽  
Oriane Cédile ◽  
Maja Ludvigsen ◽  
Eigil Kjeldsen ◽  
Peter L. Møller ◽  
...  
Keyword(s):  
Chromosomal Aberrations ◽  
Neutral Loss ◽  
Low Frequency ◽  
Read Depth ◽  
Low Complexity ◽  
Supplementary Information ◽  
Simple Method ◽  
Exact Test ◽  
Paired Samples ◽  
Depth Ratio

AbstractChromosomal aberrations are common features of hematological malignancies, with several recurrent aberrations recognized as important diagnostic or prognostic molecular markers. While genome-wide genotyping and genomic hybridization microarray analyses have been implemented in clinical laboratories for several years the usage of next generation sequencing for detection of acquired copy number alterations has not yet reached full clinical integration. One evident problem is the identification of copy neutral loss of heterozygosity (CN-LoH), which is not detectable by sequencing read depth correlation or the analogous microarray CGH. We selected 23 paired samples of hematological disorders from 14 individuals, focusing on leukemia and lymphomas, and tested whether a low complexity approach, relying on Fisher’s exact test or χ2, is efficient for the analysis of variant allele frequencies with read-depth ratio correlations in order to resolve both copy-altering and neutral chromosomal aberrations. This combination helped to identify 69 altered chromosomes and offered mutual confirmation. Moreover, six CN-LoHs (>1% AF shifts, p<0.01) were found with one additional suspected low frequency deletion (~10-15% burden) in a case of CLL. We conclude that this simple method is directly clinically applicable for the detection of copy neutral chromosomal loss of single genes from WES with intermediate coverage.AvailabilityMentioned plot software is available at Harvard Dataverse http://doi.org/10.7910/DVN/[email protected] or [email protected] informationSupplementary plots are available

scholarly journals CNV-BAC: Copy number Variation Detection in Bacterial Circular Genome

2020 ◽  
Vol 36 (12) ◽  
pp. 3890-3891
Author(s):  
Linjie Wu ◽  
Han Wang ◽  
Yuchao Xia ◽  
Ruibin Xi
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Genome Structure ◽  
Real Data ◽  
Read Depth ◽  
Supplementary Information ◽  
Circular Genome ◽  
Number Variation ◽  
Copy Number Variation Detection ◽  
Cnv Detection

Abstract Motivation Whole-genome sequencing (WGS) is widely used for copy number variation (CNV) detection. However, for most bacteria, their circular genome structure and high replication rate make reads more enriched near the replication origin. CNV detection based on read depth could be seriously influenced by such replication bias. Results We show that the replication bias is widespread using ∼200 bacterial WGS data. We develop CNV-BAC (CNV-Bacteria) that can properly normalize the replication bias and other known biases in bacterial WGS data and can accurately detect CNVs. Simulation and real data analysis show that CNV-BAC achieves the best performance in CNV detection compared with available algorithms. Availability and implementation CNV-BAC is available at https://github.com/XiDsLab/CNV-BAC. Supplementary information Supplementary data are available at Bioinformatics online.

Determination of Electric and Magnetic Properties of Commercial LTCC Soft Ferrite Material

2011 ◽  
Vol 8 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Nelu Blaž ◽  
Andrea Marić ◽  
Goran Radosavljević ◽  
Nebojša Mitrović ◽  
Ibrahim Atassi ◽  
...  
Keyword(s):  
Electrical Properties ◽  
Low Frequency ◽  
Hysteresis Loops ◽  
Frequency Range ◽  
Dispersion Parameters ◽  
Simple Method ◽  
Component Design ◽  
Microwave Engineering ◽  
Characterization Procedure

This paper offers an effective, accurate, and simple method for permittivity and permeability determination of an LTCC (low temperature cofired ceramic) ferrite sample. The presented research can be of importance in the fields of ferrite component design and application, as well as for RF and microwave engineering. The characterization sample is a stack of LTCC tapes forming a toroid. Commercially available ferrite tape ESL 40012 was used and standard LTCC processing was applied for the sample fabrication. For the first time, the electrical properties of a ferrite toroid sample of ESL 40012 LTCC ferrite tape is presented at various frequencies. The electrical properties of LTCC ferrite materials, permittivity and specific resistivity, are shown in a frequency range from 10 kHz to 1 MHz using the capacitive method. The hysteresis properties of this material are also determined. B-H hysteresis loops were measured applying a maximum excitation of 2 kA/m and frequencies of 50 Hz, 500 Hz, and 1000 Hz. Permeability is determined in the frequency range from 10 kHz to 1 GHz and a characterization procedure is divided in two segments, for low and high frequencies. Low frequency measurements (from 10 kHz to 1 MHz) are performed using LCZ meter and discrete turns of wire, while a short coaxial sample holder and vector network analyzer were used for the higher frequency range (from 300 kHz to 1 GHz). In addition, another important factor required for the practical design of devices is presented, the temperature variation of the permeability dispersion parameters.

scholarly journals A Simple Method for Assessing Diversity and Dynamics of Microbial Community: Comparison of Dairy Phages from Industrial and Spontaneous Fermentation

2021 ◽  
Vol 11 (19) ◽  
pp. 8915
Author(s):  
Agnieszka Olejnik-Schmidt ◽  
Bernadeta Pietrzak ◽  
Iwona Kawacka ◽  
Klaudia Malak ◽  
Weronika Wawrzyniak ◽  
...  
Keyword(s):  
Phage Type ◽  
Low Complexity ◽  
Universal Primers ◽  
Spontaneous Fermentation ◽  
Simple Method ◽  
Protective Measures ◽  
Production Methods ◽  
Phage Types ◽  
Quality Product ◽  
Sanger Method

Background: The dairy industry heavily relies on fermentation processes driven in high proportion by Lactococcus lactis. The fermentation process can be perturbed or even stopped by bacteriophage activity, leading to complete loss of fermentation batch or decreased quality product. The monitoring of the phage diversity and dynamics in the process allows implementing protective measures (e.g., starter rotation) to maintain unperturbed production. Methods: Universal primers were used to amplify sequences of the 936, c2, and P335 Lactococcus phage types. The amplicons were sequenced with the Sanger method and obtained degenerate sequences were analyzed using a simple bioinformatic pipeline in the R environment. Results: The most prevalent phage type is 936, followed by P335, whereas the c2 type is less frequent. Conclusions: Curd cheeses prepared on non-pasteurized milk based on native milk microbiota had a higher diversity of phages distinct from those found in dairy plants. Sanger sequencing of heterogenous amplicons generated on metagenome DNA can be used to assess low-complexity microbiota diversity.

scholarly journals γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites

2019 ◽  
Author(s):  
Andrea Calabria ◽  
Stefano Beretta ◽  
Ivan Merelli ◽  
Giulio Spinozzi ◽  
Stefano Brasca ◽  
...  
Keyword(s):  
Predictive Power ◽  
Graph Algorithm ◽  
Low Complexity ◽  
Host Cells ◽  
Supplementary Information ◽  
Dna Junctions ◽  
Alignment Tool ◽  
Insertion Sites ◽  
Cell Genome

Abstract Summary Retroviruses and their vector derivatives integrate semi-randomly in the genome of host cells and are inherited by their progeny as stable genetic marks. The retrieval and mapping of the sequences flanking the virus-host DNA junctions allows the identification of insertion sites in gene therapy or virally infected patients, essential for monitoring the evolution of genetically modified cells in vivo. However, since ∼30% of insertions land in low complexity or repetitive regions of the host cell genome, they cannot be correctly assigned and are currently discarded, limiting the accuracy and predictive power of clonal tracking studies. Here, we present γ-TRIS, a new graph-based genome-free alignment tool for identifying insertion sites even if embedded in low complexity regions. By using γ-TRIS to reanalyze clinical studies, we observed improvements in clonal quantification and tracking. Availability and implementation Source code at https://bitbucket.org/bereste/g-tris. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals AmpliCI: a high-resolution model-based approach for denoising Illumina amplicon data

2020 ◽  
Author(s):  
Xiyu Peng ◽  
Karin S Dorman
Keyword(s):  
Sequence Similarity ◽  
Low Frequency ◽  
Computation Time ◽  
Amplicon Sequencing ◽  
Supplementary Information ◽  
Quality Information ◽  
Model Based ◽  
Main Challenge ◽  
Sequencing Quality ◽  
Resolution Model

Abstract Motivation Next-generation amplicon sequencing is a powerful tool for investigating microbial communities. A main challenge is to distinguish true biological variants from errors caused by amplification and sequencing. In traditional analyses, such errors are eliminated by clustering reads within a sequence similarity threshold, usually 97%, and constructing operational taxonomic units, but the arbitrary threshold leads to low resolution and high false-positive rates. Recently developed ‘denoising’ methods have proven able to resolve single-nucleotide amplicon variants, but they still miss low-frequency sequences, especially those near more frequent sequences, because they ignore the sequencing quality information. Results We introduce AmpliCI, a reference-free, model-based method for rapidly resolving the number, abundance and identity of error-free sequences in massive Illumina amplicon datasets. AmpliCI considers the quality information and allows the data, not an arbitrary threshold or an external database, to drive conclusions. AmpliCI estimates a finite mixture model, using a greedy strategy to gradually select error-free sequences and approximately maximize the likelihood. AmpliCI has better performance than three popular denoising methods, with acceptable computation time and memory usage. Availability and implementation Source code is available at https://github.com/DormanLab/AmpliCI. Supplementary information Supplementary material are available at Bioinformatics online.

CluMSID: an R package for similarity-based clustering of tandem mass spectra to aid feature annotation in metabolomics

2019 ◽  
Vol 35 (17) ◽  
pp. 3196-3198 ◽  
Author(s):  
Tobias Depke ◽  
Raimo Franke ◽  
Mark Brönstrup
Keyword(s):  
Mass Spectra ◽  
Neutral Loss ◽  
Metabolite Identification ◽  
R Package ◽  
Supplementary Information ◽  
Tandem Mass ◽  
Compound Identification ◽  
Feature Identification ◽  
Tandem Mass Spectra ◽  
Interactive Visualizations

Abstract Summary Compound identification is one of the most eminent challenges in the untargeted analysis of complex mixtures of small molecules by mass spectrometry. Similarity of tandem mass spectra can provide valuable information on putative structural similarities between known and unknown analytes and hence aids feature identification in the bioanalytical sciences. We have developed CluMSID (Clustering of MS2 spectra for metabolite identification), an R package that enables researchers to make use of tandem mass spectra and neutral loss pattern similarities as a part of their metabolite annotation workflow. CluMSID offers functions for all analysis steps from import of raw data to data mining by unsupervised multivariate methods along with respective (interactive) visualizations. A detailed tutorial with example data is provided as supplementary information. Availability and implementation CluMSID is available as R package from https://github.com/tdepke/CluMSID/and from https://bioconductor.org/packages/CluMSID/. Supplementary information Supplementary data are available at Bioinformatics online.

A Note on Testing for Intervention Effects on Binary Responses

2006 ◽  
Vol 45 (04) ◽  
pp. 435-440 ◽  
Author(s):  
R. Henderson ◽  
C.-F. Kao ◽  
T. Friede
Keyword(s):  
Approximate Method ◽  
Change Point ◽  
Binary Data ◽  
Brownian Bridge ◽  
Population Characteristics ◽  
P Value ◽  
Calendar Time ◽  
Simple Method ◽  
Exact Test ◽  
Clinical Databases

Summary Objectives: In some circumstances controlled trials are not feasible and treatments can only be evaluated using clinical databases. Here we consider the situation where treatment is introduced at a particular calendar time and can only be evaluated by comparison with historical controls. In these circumstances Heuer and Abel recommended using change-point methods to search for change in characteristics over the whole study period rather than simply comparing treated and untreated patients. Their recommendation is to only conclude that the intervention had an effect if a change-point could be demonstrated close in time to the introduction of the new treatment. This reduces the risk of false positives caused by confounding changes in population characteristics or changes in patient management. For binary data we develop a method that follows their philosophy and apply it to an observational study in the treatment of pin sites after orthopaedic surgery. Methods: Tests for change in binomial probabilities based on Brownian bridge and Hansen’s approximation for maximally selected X 2 statistics are compared to an exact test by Worsley. The approximate method is generalized to logistic regression models allowing for covariates. Results: The agreement of the exact and approximate method is good for sample sizes of 100 or more. The actual test size of the Hansen approximate test allowing for covariates is close to the nominal level, whereas the Brownian bridge approximation is slightly conservative. The change in pin site treatment significantly reduces the risk of infection for both adults and children. Conclusions: We consider the Hansen approximation to provide a very good and very simple method for obtaining the p-value when testing for a change in binary data event probabilities, with or without covariates.

Coarse graining spectral analysis of HR and BP variability in patients with autonomic failure

1996 ◽  
Vol 271 (4) ◽  
pp. H1555-H1564 ◽  
Author(s):  
A. P. Blaber ◽  
R. L. Bondar ◽  
R. Freeman
Keyword(s):  
Heart Rate ◽  
Autonomic Failure ◽  
Spectral Power ◽  
Low Frequency ◽  
Coarse Graining ◽  
Low Complexity ◽  
System Response ◽  
High Signal ◽  
Neural Input ◽  
Signal Complexity

We examined heart rate and blood pressure variability (HRV and BPV) during graded tilt (5 min in each position: supine, -10 degrees, 10 degrees, 30 degrees, 60 degrees, -10 degrees, supine) in autonomic failure patients and age-matched controls. Heart rate was not different between patients and controls and increased with tilt (P < 0.001). Total HRV was reduced in patients (P < 0.03). Patients had reduced low-frequency (0-0.15 Hz) HRV and BPV (P < 0.005). With tilt, low-frequency BPV increased in controls, whereas high-frequency (> 0.15 Hz) BPV increased in patients. The slope of the fractal component (beta) for HRV and BPV was not different between patients and controls. HRV-beta increased (1.5-1.9, P < 0.01) with tilt, but BPV-beta (approximately 1.8) was unaffected. Values of beta close to 1 indicate high signal regulatory complexity, and values of beta close to 2 indicate low complexity. HRV and BPV provide clear evidence of impaired sympathetic and parasympathetic autonomic nervous system response to tilt with autonomic failure. The similarity in signal complexity with reduced fractal and harmonic spectral power, in patients compared with controls, suggests unchanged cardiovascular neural input and integration with reduced output in autonomic failure.

Simple NMR Determination of 5α/5β Configuration of 3-Oxosteroids

2001 ◽  
Vol 66 (10) ◽  
pp. 1529-1544 ◽  
Author(s):  
Hana Chodounská ◽  
Miloš Buděšínský ◽  
Romana Šídová ◽  
Miroslav Šíša ◽  
Alexander Kasal ◽  
...  
Keyword(s):  
Nmr Spectra ◽  
Low Frequency ◽  
Simple Method ◽  
H Nmr ◽  
Steroid Skeleton ◽  
C Nmr

A simple method to distinguish the 5α- from the 5β-isomers of 3-oxosteroids based on low-frequency 1H NMR spectra was proposed. Additional 1H and 13C NMR characteristics were derived from the comparison of completely assigned spectra of the 5α- and 5β-isomers. The effect of substitution at different positions of steroid skeleton was evaluated on a series of isomeric 3-oxosteroids, prepared for this purpose.

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