scholarly journals Alternative splicing QTLs in European and African populations using Altrans, a novel method for splice junction quantification

2015 ◽  
Author(s):  
Halit Ongen ◽  
Emmanouil T Dermitzakis
Keyword(s):  
Alternative Splicing ◽  
Rna Sequencing ◽  
Active Regions ◽  
Splice Junction ◽  
Population Based ◽  
Transcript Quantification ◽  
Novel Approach ◽  
African Populations ◽  
Different Types ◽  
Novel Method

With the advent of RNA-sequencing technology we now have the power to detect different types of alternative splicing and how DNA variation affects splicing. However, given the short read lengths used in most population based RNA-sequencing experiments, quantifying transcripts accurately remains a challenge. Here we present a novel method, Altrans, for discovery of alternative splicing quantitative trait loci (asQTLs). To assess the performance of Altrans we compared it to Cufflinks, a well-established transcript quantification method. Simulations show that in the presence of transcripts absent from the annotation, Altrans performs better in quantifications than Cufflinks. We have applied Altrans and Cufflinks to the Geuvadis dataset, which comprises samples from European and African populations, and discovered (FDR = 1%) 1806 and 243 asQTLs with Altrans, and 1596 and 288 asQTLs with Cufflinks for Europeans and Africans, respectively. Although Cufflinks results replicated better across the two populations, this likely due to the increased sensitivity of Altrans in detecting harder to detect associations. We show that, by discovering a set of asQTLs in a smaller subset of European samples and replicating these in the remaining larger subset of Europeans, both methods achieve similar replication levels (94% and 98% replication in Altrans and Cufflinks, respectively). We find that method specific asQTLs are largely due to different types of alternative splicing events detected by each method. We overlapped the asQTLs with biochemically active regions of the genome and observed significant enrichments for many functional marks and variants in splicing regions, highlighting the biological relevance of the asQTLs identified. All together, we present a novel approach for discovering asQTLs that is a more direct assessment of splicing compared to other methods and is complementary to other transcript quantification methods.

scholarly journals Splice junction centric approach to identify translated noncanonical isoforms in the human proteome

2018 ◽  
Author(s):  
Edward Lau ◽  
Yu Han ◽  
Maggie P. Y. Lam
Keyword(s):  
Alternative Splicing ◽  
Rna Sequencing ◽  
Splice Site ◽  
Splice Junction ◽  
Human Proteome ◽  
Protein Isoforms ◽  
Sequencing Data ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Disordered Regions

AbstractRNA sequencing has led to the discovery of many transcript isoforms created by alternative splicing, but the translational status and functional significance of most alternative splicing events remain unknown. Here we applied a splice junction-centric approach to survey the landscape of protein alternative isoform expression in the human proteome. We focused on alternative splice events where pairs of splice junctions corresponding to included and excluded exons with appreciable read counts are translated together into selective protein sequence databases. Using this approach, we constructed tissue-specific FASTA databases from ENCODE RNA sequencing data, then reanalyzed splice junction peptides in existing mass spectrometry datasets across 10 human tissues (heart, lung, liver, pancreas, ovary, testis, colon, prostate, adrenal gland, and esophagus). Our analysis reidentified 1,108 non-canonical isoforms annotated in SwissProt. We further found 253 novel splice junction peptides in 212 genes that are not documented in the comprehensive Uniprot TrEMBL or Ensembl RefSeq databases. On a proteome scale, non-canonical isoforms differ from canonical sequences preferentially at sequences with heightened protein disorder, suggesting a functional consequence of alternative splicing on the proteome is the regulation of intrinsically disordered regions. We further observed examples where isoform-specific regions intersect with important cardiac protein phosphorylation sites. Our results reveal previously unidentified protein isoforms and may avail efforts to elucidate the functions of splicing events and expand the pool of observable biomarkers in profiling studies.Acronyms and AbbreviationsA3SSalternative 3-prime splice site;A5SSalternative 5-prime splice site;FDRfalse discovery rate;IDRintrinsically disordered regions;MXEmutually exclusive exons;PSIpercent spliced in;PTCpremature termination codon;PTMpost-translational modifications;SEskipped exon;RIretained intron.

scholarly journals Leveraging transcript quantification for fast computation of alternative splicing profiles

2014 ◽  
Author(s):  
Gael P Alamancos ◽  
Amadís Pagès ◽  
Juan L Trincado ◽  
Nicolás Bellora ◽  
Eduardo Eyras
Keyword(s):  
Alternative Splicing ◽  
Rna Sequencing ◽  
De Novo ◽  
Computation Time ◽  
Sequencing Data ◽  
Standard Methods ◽  
Transcript Quantification ◽  
Cellular Processes ◽  
Reconstruction Methods ◽  
Transcript Reconstruction

Alternative splicing plays an essential role in many cellular processes and bears major relevance in the understanding of multiple diseases, including cancer. High-throughput RNA sequencing allows genome-wide analyses of splicing across multiple conditions. However, the increasing number of available datasets represents a major challenge in terms of computation time and storage requirements. We describe SUPPA, a computational tool to calculate relative inclusion values of alternative splicing events, exploiting fast transcript quantification. SUPPA accuracy is comparable and sometimes superior to standard methods using simulated as well as real RNA sequencing data compared to experimentally validated events. We assess the variability in terms of the choice of annotation and provide evidence that using complete transcripts rather than more transcripts per gene provides better estimates. Moreover, SUPPA coupled with de novo transcript reconstruction methods does not achieve accuracies as high as using quantification of known transcripts, but remains comparable to existing methods. Finally, we show that SUPPA is more than 1000 times faster than standard methods. Coupled with fast transcript quantification, SUPPA provides inclusion values at a much higher speed than existing methods without compromising accuracy, thereby facilitating the systematic splicing analysis of large datasets with limited computational resources. The software is implemented in Python 2.7 and is available under the MIT license at https://bitbucket.org/regulatorygenomicsupf/suppa

scholarly journals A novel approach to the computation of one-loop three- and four-point functions: I. The real mass case

2019 ◽  
Vol 2019 (11) ◽  
Author(s):  
J Ph Guillet ◽  
E Pilon ◽  
Y Shimizu ◽  
M S Zidi
Keyword(s):  
Building Blocks ◽  
The Real ◽  
Alternative Method ◽  
Novel Approach ◽  
Reduction Methods ◽  
Real Mass ◽  
Novel Method ◽  
Algebraic Reduction ◽  
The One ◽  
Mass Case

Abstract This article is the first of a series of three presenting an alternative method of computing the one-loop scalar integrals. This novel method enjoys a couple of interesting features as compared with the method closely following ’t Hooft and Veltman adopted previously. It directly proceeds in terms of the quantities driving algebraic reduction methods. It applies to the three-point functions and, in a similar way, to the four-point functions. It also extends to complex masses without much complication. Lastly, it extends to kinematics more general than that of the physical, e.g., collider processes relevant at one loop. This last feature may be useful when considering the application of this method beyond one loop using generalized one-loop integrals as building blocks.

scholarly journals From Multiplex Serology to Serolomics—A Novel Approach to the Antibody Response against the SARS-CoV-2 Proteome

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 749
Author(s):  
Julia Butt ◽  
Rajagopal Murugan ◽  
Theresa Hippchen ◽  
Sylvia Olberg ◽  
Monique van Straaten ◽  
...  
Keyword(s):  
Antibody Response ◽  
High Throughput ◽  
Large Population ◽  
High Sensitivity ◽  
Population Based ◽  
Antibody Responses ◽  
Hek293 Cells ◽  
Novel Approach ◽  
Assay Performance ◽  
Multiplex Serology

The emerging SARS-CoV-2 pandemic entails an urgent need for specific and sensitive high-throughput serological assays to assess SARS-CoV-2 epidemiology. We, therefore, aimed at developing a fluorescent-bead based SARS-CoV-2 multiplex serology assay for detection of antibody responses to the SARS-CoV-2 proteome. Proteins of the SARS-CoV-2 proteome and protein N of SARS-CoV-1 and common cold Coronaviruses (ccCoVs) were recombinantly expressed in E. coli or HEK293 cells. Assay performance was assessed in a COVID-19 case cohort (n = 48 hospitalized patients from Heidelberg) as well as n = 85 age- and sex-matched pre-pandemic controls from the ESTHER study. Assay validation included comparison with home-made immunofluorescence and commercial enzyme-linked immunosorbent (ELISA) assays. A sensitivity of 100% (95% CI: 86–100%) was achieved in COVID-19 patients 14 days post symptom onset with dual sero-positivity to SARS-CoV-2 N and the receptor-binding domain of the spike protein. The specificity obtained with this algorithm was 100% (95% CI: 96–100%). Antibody responses to ccCoVs N were abundantly high and did not correlate with those to SARS-CoV-2 N. Inclusion of additional SARS-CoV-2 proteins as well as separate assessment of immunoglobulin (Ig) classes M, A, and G allowed for explorative analyses regarding disease progression and course of antibody response. This newly developed SARS-CoV-2 multiplex serology assay achieved high sensitivity and specificity to determine SARS-CoV-2 sero-positivity. Its high throughput ability allows epidemiologic SARS-CoV-2 research in large population-based studies. Inclusion of additional pathogens into the panel as well as separate assessment of Ig isotypes will furthermore allow addressing research questions beyond SARS-CoV-2 sero-prevalence.

scholarly journals Red panda: a novel method for detecting variants in single-cell RNA sequencing

BMC Genomics ◽  
2020 ◽  
Vol 21 (S11) ◽  
Author(s):  
Adam Cornish ◽  
Shrabasti Roychoudhury ◽  
Krishna Sarma ◽  
Suravi Pramanik ◽  
Kishor Bhakat ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Articular Chondrocytes ◽  
Genetic Diseases ◽  
Simulated Data ◽  
Single Nucleotide ◽  
Single Cell Rna Sequencing ◽  
Red Panda ◽  
Novel Method ◽  
Rare Cells

Abstract Background Single-cell sequencing enables us to better understand genetic diseases, such as cancer or autoimmune disorders, which are often affected by changes in rare cells. Currently, no existing software is aimed at identifying single nucleotide variations or micro (1-50 bp) insertions and deletions in single-cell RNA sequencing (scRNA-seq) data. Generating high-quality variant data is vital to the study of the aforementioned diseases, among others. Results In this study, we report the design and implementation of Red Panda, a novel method to accurately identify variants in scRNA-seq data. Variants were called on scRNA-seq data from human articular chondrocytes, mouse embryonic fibroblasts (MEFs), and simulated data stemming from the MEF alignments. Red Panda had the highest Positive Predictive Value at 45.0%, while other tools—FreeBayes, GATK HaplotypeCaller, GATK UnifiedGenotyper, Monovar, and Platypus—ranged from 5.8–41.53%. From the simulated data, Red Panda had the highest sensitivity at 72.44%. Conclusions We show that our method provides a novel and improved mechanism to identify variants in scRNA-seq as compared to currently existing software. However, methods for identification of genomic variants using scRNA-seq data can be still improved.

Fuzzified time-frequency method for identification and localization of power system faults

2021 ◽  
pp. 1-13
Author(s):  
Pullabhatla Srikanth ◽  
Chiranjib Koley
Keyword(s):  
Power System ◽  
High Accuracy ◽  
Fuzzy Decision ◽  
Frequency Method ◽  
Time Frequency ◽  
Novel Approach ◽  
S Transform ◽  
Different Types ◽  
Power System Faults ◽  
Frequency Magnitude

In this work, different types of power system faults at various distances have been identified using a novel approach based on Discrete S-Transform clubbed with a Fuzzy decision box. The area under the maximum values of the dilated Gaussian windows in the time-frequency domain has been used as the critical input values to the fuzzy machine. In this work, IEEE-9 and IEEE-14 bus systems have been considered as the test systems for validating the proposed methodology for identification and localization of Power System Faults. The proposed algorithm can identify different power system faults like Asymmetrical Phase Faults, Asymmetrical Ground Faults, and Symmetrical Phase faults, occurring at 20% to 80% of the transmission line. The study reveals that the variation in distance and type of fault creates a change in time-frequency magnitude in a unique pattern. The method can identify and locate the faulted bus with high accuracy in comparison to SVM.

scholarly journals Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
pp. 54 ◽  
Author(s):  
Bin-Bin Xie ◽  
Dan Li ◽  
Wei-Ling Shi ◽  
Qi-Long Qin ◽  
Xiao-Wei Wang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Rna Sequencing ◽  
High Frequency ◽  
Trichoderma Longibrachiatum ◽  
Alternative Splicing Events

Motion estimation in vehicular environments based on Bayesian dynamic networks

2021 ◽  
pp. 1-12
Author(s):  
Lauro Reyes-Cocoletzi ◽  
Ivan Olmos-Pineda ◽  
J. Arturo Olvera-Lopez
Keyword(s):  
Real World ◽  
Dynamic Networks ◽  
Ground Truth ◽  
Change Of Direction ◽  
Prediction Rate ◽  
Different Types ◽  
Novel Method ◽  
Comparison Of The Results ◽  
Multiple Obstacles ◽  
Real Traffic

The cornerstone to achieve the development of autonomous ground driving with the lowest possible risk of collision in real traffic environments is the movement estimation obstacle. Predicting trajectories of multiple obstacles in dynamic traffic scenarios is a major challenge, especially when different types of obstacles such as vehicles and pedestrians are involved. According to the issues mentioned, in this work a novel method based on Bayesian dynamic networks is proposed to infer the paths of interest objects (IO). Environmental information is obtained through stereo video, the direction vectors of multiple obstacles are computed and the trajectories with the highest probability of occurrence and the possibility of collision are highlighted. The proposed approach was evaluated using test environments considering different road layouts and multiple obstacles in real-world traffic scenarios. A comparison of the results obtained against the ground truth of the paths taken by each detected IO is performed. According to experimental results, the proposed method obtains a prediction rate of 75% for the change of direction taking into consideration the risk of collision. The importance of the proposal is that it does not obviate the risk of collision in contrast with related work.

cis-acting elements and a trans-acting factor affecting alternative splicing of adenovirus L1 transcripts

1989 ◽  
Vol 9 (10) ◽  
pp. 4364-4371
Author(s):  
C Delsert ◽  
N Morin ◽  
D F Klessig
Keyword(s):  
Alternative Splicing ◽  
Rna Splicing ◽  
Late Phase ◽  
Simian Virus 40 ◽  
Splice Junction ◽  
Simian Virus ◽  
T Antigen ◽  
Expression Vectors ◽  
Acceptor Site ◽  
Proximal Site

Expression of the L1 region of adenovirus is temporally regulated by alternative splicing to yield two major RNAs encoding the 52- to 55-kilodalton (52-55K) and IIIa polypeptides. The distal acceptor site (IIIa) is utilized only during the late phase of infection, whereas the proximal site (52-55K) is used at both early and late times. Several parameters that might affect this alternative splicing were tested by using expression vectors carrying the L1 region or mutated versions of it. In the absence of a virus-encoded or -induced factor(s), only the 52-55K acceptor was used. Decreasing the distance between the donor and the IIIa acceptor had no effect. Removal of the 52-55K acceptor induced IIIa splicing slightly, implying competition between the two acceptors. Fusion of the IIIa exon to the 52-55K intron greatly enhanced splicing of the IIIa junction, suggesting that the IIIa exon does not contain sequences that inhibit splicing. Thus, the lack of splicing to the IIIa acceptor in the absence of a virus-encoded or -induced factor(s) is probably due to the absence of a favorable sequence and/or the presence of a negative element 5' of the IIIa splice junction, or both. The presence of several adenovirus gene products, including VA RNAs, the E2A DNA-binding protein, and the products of E1A and E1B genes, did not facilitate use of the IIIa acceptor. In contrast, the simian virus 40 early proteins, probably large T antigen, induced IIIa splicing. This result, together with those of earlier studies, suggest that T antigen plays a role in modulation of alternative RNA splicing.

Abstract 309: Vasovasorum Volume Can Be Measured by Contrast-Enhanced 3D Carotid Duplex Ultrasound: Concept and Design of a Novel Method for Predicting Stroke Risk in Patients With Carotid Artery Stenosis

2014 ◽  
Vol 34 (suppl_1) ◽  
Author(s):  
Isibor J Arhuidese ◽  
Alexander Nodel ◽  
Umair Qazi ◽  
Diana Call ◽  
Bruce Perler ◽  
...  
Keyword(s):  
Stroke Risk ◽  
Duplex Ultrasound ◽  
Population Based ◽  
Severe Stenosis ◽  
Asymptomatic Patients ◽  
Grant Support ◽  
Contrast Enhanced ◽  
Novel Method ◽  
Preliminary Study ◽  
Selection For

Introduction: Stroke remains a leading cause of death and disability. The reliance on the occurrence of symptoms and degree of stenosis for selecting patients with carotid stenosis for intervention is not ideal because it is often seen that patients with severe stenosis remain asymptomatic while many patients with moderate stenosis experience stroke. Furthermore, the majority of patients are asymptomatic until they experience stroke. It is known that intimal neovascularization flourishes as atherosclerotic disease progresses; however no technique in current use adequately correlates neovascularization to stroke risk. Objective: With seed grant support from the Society for Vascular Surgery Foundation we are executing a study based on our hypothesis that Vasovasorum Volume (VVV) measured using CE-3DCDU as a valid tool for mapping stroke risk. Method: We are recruiting symptomatic and asymptomatic patients adjudged to have >50% and >70% stenosis respectively on routine duplex ultrasound. Vasovasorum volume is measured using CE-3DCDU in patients who are eligible for carotid endarterectomy. Plaque removed during surgery is marked, decalcified and immunostained with CD34. Thereafter, VVV is measured in the excised plaque using 3D reconstruction histometry. We then evaluate the reliability and accuracy of CE-3DCDU in relation to the histopathology and compare VVV in symptomatic and asymptomatic patients. Results: The preliminary study included six patients and the results show that VVV measurement in carotid ultrasound and histopathology is feasible and reproducible (Figures 1 and 2). Conclusion: Vasovasorum volume is a promising predictor of stroke risk. By identifying patients who are truly at high risk for stroke, VVV measured by CE-3DCDU will aid precise patient selection for intervention, thus prevent stroke, save lives, limit disability and expend health care resources in an informed manner. The next phase of this project involves the establishment of efficacy and a population based multi-center clinical trial to generate evidence required to incorporate VVV measured using CE-3DCDU into clinical practice.

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