scholarly journals VarStack: a web tool for data retrieval to interpret somatic variants in cancer

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Morgan Howard ◽  
Bruce Kane ◽  
Mary Lepry ◽  
Paul Stey ◽  
Ashok Ragavendran ◽  
...  
Keyword(s):  
User Interface ◽  
Somatic Mutations ◽  
Ucsc Genome Browser ◽  
Data Retrieval ◽  
Web Tool ◽  
Somatic Variant ◽  
Search Feature ◽  
Variant Information ◽  
Tumor Genome ◽  
Excel File

Abstract Advances in tumor genome sequencing created an urgent need for bioinformatics tools to support the interpretation of the clinical significance of the variants detected. VarStack is a web tool which is a base to retrieve somatic variant data relating to cancer from existing databases. VarStack incorporates data from several publicly available databases and presents them with an easy-to-navigate user interface. It currently supports data from the Catalogue of Somatic Mutations in Cancer, gnomAD, cBioPortal, ClinVar, OncoKB, CiViC and UCSC Genome Browser. It retrieves the data from these databases and returns them back to the user in a fraction of the time it would take to manually navigate each site independently. Users submit a variant with a gene symbol, peptide change and coding sequence change. They may select a variety of tumor-specific studies in cBioPortal to search through in addition to their original query. The results from the databases are presented in tabs. Users can export the results as an Excel file. VarStack also has the batch search feature in which the user can submit a list of variants and download an Excel file with the data from the databases. With the batch search and data download options, users can easily incorporate VarStack into their workflow or tools. VarStack saves time by providing somatic variant information to the user from multiple databases in an easy-to-export and interpretable format. VarStack is freely available under https://varstack.brown.edu.

scholarly journals VarStack: a Web Tool for Data Retrieval to Interpret Somatic Variants in Cancer

2020 ◽  
Author(s):  
Morgan Howard ◽  
Bruce Kane ◽  
Mary Lepry ◽  
Paul Stey ◽  
Ashok Ragavendran ◽  
...  
Keyword(s):  
User Interface ◽  
Clinical Significance ◽  
Genome Sequencing ◽  
Somatic Mutations ◽  
Ucsc Genome Browser ◽  
Data Retrieval ◽  
Web Tool ◽  
Somatic Variant ◽  
Search Feature ◽  
Tumor Genome

AbstractBackground and objectiveAdvances in tumor genome sequencing created an urgent need for bioinformatics tools to support the interpretation of the clinical significance of the variants detected. VarStack is a web tool which is a base to retrieve somatic variant data in cancer from existing databases.MethodsVarStack incorporates data from several publicly available databases and presents them with an easy-to-navigate user-interface. It currently supports data from the Catalogue of Somatic Mutations in Cancer (COSMIC), gnomAD, cBioPortal, ClinVar, OncoKB and UCSC Genome browser. It retrieves the data from these databases and returns back to the user in a fraction of the time it would take to manually navigate each site independently.ResultsUsers submit a variant with gene symbol, peptide change, and coding sequence change. They may select a variety of tumor specific studies in cBioportal to search through in addition to their original query. The results from the databases are presented in tabs. Users can export the results as a CSV file. VarStack also has the batch search feature in which user submits a list of variants and download a CSV file with the data from the databases. With the batch search and data download options users can easily incorporate VarStack into their workflow or tools. VarStack saves time by providing variant data to the user from multiple databases in an easy-to-export and interpretable format.AvailabilityVarStack is freely available under https://varstack.brown.edu.

scholarly journals PathScore: a web tool for identifying altered pathways in cancer data

2016 ◽  
Author(s):  
Stephen G. Gaffney ◽  
Jeffrey P. Townsend
Keyword(s):  
Web Application ◽  
Somatic Mutations ◽  
Supplementary Information ◽  
Web Tool ◽  
Cancer Data ◽  
Link Type ◽  
Novel Approach ◽  
Supplementary Material ◽  
User Friendly ◽  
Pathway Effect

ABSTRACTSummaryPathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects.Availability and ImplementationWeb application available at pathscore.publichealth.yale.edu. Site implemented in Python and MySQL, with all major browsers supported. Source code available at github.com/sggaffney/pathscore with a GPLv3 [email protected] InformationAdditional documentation can be found at http://pathscore.publichealth.yale.edu/faq.

scholarly journals MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data

2017 ◽  
Vol 34 (2) ◽  
pp. 300-302 ◽  
Author(s):  
Christopher J Green ◽  
Matthew R Gazzara ◽  
Yoseph Barash
Keyword(s):  
Experimental Validation ◽  
Ucsc Genome Browser ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Rna Seq ◽  
Web Tool ◽  
Rt Pcr ◽  
Design Algorithm ◽  
Gene Isoforms ◽  
Downstream Analysis

Abstract Summary Analysis of RNA sequencing (RNA-Seq) data have highlighted the fact that most genes undergo alternative splicing (AS) and that these patterns are tightly regulated. Many of these events are complex, resulting in numerous possible isoforms that quickly become difficult to visualize, interpret and experimentally validate. To address these challenges we developed MAJIQ-SPEL, a web-tool that takes as input local splicing variations (LSVs) quantified from RNA-Seq data and provides users with visualization and quantification of gene isoforms associated with those. Importantly, MAJIQ-SPEL is able to handle both classical (binary) and complex, non-binary, splicing variations. Using a matching primer design algorithm it also suggests to users possible primers for experimental validation by RT-PCR and displays those, along with the matching protein domains affected by the LSV, on UCSC Genome Browser for further downstream analysis. Availability and implementation Program and code will be available athttp://majiq.biociphers.org/majiq-spel. Supplementary information Supplementary data are available atBioinformatics online.

scholarly journals TNscope: Accurate Detection of Somatic Mutations with Haplotype-based Variant Candidate Detection and Machine Learning Filtering

2018 ◽  
Author(s):  
Donald Freed ◽  
Renke Pan ◽  
Rafael Aldana
Keyword(s):  
Machine Learning ◽  
Normal Tissue ◽  
Structural Variation ◽  
Somatic Mutations ◽  
Variant Calling ◽  
Somatic Variant ◽  
Accurate Detection ◽  
Machine Learning Model ◽  
Early Engineering ◽  
Somatic Mutation Calling

AbstractDetection of somatic mutations in tumor samples is important in the clinic, where treatment decisions are increasingly based upon molecular diagnostics. However, accurate detection of these mutations is difficult, due in part to intra-tumor heterogeneity, contamination of the tumor sample with normal tissue and pervasive structural variation. Here, we describe Sentieon TNscope, a haplotype-based somatic variant caller with increased accuracy relative to existing methods. An early engineering version of TNscope was used in our submission to the most recent ICGC-DREAM Somatic Mutation calling challenge. In that challenge, TNscope is the leader in accuracy for SNVs, indels and SVs. To further improve variant calling accuracy, we combined the improvements in the variant caller with machine learning. We benchmarked TNscope using in-silico mixtures of well-characterized Genome in a Bottle (GIAB) samples. TNscope displays higher accuracy than the other benchmarked tools and the accuracy is substantially improved by the machine learning model.

scholarly journals MAJIQ-SPEL: Web-Tool to interrogate classical and complex splicing variations from RNA-Seq data

2017 ◽  
Author(s):  
Christopher J. Green ◽  
Matthew R. Gazzara ◽  
Yoseph Barash
Keyword(s):  
Alternative Splicing ◽  
Rna Sequencing ◽  
Experimental Validation ◽  
Ucsc Genome Browser ◽  
Rna Seq ◽  
Web Tool ◽  
Rt Pcr ◽  
Design Algorithm ◽  
Gene Isoforms ◽  
Downstream Analysis

AbstractAnalysis of RNA sequencing (RNA-Seq) data have highlighted the fact that most genes undergo alternative splicing (AS) and that these patterns are tightly regulated. Many of these events are complex, resulting in numerous possible isoforms that quickly become difficult to visualize, interpret, and experimentally validate. To address these challenges, We developed MAJIQ-SPEL, a web-tool that takes as input local splicing variations (LSVs) quantified from RNA-Seq data and provides users with visualization and quantification of gene isoforms associated with those. Importantly, MAJIQ-SPEL is able to handle both classical (binary) and complex (non-binary) splicing variations. Using a matching primer design algorithm it also suggests users possible primers for experimental validation by RT-PCR and displays those, along with the matching protein domains affected by the LSV, on UCSC Genome Browser for further downstream analysis.Availability: Program and code will be available at http://majiq.biociphers.org/majiq-spel

scholarly journals The ARMC5 gene shows extensive genetic variance in primary macronodular adrenocortical hyperplasia

2015 ◽  
Vol 173 (4) ◽  
pp. 435-440 ◽  
Author(s):  
Ricardo Correa ◽  
Mihail Zilbermint ◽  
Annabel Berthon ◽  
Stephanie Espiard ◽  
Maria Batsis ◽  
...  
Keyword(s):  
Germline Mutation ◽  
Genetic Variance ◽  
Somatic Mutations ◽  
Adrenal Glands ◽  
Suppressor Gene ◽  
Single Patient ◽  
Rare Type ◽  
Somatic Variant ◽  
Site Variation ◽  
Sanger Method

ObjectivePrimary macronodular adrenal hyperplasia (PMAH) is a rare type of Cushing's syndrome (CS) that results in increased cortisol production and bilateral enlargement of the adrenal glands. Recent work showed that the disease may be caused by germline and somatic mutations in the ARMC5 gene, a likely tumor suppressor gene (TSG). We investigated 20 different adrenal nodules from one patient with PMAH for ARMC5 somatic sequence changes.DesignAll of the nodules were obtained from a single patient who underwent bilateral adrenalectomy. DNA was extracted by standard protocol and the ARMC5 sequence was determined by the Sanger method.ResultsSixteen of 20 adrenocortical nodules harbored, in addition to what appeared to be the germline mutation, a second somatic variant. The p.Trp476* sequence change was present in all 20 nodules, as well as in normal tissue from the adrenal capsule, identifying it as the germline defect; each of the 16 other variants were found in different nodules: six were frame shift, four were missense, three were nonsense, and one was a splice site variation. Allelic losses were confirmed in two of the nodules.ConclusionThis is the most genetic variance of the ARMC5 gene ever described in a single patient with PMAH: each of 16 adrenocortical nodules had a second new, ‘private,’ and – in most cases – completely inactivating ARMC5 defect, in addition to the germline mutation. The data support the notion that ARMC5 is a TSG that needs a second, somatic hit, to mediate tumorigenesis leading to polyclonal nodularity; however, the driver of this extensive genetic variance of the second ARMC5 allele in adrenocortical tissue in the context of a germline defect and PMAH remains a mystery.

scholarly journals CLINE: a web-tool for the comparison of biological dendrogram structures

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Rodolfo S. Allendes Osorio ◽  
Lokesh P. Tripathi ◽  
Kenji Mizuguchi
Keyword(s):  
User Interface ◽  
Open Access ◽  
Special Interest ◽  
Web Application ◽  
Source Code ◽  
Visualization Tool ◽  
Web Tool ◽  
Link Type ◽  
Multiple Structures ◽  
Biological Interpretation

Abstract Background When visually comparing the results of hierarchical clustering, the differences in the arrangements of components are of special interest. However, in a biological setting, identifying such differences becomes less straightforward, as the changes in the dendrogram structure caused by permuting biological replicates, do not necessarily imply a different biological interpretation. Here, we introduce a visualization tool to help identify biologically similar topologies across different clustering results, even in the presence of replicates. Results Here we introduce CLINE, an open-access web application that allows users to visualize and compare multiple dendrogram structures, by visually displaying the links between areas of similarity across multiple structures. Through the use of a single page and a simple user interface, the user is able to load and remove structures form the visualization, change some aspects of their display and set the parameters used to match cluster topology across consecutive pairs of dendrograms. Conclusions We have implemented a web-tool that allows the users to visualize different dendrogram structures, showing not only the structures themselves, but also linking areas of similarity across multiple structures. The software is freely available at http://mizuguchilab.org/tools/cline/. Also, the source code, documentation and installation instructions are available on GitHub at https://github.com/RodolfoAllendes/cline/.

scholarly journals Next Generation Sequencing for Detecting Somatic FAS Mutations in Patients With Autoimmune Lymphoproliferative Syndrome

2021 ◽  
Vol 12 ◽  
Author(s):  
Marta López-Nevado ◽  
Jorge Docampo-Cordeiro ◽  
José T. Ramos ◽  
Rebeca Rodríguez-Pena ◽  
Celia Gil-López ◽  
...  
Keyword(s):  
Somatic Mutations ◽  
Genetic Defect ◽  
Autoimmune Lymphoproliferative Syndrome ◽  
Apoptotic Pathway ◽  
Somatic Variant ◽  
Panel Testing ◽  
Increased Risk ◽  
Lymphoproliferative Syndrome ◽  
Generation Sequencing ◽  
Blood Data

Autoimmune lymphoproliferative syndrome (ALPS) is a primary immune regulatory disorder clinically defined by chronic and benign lymphoproliferation, autoimmunity and an increased risk of lymphoma due to a genetic defect in the FAS-FASL apoptotic pathway. Genetic defects associated with ALPS are germinal and somatic mutations in FAS gene, in addition to germinal mutations in FASLG, FADD, CASP8 and CASP10 genes. The accumulation of CD3+TCRαβ+CD4-CD8- double negative T-cells (DNT) is a hallmark of the disease and 20-25% of ALPS patients show heterozygous somatic mutations restricted to DNT in the FAS gene (ALPS-sFAS patients). Nowadays, somatic mutations in the FAS gene are detected through Sanger sequencing in isolated DNT. In this study, we report an ALPS-sFAS patient fulfilling clinical and laboratory ALPS criteria, who was diagnosed through NGS with a targeted gene panel using DNA from whole blood. Data analysis was carried out with Torrent Suite Software and variant detection was performed by both germinal and somatic variant caller plugin. The somatic variant caller correctly detected other six ALPS-sFAS patients previously diagnosed in the authors’ laboratories. In summary, this approach allows the detection of both germline and somatic mutations related to ALPS by NGS, avoiding the isolation of DNT as the first step. The reads of the somatic variants could be detected even in patients with DNT in the cut off limit. Thus, custom-designed NGS panel testing may be a faster and more reliable method for the diagnosis of new ALPS patients, including those with somatic FAS mutations (ALPS-sFAS).

A web tool for STORET/WQX water quality data retrieval and Best Management Practice scenario suggestion

2015 ◽  
Vol 150 ◽  
pp. 21-27
Author(s):  
Youn Shik Park ◽  
Bernie A. Engel ◽  
Jonggun Kim ◽  
Larry Theller ◽  
Indrajeet Chaubey ◽  
...  
Keyword(s):  
Water Quality ◽  
Management Practice ◽  
Data Retrieval ◽  
Best Management Practice ◽  
Quality Data ◽  
Web Tool ◽  
Water Quality Data ◽  
Best Management

scholarly journals DNAvisualization.org: a serverless web tool for DNA sequence visualization

2019 ◽  
Vol 47 (W1) ◽  
pp. W20-W25 ◽  
Author(s):  
Benjamin D Lee ◽  
Michael A Timony ◽  
Pablo Ruiz
Keyword(s):  
Parallel Computing ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Cost Effective ◽  
Data Retrieval ◽  
Biological Information ◽  
Two Dimensional ◽  
Web Tool ◽  
Recent Developments

Abstract Raw DNA sequences contain an immense amount of meaningful biological information. However, these sequences are hard for humans to intuitively interpret. To solve this problem, a number of methods have been proposed to transform DNA sequences into two-dimensional visualizations. DNAvisualization.org implements several of these methods in a cost effective and performant manner via a novel, entirely serverless architecture. By taking advantage of recent developments in serverless parallel computing and selective data retrieval, the website is able to offer users the ability to visualize up to thirty 4.5 Mb DNA sequences simultaneously using one of five supported methods and to export these visualizations in a variety of publication-ready formats.

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