scholarly journals EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies

2019 ◽  
Vol 47 (W1) ◽  
pp. W166-W170 ◽  
Author(s):  
Julie Krainer ◽  
Andreas Weinhäusel ◽  
Karel Hanak ◽  
Walter Pulverer ◽  
Seza Özen ◽  
...  
Keyword(s):  
Bisulfite Sequencing ◽  
Cost Effective ◽  
Analysis Tool ◽  
Sequencing Data ◽  
Targeted Bisulfite Sequencing ◽  
Cost Effective Approach ◽  
Analysis Workflow ◽  
Complete Data Analysis ◽  
User Friendly ◽  
Validation Research

Abstract DNA methylation is one of the major epigenetic modifications and has frequently demonstrated its suitability as diagnostic and prognostic biomarker. In addition to chip and sequencing based epigenome wide methylation profiling methods, targeted bisulfite sequencing (TBS) has been established as a cost-effective approach for routine diagnostics and target validation applications. Yet, an easy-to-use tool for the analysis of TBS data in combination with array-based methylation results has been missing. Consequently, we have developed EPIC-TABSAT, a user-friendly web-based application for the analysis of targeted sequencing data that additionally allows the integration of array-based methylation results. The tool can handle multiple targets as well as multiple sequencing files in parallel and covers the complete data analysis workflow from calculation of quality metrics to methylation calling and interactive result presentation. The graphical user interface offers an unprecedented way to interpret TBS data alone or in combination with array-based methylation studies. Together with the computation of target-specific epialleles it is useful in validation, research, and routine diagnostic environments. EPIC-TABSAT is freely accessible to all users at https://tabsat.ait.ac.at/.

scholarly journals A simple and cost-effective approach for technical validation of next generation methylation sequencing data

2019 ◽  
Author(s):  
Ali Javadmanesh ◽  
Afsaneh Mojtabanezhad Shariatpanahi ◽  
Ehsan Shams Davodly ◽  
Marjan Azghandi ◽  
Maryam Yassi ◽  
...  
Keyword(s):  
Dna Methylation ◽  
High Resolution ◽  
High Resolution Melting ◽  
Cost Effective ◽  
Next Generation ◽  
Sequencing Data ◽  
Cost Effective Approach ◽  
Technical Validation ◽  
R Programming ◽  
And Control

Abstract Background DNA methylation is a fundamental epigenetic process that, in most cases, modulates genetic expression levels. Changes in DNA methylation, either hypo- or hypermethylation, have a key role in many biological processes and several human diseases such as cancer. In the current study, we offered an approach to validate the next generation methylation sequencing data.Methods Genomic DNA was extracted from target and control samples (6 in each group), followed by bisulfite conversion. Next generation methylation sequencing and methylation sensitive high-resolution melting assay were carried out. The primers for methylation sequencing validation were designed by R programming language.Results In the current study, two groups, case and control, were discriminated based on methylation sequencing results and the real time PCR-based results were in accordance with the next generation methylation sequencing.Discussion Methylation sensitive high-resolution melting validation assay is a simple and cost-effective method, which confirmed next generation methylation sequencing results.

scholarly journals Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data

2021 ◽  
Vol 9 ◽  
Author(s):  
Xubin Zheng ◽  
Qiong Wu ◽  
Haonan Wu ◽  
Kwong-Sak Leung ◽  
Man-Hon Wong ◽  
...  
Keyword(s):  
Liver Cancer ◽  
Dna Sequences ◽  
Bisulfite Sequencing ◽  
Differentially Methylated Region ◽  
Sequencing Data ◽  
Reduced Representation ◽  
Targeted Bisulfite Sequencing ◽  
Differentially Methylated Genes ◽  
Genome Bisulfite Sequencing ◽  
Bisulfite Sequencing Data

Bisulfite sequencing is considered as the gold standard approach for measuring DNA methylation, which acts as a pivotal part in regulating a variety of biological processes without changes in DNA sequences. In this study, we introduced the most prevalent methods for processing bisulfite sequencing data and evaluated the consistency of the data acquired from different measurements in liver cancer. Firstly, we introduced three commonly used bisulfite sequencing assays, i.e., reduced-representation bisulfite sequencing (RRBS), whole-genome bisulfite sequencing (WGBS), and targeted bisulfite sequencing (targeted BS). Next, we discussed the principles and compared different methods for alignment, quality assessment, methylation level scoring, and differentially methylated region identification. After that, we screened differential methylated genes in liver cancer through the three bisulfite sequencing assays and evaluated the consistency of their results. Ultimately, we compared bisulfite sequencing to 450 k beadchip and assessed the statistical similarity and functional association of differentially methylated genes (DMGs) among the four assays. Our results demonstrated that the DMGs measured by WGBS, RRBS, targeted BS and 450 k beadchip are consistently hypo-methylated in liver cancer with high functional similarity.

scholarly journals MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection

2020 ◽  
Author(s):  
Phuc-Loi Luu ◽  
Phuc-Thinh Ong ◽  
Tran Thai Huu Loc ◽  
Dilys Lam ◽  
Ruth Pidsley ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Supplementary Information ◽  
Complete Analysis ◽  
Analysis Tool ◽  
Sequencing Data ◽  
Interactive Analysis ◽  
Disease States ◽  
Parallel Pipeline ◽  
Analysis Workflow ◽  
A Cell

Abstract Summary DNA methylation patterns in a cell are associated with gene expression and the phenotype of a cell, including disease states. Bisulphite PCR sequencing is commonly used to assess the methylation profile of genomic regions between different cells. Here we have developed MethPanel, a computational pipeline with an interactive graphical interface to rapidly analyse multiplex bisulphite PCR sequencing data. MethPanel comprises a complete analysis workflow from genomic alignment to DNA methylation calling and supports an unlimited number of PCR amplicons and input samples. MethPanel offers important and unique features, such as calculation of a epipolymorphism score and bisulphite PCR bias correction capabilities, and is designed so that the methylation data from all samples can be processed in parallel. The outputs are automatically forwarded to a shinyApp for convenient display, visualisation and remotely sharing data with collaborators and clinicians. Availability MethPanel is freely available at https://github.com/thinhong/MethPanel. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals rCASC: reproducible Classification Analysis of Single Cell sequencing data

2018 ◽  
Author(s):  
Luca Alessandrì ◽  
Marco Beccuti ◽  
Maddalena Arigoni ◽  
Martina Olivero ◽  
Greta Romano ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cells ◽  
R Package ◽  
Cellular Heterogeneity ◽  
Supplementary Information ◽  
Sequencing Data ◽  
Single Cell Sequencing ◽  
Analysis Workflow ◽  
User Friendly ◽  
Bioinformatics Workflows

AbstractSummarySingle-cell RNA sequencing has emerged as an essential tool to investigate cellular heterogeneity, and highlighting cell sub-population specific signatures. Nowadays, dedicated and user-friendly bioinformatics workflows are required to exploit the deconvolution of single-cells transcriptome. Furthermore, there is a growing need of bioinformatics workflows granting both functional, i.e. saving information about data and analysis parameters, and computation reproducibility, i.e. storing the real image of the computation environment. Here, we present rCASC a modular RNAseq analysis workflow allowing data analysis from counts generation to cell sub-population signatures identification, granting both functional and computation reproducibility.Availability and ImplementationrCASC is part of the reproducible bioinfomatics project. rCASC is a docker based application controlled by a R package available at https://github.com/kendomaniac/rCASC.Supplementary informationSupplementary data are available at rCASC github

scholarly journals Performance comparison and in-silico harmonization of commercial platforms for DNA methylome analysis by targeted bisulfite sequencing

2021 ◽  
Author(s):  
Miljana Tanic ◽  
Ismail Moghul ◽  
Simon Rodney ◽  
Pawan Dhami ◽  
Heli Vaikkinen ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Fate ◽  
Bisulfite Sequencing ◽  
Epigenetic Modification ◽  
Cost Effective ◽  
Performance Comparison ◽  
Performance Criteria ◽  
Targeted Bisulfite Sequencing ◽  
Cpg Sites ◽  
Targeted Analysis

Abstract DNA methylation is a key epigenetic modification in the regulation of cell fate and differentiation, and its analysis is gaining increasing importance in both basic and clinical research. Targeted Bisulfite Sequencing (TBS) has become the method of choice for the cost-effective, targeted analysis of the human methylome at base-pair resolution. Here we benchmarked five commercially available TBS platforms, including three hybridization capture-based (Agilent, Roche, and Illumina) and two RRBS-based (Diagenode and NuGen), across 11 samples. A subset of these were also compared to whole-genome DNA methylation sequencing with the Illumina and Oxford Nanopore platforms. We assessed performance with respect to workflow complexity, on/off-target performance, coverage, accuracy, and reproducibility. We find all platforms able to produce usable data but with major differences for some performance criteria, especially in the number and identity of the CpG sites covered, which affects the interoperability of datasets generated on these different platforms. To overcome this limitation, we used imputation and show that it improves the interoperability from an average of 10.35% (0.8M CpG sites) to 97% (7.6M CpG sites). Our study provides cross-validated guidance on which TBS platform to use for different features of the methylome and offers an imputation-based harmonization solution for improved interoperability between platforms, allowing comparative and integrative analysis.

scholarly journals HAM-TBS: High accuracy methylation measurements via targeted bisulfite sequencing

2017 ◽  
Author(s):  
Simone Röh ◽  
Tobias Wiechmann ◽  
Susann Sauer ◽  
Maik Ködel ◽  
Elisabeth B. Binder ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Cost Effective ◽  
Accurate Method ◽  
High Accuracy ◽  
Ctcf Binding ◽  
Stress System ◽  
Robust Detection ◽  
Targeted Bisulfite Sequencing ◽  
Effective Manner

AbstractBackgroundThe ability to accurately and efficiently measure DNA methylation is vital to advance the understanding of this mechanism and its contribution to common diseases. Here, we present a highly accurate method to measure methylation using bisulfite sequencing (termed HAM-TBS). This novel method is able to assess DNA methylation in multiple samples with high accuracy in a cost-effective manner. We developed this assay for the FKBP5 locus, an important gene in the regulation of the stress system and previously linked to stress-related disorders, but the method is applicable to any locus of interest.ResultsHAM-TBS enables multiplexing of up to 96 samples spanning a region of ~10 kb using the llumina MiSeq. It incorporates a triplicate bisulfite conversion step, pooled target enrichment via PCR, PCR-free library preparation and a minimum coverage of 1,000x. Furthermore, we designed and validated a targeted panel to specifically assess regulatory regions within the FKBP5 locus including the transcription start site, topologically associated domain boundaries, intergenic and proximal enhancers as well as glucocorticoid receptor and CTCF binding sites that are not covered in commercially available DNA methylation arrays.ConclusionsHAM-TBS represents a highly accurate, medium-throughput sequencing approach for robust detection of DNA methylation changes in specific target regions.

scholarly journals Deconvolution of nucleic-acid length distributions: a gel electrophoresis analysis tool and applications

2019 ◽  
Vol 47 (16) ◽  
pp. e92-e92
Author(s):  
Riccardo Ziraldo ◽  
Massa J Shoura ◽  
Andrew Z Fire ◽  
Stephen D Levene
Keyword(s):  
Quality Control ◽  
Software Tool ◽  
Cost Effective ◽  
Analysis Tool ◽  
Dna Fragments ◽  
Line Profiles ◽  
Limited Information ◽  
Sequencing Data ◽  
Dna And Rna ◽  
Average Size

Abstract Next-generation DNA-sequencing (NGS) technologies, which are designed to streamline the acquisition of massive amounts of sequencing data, are nonetheless dependent on various preparative steps to generate DNA fragments of required concentration, purity and average size (molecular weight). Current automated electrophoresis systems for DNA- and RNA-sample quality control, such as Agilent’s Bioanalyzer® and TapeStation® products, are costly to acquire and use; they also provide limited information for samples having broad size distributions. Here, we describe a software tool that helps determine the size distribution of DNA fragments in an NGS library, or other DNA sample, based on gel-electrophoretic line profiles. The software, developed as an ImageJ plug-in, allows for straightforward processing of gel images, including lane selection and fitting of univariate functions to intensity distributions. The user selects the option of fitting either discrete profiles in cases where discrete gel bands are visible or continuous profiles, having multiple bands buried under a single broad peak. The method requires only modest imaging capabilities and is a cost-effective, rigorous alternative characterization method to augment existing techniques for library quality control.

scholarly journals Using a Telegram chatbot as cost-effective software infrastructure for ambulatory assessment studies with iOS and Android devices

2020 ◽  
Author(s):  
Michael Barthelmäs ◽  
Marcel Killinger ◽  
Johannes Keller
Keyword(s):  
Data Security ◽  
Cost Effective ◽  
Ambulatory Assessment ◽  
The Internet ◽  
Software Infrastructure ◽  
New Approach ◽  
Python Script ◽  
Cost Effective Approach ◽  
User Friendly ◽  
General Public License

Abstract In this work, we present an innovative and cost-effective approach to run ambulatory assessment (AA) studies on participants’ smartphones via Telegram Messenger. Our approach works both for Android and iOS devices. The population of potential participants in a given country or region consists of all individuals who (a) are in possession of a smartphone, (b) are willing to install Telegram Messenger, and (c) live in an environment providing constant connection to the Internet. In our new approach to AA, participants are asked to subscribe to a Telegram chatbot that provides them with links to brief surveys at specified points in time in their everyday lives via short notifications. We developed a user-friendly Python script that allows for the flexible editing of the chatbot’s settings, e.g., the number of surveys per day. All common survey software designed for mobile devices can be used to present surveys to participants. This means that data collection takes place exclusively via the selected survey software, not via Telegram. With our approach, AA studies can be carried out among iOS and Android users cost-effectively and reliably while data security is ensured. Initial data from a pilot study show that studies of this kind are feasible, and the procedure is accepted by participants. Our Python script is licensed under General Public License (GPLv3) and therefore freely available and editable: https://github.com/Raze97/Telegram-Survey-Bot

scholarly journals Deconvolution of Nucleic-acid Length Distributions: A Gel Electrophoresis Analysis Tool and Applications

2019 ◽  
Author(s):  
Riccardo Ziraldo ◽  
Massa J. Shoura ◽  
Andrew Z. Fire ◽  
Stephen D. Levene
Keyword(s):  
Quality Control ◽  
Software Tool ◽  
Cost Effective ◽  
Analysis Tool ◽  
Dna Fragments ◽  
Line Profiles ◽  
Limited Information ◽  
Sequencing Data ◽  
Dna And Rna ◽  
Average Size

ABSTRACTNext-generation DNA-sequencing (NGS) technologies, which are designed to streamline the acquisition of massive amounts of sequencing data, are nonetheless dependent on various preparative steps to generate DNA fragments of required concentration, purity, and average size (molecular weight). Current automated electrophoresis systems for DNA- and RNA-sample quality control, such as Agilent’s Bioanalyzer ®and TapeStation ® products, are costly to acquire and use; they also provide limited information for samples having broad size distributions. Here we describe a software tool that helps determine the size distribution of DNA fragments in an NGS library, or other DNA sample, based on gel-electrophoretic line profiles. The software, developed as an ImageJ plug-in, allows for straightforward processing of gel images, including lane selection and fitting of univariate functions to intensity distributions. The user selects the option of fitting either discrete profiles in cases where discrete gel bands are visible, or continuous profiles, having multiple bands buried under a single broad peak. The method requires only modest imaging capabilities and is a cost-effective, rigorous alternative characterization method to augment existing techniques for library quality control.

Sign in / Sign up

Export Citation Format

Share Document