GeneTalk
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Application data |
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| Created by | Krawitz PM, Kamphans T |
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| Biological application domain(s) | Structural variation |
| Principal bioinformatics method(s) | Variant calling, Genetic variation analysis, Sequence contamination filtering, Annotation, Exome analysis, Sequence analysis, Variant classification, Plotting and rendering |
| Created at | Charité-Universitätsmedizin Berlin |
| Maintained? | Yes |
| Input format(s) | VCF |
| Output format(s) | VCF, XLS, XLSX |
| Software features | Easy-to-use point-and-click web interface, data visualization, data filtering, Fast, SNP annotation, SNP calling, Variant annotation and analysis, variant counting |
| Programming language(s) | Ruby, JavaScript |
| Software libraries | dbSNP, GeneTalk |
| Licence | Freemium |
Summary: GeneTalk, a web-based platform, that can filter, reduce and prioritize human sequence variants from NGS data and assist in the interpretation of personal variants in clinical context. 200px|right
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Description
GeneTalk, a web-based platform, that can filter, reduce and prioritize human sequence variants from NGS data and assist in the time consuming and costly interpretation of personal variants in clinical context. It serves as an expert exchange platform for clinicians and scientists who are searching for information about specific sequence variants and connects them to share and exchange expertise on variants that are potentially disease-relevant.
GeneTalk is...
...a web-based software
- for the analysis and interpretation of human sequence variants
- for human geneticists, physicians, scientists
- filter and reduce huge VCF files with powerful and easily usable tools
...a database and network
- where users can create annotation about sequence variants
- where users can find experts
...a communication platform
- where users can exchange expertise and knowledge
- where users can assist in the interpretation of NGS data
GeneTalk, is a web-based platform, tool, and database, for filtering, reduction and prioritisation of human sequence variants from NGS data. Users can edit annotation about sequence variants and build up a crowd sourced database with clinically relevant information for diagnostics of genetic disorders. GeneTalk also serves as an expert exchange platform for clinicians and scientists who are searching for information about specific sequence variants and connects them to share and exchange expertise on variants that are potentially disease-relevant.
Users can register at www.gene-talk.de and use basic feature for free.
Application in diagnostics
GeneTalk is used by human geneticists, scientists, and clinicians for analysis and interpretation of sequence data from NGS for diagosicts of genetic disorders.
Registred users can upload NGS data (in VCF format) of a patient onto the GeneTalk server. All entries of the file are listed in the integrated VCF viewer. A user has the possibility to edit a family tree for pedigree_analysis. Using the intuitive filtering tools the user can reduce the number of clinically nonrelevant variants. After filtering and prioritisation users can interpret the relevant variants by retrieving information (annotations) about variants from the GeneTalk database. Useres have the option to provide annotations to disease causing variants, by providing publications, comments, and further details about the variant.
Using the communication platform a user can contact experts about specific variants, genes, or genetic disorders, to exchange knowledge and expertise.
Tools
GeneTalk offers a variety of filtering option to reduce the non-relevant sequence variants in VCF files.
- Functional filter (filter out variants that have effects on protein level)
- Linkage filter (filter out variants that are on specified chromosomes)
- Gene panel filter (filter variants by genes or gene panles, subscribe to publically available gene panels or create own ones)
- Frequency filter (show only variants with a genotype frequency lower than specified)
- Inheritance filter (filter out variants by presumed mode of inheritance)
- Annotation filter (show only variants that are listed in databases)
Links
References
To add a reference for GeneTalk, enter the PubMed ID in the field below and click 'Add'.
Search for "GeneTalk" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
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