# Next Generation Sequencing (NGS)/Bioinformatics from the outside/GeneTalk
## Description

GeneTalk, is a web-based platform, tool, and database, for filtering, reduction and prioritization 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 diagnostics of genetic disorders.
Registerd 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 prioritization 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.

### Analysis procedure

5 easy steps to analyze VCF files
* Upload VCF file
* Edit pedigree and phenotype information for segregation filtering
* Filter your VCF file by editing the filtering options
* View results and annotations
* Write your own annotations

### Filtering 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 panels, 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)

## Communication platform & expert network

Users can share VCF files with colleagues and coworkers. The integrated mailig systems allows users to contact experts easily. Users can create annotations and comments and rate annotations regarding disease causing and trustworthiness. This information is helpful for interpretation of human sequence variants and diagnosis of genetic disorders. Registered users provide information about their field of knowledge in their profile and can be contacted by other users. Expertise of a user can consist of genetic disease, gene panels, or single genes.

## Benefit for the user

* Saving time during data interpretation
* Reducing costs in diagnostics
* Professionalization of genetic analysis
* Up to date data generated by community
* Communication and exchange of knowledge and expertise
* Outsourcing of bioinformatic

## References

* ↑ Kamphans, Tom (23 July 2012). "GeneTalk: an expert exchange platform for assessing rare sequence variants in personal genomes". Bioinformatics. 28 (19): 2515–20156. doi:10.1093/bioinformatics/bts462. PMC 3463119. PMID 22826540. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help); Unknown parameter |month= ignored (help)CS1 maint: date and year (link)
* ↑ [www.gene-talk.de [http://www.gene-talk.de www.gene-talk.de]] {{citation}}: Check |url= value (help); Missing or empty |title= (help)

## External links

gene-talk.de