GeneTalk statistics

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Protocols

GeneTalk specifications

Information


Unique identifier OMICS_00270
Name GeneTalk
Interface Web user interface
Restrictions to use None
Input format VCF
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/GeneTalk

Taxon


  • Primates
    • Homo sapiens

Publication for GeneTalk

GeneTalk citations

 (10)
call_split

Characterization of a variant of gap junction protein α8 identified in a family with hereditary cataract

2017
PLoS One
PMCID: 5565107
PMID: 28827829
DOI: 10.1371/journal.pone.0183438
call_split See protocol

[…] f interest was eluted and subjected to 18 cycles of DNA amplification. The sample was then sequenced using an Illumina HiSeq2000 sequencer (Illumina, San Diego, CA, USA). The data were filtered using GeneTalk (http://www.gene-talk.de) []. Variants were analyzed with Polyphen-2 (http://genetics.bwh.harvard.edu/pph2/) and SIFT (Sorting Intolerant From Tolerant Web Server, version 5.1.1, database rel […]

library_books

MyGeneFriends: A Social Network Linking Genes, Genetic Diseases, and Researchers

2017
J Med Internet Res
PMCID: 5493784
PMID: 28623182
DOI: 10.2196/jmir.6676

[…] , with wiki-inspired approaches like Proteopedia [] or WikiGene [], collaborative sequence annotations such as WebApollo [], or voting for medical relevance and scientific evidence of variations with GeneTalk []. Recent initiatives such as Coremine or MAGI [] combine these trends. Coremine allows exploration of various biomedical concepts and connections between them, addition of private or public […]

call_split

Exome Sequencing in a Family with Luminal Type Breast Cancer Underpinned by Variation in the Methylation Pathway

2017
Int J Mol Sci
PMCID: 5343999
PMID: 28241424
DOI: 10.3390/ijms18020467
call_split See protocol

[…] on loci led to repeat mapping of the reads to a synthetic Caucasian major allele reference sequence (CEU-MARS) [], following the same process illustrated in . Resulting VCFs were then processed using GeneTalk [], a web-based tool for filtering and annotation of uploadable VCFs.A coverage depth of 15× was used for detection of potentially causative gene variants, prior to confirmation by Sanger seq […]

library_books

A likelihood ratio based method to predict exact pedigrees for complex families from next generation sequencing data

2016
Bioinformatics
PMCID: 5408770
PMID: 27565584
DOI: 10.1093/bioinformatics/btw550

[…] ding as well as increasing degrees of error rates we also simulated samples based on sequencing data from real individuals. The java application, as well as the visualizing R script, is integrated in GeneTalk (), and also available as a standalone application at www.gene-talk.de/vcf2ped. We analyzed the performance of our approach for a decreasing number of exomic and genomic markers. For exomic m […]

library_books

Crowdsourced direct to consumer genomic analysis of a family quartet

2015
BMC Genomics
PMCID: 4636840
PMID: 26547235
DOI: 10.1186/s12864-015-1973-7

[…] ound population (in cases where such numbers are known), variant predicted to be deleterious by several prediction tools and an exact match of the variant for the nucleotide change (Additional file ).GeneTalk: Various filter settings were implemented for analysis using GeneTalk []. First, variants of Father and Mother were analysed to look for screening of pathogenic heterozygous risk alleles that […]

call_split

A nonsense mutation of human XRCC4 is associated with adult onset progressive encephalocardiomyopathy

2015
PMCID: 4520657
PMID: 25872942
DOI: 10.15252/emmm.201404803
call_split See protocol

[…] nd 300 bp. In-solution targeted enrichment of exonic sequences was performed using the 64 Mb Exon Capture kit from Nimblgen. Then, the captured library was sequenced on Hiseq2000 platform (Illumina). GeneTalk (www.gene-talk.de) and Ingenuity Variant Analysis (www.ingenuity.com) web applications were used for variant filtering. Polyphen2, SIFT, and Mutation taster were used for pathogenicity predic […]

Citations

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GeneTalk institution(s)
GeneTalk, Berlin, Germany; Department of Medical and Human Genetics, Charité, Univfersitätsmedizin Berlin,Berlin, Germany

GeneTalk review

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Anonymous user #122

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Web
GeneTalk is a perfect platform to analyze VCF files and to get into contact with experts: We needed a to be able to contact any geneticist in the world that’s an expert for a specific gene. Now we can make use of social web technology at GeneTalk to find second patients with a particular variant or colleagues to collaborate with.