GeneTalk Annotation Whitepaper

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Information about GeneTalk Annotation Whitepaper

Published on February 28, 2014

Author: AlexejKnaus


VARIANT SPECIFIC ANNOTATIONS AN ANNOTATIONS in GeneTalk is a user-generated content that is specific to a genomic position. It can contain information about a genetic disorder or a link to a scientific article. Users can rate annotations in the category MEDICAL RELEVANCE and SCIENTIFIC EVIDENCE. Additionally users can provide comments to provide information or start a discussion. 1. 2. 3. Genomic position of the first nucleotide affected Genotype or allele Gene name and Entrez ID 4. HGVS codes for DNA and protein level 5. 6. 7. 8. 9. Author of annotation Visibility to GeneTalk community Annotation Text Your rating for medical relevance and scientific evidence User who provided a comment Opens a new window at 13. Link to publication in Pubmed Opens the gene info viewer Referring to the first affected letter in cDNA or protein Contact user directly by clicking the mail button 10. Add your comment 11. Link to external source or website 12. OMIM-ID Opens a new window at 14. Link to MutationTaster Opens a new window at to evaluates disease-causing potential of sequence alterations 15. 16. 17. 18. 19. Star rating for medical relevance Star rating for scientific evidence Votes of all users Click the VOTE button to apply your rating Comment of a user

ANNOTATION RATING AND FILTERING RATING OF ANNOTATIONS: The ratings in the category MEDICAL RELEVANCE range from one star (irrelevant or artifact) to five stars (disease causing) and in the category SCIENTIFIC EVIDENCE from one star (very low (e.g. incidental finding)) to five stars (very high (e.g. therapy studies)). Newly created annotations have to be rated by the user for medical relevance and scientific evidence. The initial rating of user counts as three votes and every further rating as one. Irrelevant or artifact Suspicious Disease associated Disease modifying Disease causing Very low (e.g. incidental finding) THE STAR RATING OF THE CATEGORIES medical relevance and scientific evidence is based on the majority vote of the user community. Users can adjust their rating at any time. The rating of the category changes as soon as a new majority of users is found. The displayed star rating of an annotation represents the majority of votes. All ratings are anonymous but a vote counter shows the distribution of all ratings of the users. GENETALK’S KOWLEDGEBASE: GeneTalk combined existing annotations from publicly available databases such as HGMD, dbSNP and the 1000 genomes project (1kGP). All annotations from the dbSNP that are flagged as clinically precious and HGMD annotations that are termed disease causing are initially rated with five stars for medical relevance and scientific evidence. Technical sequencing artifacts from the 1kGP blacklist were initially rated with one star for medical relevance and five stars for scientific evidence. FILTER VARIANTS BY MEDICAL RELEVANCE AND SCI- ENTIFIC EVIDENCE: You can set the annotation filter to any level of medical relevance and scientific evidence. If the filter is set to two stars in medical relevance for example all sequencing artifacts and irrelevant variants will be removed. As a first approach in a diagnostic filtering procedure it might be reasonable to start with a five star rating for medical relevance and at least a two star rating for scientific evidence. The total number of variants is most effectively reduced when only variants with annotations are kept. This setting can be used to check whether there are variants in a data set with already annotated mutation. If a patient cannot be diagnosed with this setting it is a more complicated research question and other filtering parameters have to be carefully chosen. Low (e.g. multiple cases) Medium (e.g. functional assays) High (e.g. animal models) Very high (e.g. therapy studies)

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