Tagging genetic variants in the RD-Connect Genome-Phenome Analysis Platform


This video is going to show how to tag a
variant of interest in the RD-Connect Platform. Once you have identified a
variant of interest, you can tag it in the genomic platform selecting the tag feature directly from the results section. A disclaimer will appear stating
that this tag will be visible to all the RD-Connect users. A form is then displayed with different fields to be filled in. The first two concerning the user and the date are automatically filled in and for the other one you would have to choose between the options offered in the different dropdowns. First, you will have to select in which sample of the query, if there is more than one,
you would like to tag the variant. In this case we select the first one, which
correspond to the index case. The gene name is also prefilled in, but you can select another one if the position is covered by more than one gene. Then you have to enter the mode of inheritance also selecting from the drop down. For this case, we select an autosomal dominant inheritance. Now you will have to enter the origin, which is in this example is a de novo variant. Then you would have to select the clinical significance according to your variant interpretation. The options displayed are the ones used in ClinVar database, and we strongly recommend you to apply ACMG guidelines to define the clinical
significance of your variant. In this case, and according to the ACMG criteria, the variant will be classified as photogenic. Finally, you can also enter evidences
adding specific PubMed IDs or using the comments section. You can now submit your variant. Once the variant is submitted, you would be able to filter your data by variants that have been tagged in your samples or in the whole RD-Connect database. To do so, go to the filters section and in the “Variant Type” field, select “selected samples” if you want to retrieve only the variants tagged in the samples of the query or select “any samples” if you want to retrieve any variant tagged in the RD-Connect database. In this case, if we select “in the selected samples” and we rerun the query we will retrieve the variant we
have just tagged. Now, if you select the variant, and go to the candidate tab, you
will see all the information that have been entered for this variant. Script and recording: Leslie Matalonga
Editing: Dorota Badowska

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