Using GTGT ========== .. _usage: GTGT is accessible online via `https://gtgt.rnatherapy.nl `_. Users can specify their transcript and mutation of interest in `HGVS `_ format. For the best results, users should specify all variants that were observed on the affected allele, since the exact patient sequence is taken into account when assessing therapies. However, if only the pathogenic variant is known, this will also work. .. figure:: figures/gtgt-input.png Input screen for the GTGT website. Users can describe their variant(s) of itnerest, and configure the parameters of the analysis. Please refer to the :ref:`transcripts ` section for more information on which transcripts can be used with GTGT. Settings -------- There are a number of settings that the user can change to control the analysis by GTGT. Include protein domains ~~~~~~~~~~~~~~~~~~~~~~~ For transcripts encoded on HG38, GTGT can also access the protein features which are available from the UCSC, and determine the effect of the therapy on protein features. For example, GTGT will correctly determine if a protein domain is lost due to an exon skip, and will also update the protein domain if (part of) the domain has been lost due to a frameshift. Show all evaluated therapies ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GTGT will always evaluate all possible therapies to simulate their effect on the transcript. Select this option if you want to see output for all considered therapies. By default, GTGT will only display a therapy when one of two conditions is met: #. A therapy changes or removes at least one of the input variants #. A therapy improves at least one of the features of the transcript, when compared to the input transcript Option 2 can sometimes give surprising results, especially when protein domains are included in the analysis. If a therapy introduces a frameshift in the transcript, the region of the protein after the frameshift but before the STOP will sometimes contain motifs which match the wildtype protein. GTGT will interpret this as an improvement of that feature, and hence show this therapy in the results. In these cases, we rely on the users to recognize that the benefits of this therapy are extremely minimal. Results ------- The GTGT results page will show the input transcript, the wildtype (as a reference) and any of the proposed therapies. .. figure:: figures/gtgt-result.png Result section of GTGT for the specified input variant Variant description ~~~~~~~~~~~~~~~~~~~ This lists the description of the variant(s) in HGVS format for the coding, RNA and protein level. Clicking these descriptions will take you to Mutalyzer where you can find more information regarding the HGVS descriptions. Therapy description ~~~~~~~~~~~~~~~~~~~ This is a human readable description of the therapy. In the case of the input variant, this will just hold a short description that this is the input variant. In the case of exon skip therapies, this description will explain which exons have been skipped, and optionally also if any of the exons are especially vulnerable to exon skipping. Transcript visualization ~~~~~~~~~~~~~~~~~~~~~~~~ Only in case of the input variant, GTGT also shows a figure indicating the location of the specified variants on the transcript. Changed annotations ~~~~~~~~~~~~~~~~~~~ This lists all annotations that have changed as a result of the variant(s) that were specfied. The ``Exons`` and ``Coding exons`` annotations are always available. Additional protein level annotations are only available for transcripts encoded on the HG38 reference genome. For each annotation, both the remaining percentage as well as the total number of (remaining) bases is listed. The protein annotations are retrieved from the UCSC, including the names which can be cryptic at times. Unchanged annotations ~~~~~~~~~~~~~~~~~~~~~ As the name suggest, these are annotations that have not been affected by the variants. By default, these are hidden in the web interface to conserve space, but you can expand them by clicking on the header. External resources ------------------ For each specified transcript, GTGT will automatically provide links to external resources in the side bar under 'External resources'. These can be related to the variant, transcript or gene of interest.