The New Analysis Wizard guides you through creating a new analysis in TGex. The process is separated into 4 stages, and information collected is summarized on the right side of the screen.
In the first stage of the analysis, you will be required to select the protocol for this analysis. A protocol is a template for analysis which includes predefined filters, the list of required and associated samples and the report template. Each new account includes a set of default protocols representing the most common cases of NGS analysis. These include:
- Germline – Single Sample – This case is commonly used to analyze germline samples when you only have access to the affected sample.
- Germline – Trio – This case is commonly used to analyze a rare genetics case when you have access to samples for the parents and the affected.
- Tumor Biopsy – Single Sample – This case is commonly used to analyze somatic samples when you have no access to the germline sample.
- Tumor Biopsy – with Germline – This case is commonly used to analyze somatic samples together with their germline counterparts.
NOTE: Premium accounts include the option of creating their own protocols to optimize their workflow.
TGex was designed as a subject-centric platform. As such, each analysis contains a single main sample with the option to be accompanied by several associated samples (for example: the parents in a trio case or the matched germline in a tumor biopsy case).
In this section of the wizard you can enter general details regarding the subject of the analysis. These details will be available during the analysis process for reference, and automatically included in the analysis report.
You can also select an existing subject if one has already been created.
For new subjects, the following information can be entered:
- Subject ID (required) – A unique identifier for your subject. Commonly it would be the patient identifier in your EMR or LIMS system, but it can be any identifier you choose.
- Name (optional) – The name of your subject
- Date of birth (optional) – The date of birth of your subject
- Gender (optional) – Male / Female. Leave blank for unknown / unspecified
- Consanguinity (optional) – Commonly used to specify parental consanguinity in cases of rare disease analysis
- Population type (optional) – Population, people or ethnic groups
In this section you can either upload a new sample or select an existing pre-loaded sample for the analysis by clicking on the “Select Sample” button next to the relevant sample. When a new VCF is uploaded into the system, TGex will automatically annotate it with the required data for analysis using its proprietary annotation pipeline (this may take a few minutes).
In the case of multiple samples, you will be required to associate or upload a sample for each associated sample, as well.
In this section you may include any clinical information about the analysis and its subject, decide which genetic models to analyze for the subject, and set phenotype terms that will be used to score and rank candidate variants during the analysis stage. Information entered here will be available during the analysis stage for reference.
The following information can be entered:
- Serial Number (required) – Specify a unique identifier for this analysis. A default value is automatically generated but can be replaced with your own identifier (for example, ID of the case in your system)
- Name (optional) – The name of this analysis, which default to
- Owner (optional) – The name of the referring clinician
- Description (optional) – Free text to describe the clinical aspects of the case
- Disease frequency (required) – Expected frequency of this disease occuring in the population. This number will populate a default filter which will not display any variants that appear more commonly during the analysis stage
- Genetic models (required) – By default, each protocol has a set of genetic models that can be used to analyze the case. For rare genetics, these would be “Recessive Homozygote”, “Recessive Compound Heterozygote” and “Dominant Heterozygote”. You can elect to remove irrelevant models from this list for the analysis stage
- Phenotype terms for VarElect (optional) – Any biological term (phenotype) that will be used by VarElect to score and rank the candidate variants. You can read more about VarElect HERE.
- Gene list (optional) – Entering a list of comma-separated genes here will automatically apply a filter on the list of variants, displaying only those occurring within the list of genes entered
Clicking on ‘Save’ in the last section of the wizard will enter this new analysis to your account and will redirect you to the Analysis Summary Page.