Geneticist Assistant Online Help : Geneticist Assistant Setup and Maintenance : Managing Objects in the Geneticist Assistant Database
Managing Objects in the Geneticist Assistant Database
An object in Geneticist Assistant holds a value or variable that can be applied for carrying out a run in Geneticist Assistant, or for processing and interpreting the resulting run data. Managing objects in Geneticist Assistant consists of adding and editing the values for these objects as well as deleting values that are no longer valid or required. Twelve objects are available in Geneticist Assistant: Chemistry, Instrument, Pathogenicity, Pathogenicity Status, Sample Status, Panel Group, Coverage Region Status, Sample Status, Run Status, Artifact Type, Phenotype, and Ethnicity. Geneticist Assistant is installed with default values for five of these objects: Pathogenicity, Pathogenicity Status, Sample Status, Coverage Region Status, and Run Status. You have the option of adding custom values for these objects, and then selecting a custom value in lieu of a default value. You must manually add values for all other objects.
 
Object
Default Values
Description
Chemistry
No
Refers to the chemistry that was used to prepare the samples for sequencing.
Instrument
No
Refers to the instrument that was used to sequence the samples.
Pathogenicity
Yes
The pathogenicity for a selected variant. Default values are Deleterious, Likely Deleterious, Unknown, Likely Benign, and Benign.
Pathogenicity Status
Yes
Indicates the status for changing the pathogenicity for a selected variant. Default values are Pending and Confirmed.
Sample Status
Yes
The status for a sample. Default values are New, QC Passed, Reviewed, and Complete
Panel Group
No
Separately tracks the pathogenicities of variants that might be found in multiple panels. For example, the pathogenicity of a selected variant is set to Deleterious for multiple cancer panels; however, the pathogenicity can be set to Benign for a cardiac panel. You can create a group for each panel, and then assign the appropriate panels to each group.
Coverage Region Status
Yes
The Coverage Regions tab (via the Run tab) lists the coverage information for every region in your panel as well as a status for each region. Default values are Passed or Failed to indicate whether a region passed or failed the coverage settings that were set for the run.
Sample Group
No
Used for a group of samples that are to be processed repeatedly over a period of time, for example, a group of control samples for which the coverage or variant frequency is to be tracked.
Run Status
Yes
The status for a run. Default values are New, QC Passed, Reviewed, and Complete.
Artifact
No
The artifact type for the sample variant, for example, a Sequencing artifact. A single default value, None, is supplied for artifact type.
Phenotype
No
The phenotype for a patient.
Ethnicity
No
The ethnicity for a run patient, for example, Caucasian (Non-Hispanic).