A list of items that require some type of follow up. In Geneticist Assistant, an Action List can be created for coverage regions on the Coverage Regions tab or for variants on the Sample tab.

A user of Geneticist Assistant to whom all available privileges are automatically assigned. Both Administrator privileges and Staff status can be assigned to the same Administrator user.

One of the allowed modes for the BED File Builder tool. Includes all the exons from all the selected transcripts in the BED file.

Indicates that the variant at is not naturally present in the sample, but instead, it is formed by artificial means, such as during preparation of the sample; for example, a Sequencing artifact. A single default value, None, is supplied for artifact type. Additional values can be specified through the Add/Edit Object function in Geneticist Assistant.

The average number of aligned reads for a region. This value is reported for all panel regions on the Coverage Regions tab and the Coverage Regions sub-tab on the Panel Statistics tab. A minimum value for the status of a region to be classified as “Passed” can be set on the Quality Control tab of the Settings dialog box.

A BED file is a tab-delimited text file. A panel can be created from a BED file for use in Geneticist Assistant. Each row in the file contains a region of the reference that is to be used in Geneticist Assistant. At a minimum, the file contains the following information:

Refers to the chemistry that was used to prepare the samples for sequencing. Values can be specified through the Add/Edit Object function in Geneticist Assistant.

Found on the Variants tab. Displays information for the variant from the CIViC (Clinical Interpretations of Variants in Cancer) database.. See https://civicdb.org/home.

Contains the information for the reference that was used for aligning data and/or detecting variants. If the Geneticist Assistant client and server reside on the same computer, then you can set the Client Reference directory and the Server Reference directory to the same directory.

Found on the Variant tab. Displays the information for a variant from the ClinVar database. See http://www.ncbi.nlm.nih.gov/clinvar/intro/.

The number of base pairs after the end of a panel region to which the quality control settings must apply. The quality control settings are specified on the Quality Control tab of the Settings dialog box.

Indicates whether a panel region passed or failed the coverage settings that were set for the run. The status for every region in a panel is displayed on the Coverage Regions tab. Default values are Passed or Failed. Additional values can be specified through the Add/Edit Object function in Geneticist Assistant.

The minimum required coverage values that a panel region must meet, or it is flagged as failed region for a run. Thresholds can be set globally (applies to all panel regions in all runs) on the Quality Control tab on the Settings dialog box, or it can set on a per panel basis.

The number of base pairs before the start of a panel region to which the quality control settings must apply. The quality control settings are specified on the Quality Control tab of the Settings dialog box.

Contains only user-specified data.

Specifies not only the data that a Sample PDF report is to contain, but also the layout of the report. You build a custom report template in the Report Designer.

Found on the Variant tab. Displays the information from the dbNSFP database for a variant. See https://sites.google.com/site/jpopgen/dbNSFP.

Found on the Variant tab. Displays the information from the dbSNP database for a variant. See http://www.ncbi.nlm.nih.gov/SNP/get_html.cgi?whichHtml=overview.

The ethnicity (for example, Caucasian/Non-Hispanic) for a patient in your Geneticist Assistant database. Values can be specified through the Add/Edit Object function in Geneticist Assistant.

Found on the Variant tab. Displays the information for the variant from the Exome Aggregation Consortium database for selected global sequencing projects. See
http://exac.broadinstitute.org/.

Found on the Variant tab. Displays the information from the Exome Variant Server database for the NHLBI GO Exome Sequencing project for a variant. See
http://evs.gs.washington.edu/EVS/.

The default mode for the BED File Builder tool. Allows for the inclusion of the coding regions in the BED file, the untranslated regions, or both.

A display setting for sample variants’ reference alleles and observed alleles. Display the reference alleles and observed alleles based on the gene orientation. Set on the Variant Preferences tab for the Settings dialog box.

Found on the Variant tab. Displays information for the variant from the gnomAD (Genome Aggregation Database) database. See http://reusabledata.org/gnomad.html.

Two or more users considered a single unit for the purpose of applying the same permissions in a single step.

The minimum variant frequency for a variant to be considered heterozygous. Set on the Variant Preferences tab of the Settings dialog box. The default value is 20%.

The maximum variant frequency for a variant to be considered heterozygous. Set on the Variant Preferences tab of the Settings dialog box. The default value is 80%.

Refers to the instrument that was used to sequence the samples. Values can be specified through the Add/Edit Object function in Geneticist Assistant.

A description or explaining comment for a variant. A variant can have one or more single interpretations associated with it, or it can be part of a compound interpretation, which means that the interpretation describes or explains multiple variants.

Found on the Variant tab. Displays the information from the LOVD (Leiden Open Variation Database) for the variant. See http://www.lovd.nl/3.0/docs/.

The minimum coverage depth for a region. This value is reported for all panel regions on the Coverage Regions sub-tab on the Panel Statistics tab and the Coverage Regions tab. A minimum value for the status of a region to be classified as “Passed” can be set on the Quality Control tab of the Settings dialog box.

Holds a value or variable that can be applied for carrying out runs in Geneticist Assistant.

Found on the Variants tab. Displays the information for the variant from the OMIM (Online Mendelian Inheritance in Man) database. See http://www.omim.org/.

A collection of genomic regions that are targeted for a specific genomic test or study. Panels are added to Geneticist Assistant by providing a BED file that defines the targeted regions, known as panel regions. Each sample that is submitted in Geneticist Assistant is assigned to a specific panel.

Separately tracks the pathogenicities of variants that might be found in multiple panels. For example, the pathogenicity of a selected variant might be 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.

The regions that have been targeted for a specific panel/test as defined by the BED file that was used to create the panel.

The pathogenicity for a selected variant, which is the likelihood that the variant will cause a disease. Default values are Deleterious, Likely Deleterious, Unknown, Likely Benign, and Benign. Additional values can be specified through the Add/Edit Object function in Geneticist Assistant.

Indicates the status for changing the pathogenicity for a selected variant; for example, from Unknown to Benign. Default values are Pending and Confirmed. Additional values can be specified through the Add/Edit Object function in Geneticist Assistant.

Refers to an individual from whom a sample was taken. Any sample that is submitted to Geneticist Assistant can be associated with a patient.

The percent of a panel region that has reads aligned to it. This value is reported for all panel regions on the Coverage Regions sub-tab on the Panel Statistics tab and the Coverage Regions tab. A minimum value for the status of a region to be classified as “Passed” can be set on the Quality Control tab of the Settings dialog box.

The phenotype for a patient. Values can be specified through the Add/Edit Object function in Geneticist Assistant.

A tab-delimited text file that defines the specific transcript or isoform that is to be used for a gene. You can use different transcripts for different panels. The first column in the text file contains the gene name. The second column in the text file specifies the transcript by its nm_accession number.

The balance in forward and reverse oriented reads with the variant as reported in the VCF file.

Refers to loading a BAM file and a sorted VCF file or just a sorted VCF file into Geneticist Assistant for the purposes of importing a list of variants into the Geneticist Assistant database and/or reviewing a list of variants.

The status for a run. Default values are New, QC Passed, Reviewed, and Complete. Additional values can be specified through the Add/Edit Object function in Geneticist Assistant.

Two or more samples considered a single unit for the purpose of repeated processing over a period of time; for example, a group of control samples for which the coverage or variant frequency is to be tracked. Values can be specified through the Add/Edit Object function in Geneticist Assistant.

Various statistics that can be displayed for a sample group. Displayed on the Sample Variant Data sub-tab for the Sample tab.

The status for a sample. Default values are New, QC Passed, Reviewed, and Complete. Additional values can be specified through the Add/Edit Object function in Geneticist Assistant.

The directory on the Geneticist Assistant database server that hosts the reference files. If the Geneticist Assistant client and server reside on the same computer, then you can set the Client Reference directory and the Server Reference directory to the same directory.

A user who can log into the django web administrator site. The actions that the Staff user can carry out depend upon the permissions assigned to him/her. Both Administrator privileges and Staff status can be assigned to the same user.

A report that includes all the data that is displayed in a selected pane on a data tab, for example, the Samples pane on the Run tab. Six different standard reports are available in Geneticist Assistant—Run, Coverage Regions, Panel Statistics, Sample, Variant, and Action List.

A Geneticist Assistant user who has neither Administrator privileges nor Staff status.

Contains a fixed number of regions that are contained within a selected panel. To verify coverage for a smaller number of regions that are within the panel that has been selected for a run, you can use a subpanel.

Reference information and/or links to the appropriate websites that have been submitted to support the pathogenicity that is specified for a variant. Displayed in the Supporting Information pane on the Variant tab.

A column on the Sample Variant Data sub-tab on the Sample tab. Indicates whether the variant is Transition (Ti) or Transversion (Tv).

One of the allowed modes for the BED File Builder tool. Adds the full transcript, including introns, to the BED file.

A person who logs into Geneticist Assistant either to add and review content, or use Geneticist Assistant in a read-only capacity. Three types of users are available in Geneticist Assistant—an Administrator user, a Staff user, and a standard user.

The frequency at which a variant is detected in a sample. In Geneticist Assistant, any value< 1 is allowed, with 1 = 100%, 0.5 = 50%, and so on.

Determines how information about the variants is displayed in all the variant sub-tabs or panes in Geneticist Assistant. Set on the Variant Preferences tab for the Settings dialog box.

A person who can log in and submit information to the Geneticist Assistant customer portal.

Indicates whether the variant is heterozygous or homozygous. In Geneticist Assistant, the selected zygosity is based on the Zygosity settings that are specified on the Variant Preferences tab of the Settings dialog box.