New Flexible Family Report

Charlene Son-Rigby -

The New Flexible Family Report page launches a new test and clinical report for a family of up to five members. The family members can be nuclear or extended family members of the proband that are either affected or unaffected. The Flexible Family test uses the VAAST algorithm to prioritize the most damaged genes and their disease-causing variants.

Navigation

You can reach the New Flexible Family Report page from:
-  Clinical Reports  >>  New Report  button  >>  Flexible Family option

Features

Enter Patient Accession ID
Providing an external identifier for the sample to link the genome to a patient in your LIS system is optional if a Genome is selected to launch the test.
Choose Assay Type- Optional
This dropdown menu allows you to specify an Assay Type defined in the Assay Type module. Selecting an Assay Type is not required to launch but allows you to enter Quality Control data for the test. 
Include COSMIC Evidence
For cancer samples click the checkbox to include COSMIC evidence into the test/clinical report.
Choose Panel - Optional
This dropdown menu contains all workspace panels defined the Panel Builder. When selecting an optional Panel only variants within the panel genes are included in the test. 
Choose Filter- Optional
Selecting an optional Filter will pre-filter the variants when the report launches. Filters are defined in the Filtering Protocols module and are typically used in conjunction with Panels. Only variants that pass the applied filter are included in the test.
Choose Project
Select the Project containing the genomes you want to test. Once the Project is selected the Proband selection will be displayed. 
Proband
The first family member is always the Proband with the status affected.
Sex
Select the Sex of the Proband. Setting Sex before selecting a genome will limit the available genomes to that sex or unspecified sex. Selecting a genome first will automatically set the Sex if Male or Female was specified during upload of the genome.
Select Genome
The Select Genome button will open the Select Genome for Family Member dialog box. 
Add Family Member
Click this button to add another family member. Up to 4 family member besides the Proband can be added to the test. For each additional family member a new row is displayed with these fields:
Select Relationship
Choose the relationship of this family member to the proband, Mother, Father, Sibling or Other. If Other is selected a text field appears to further specify the relationship.
Sex
Select the Sex of the Proband. Setting Sex before selecting a genome will limit the available genomes to that sex or unspecified sex. Selecting a genome first will automatically set the Sex if Male or Female was specified during upload of the genome.
Status
Specify whether the family member is affected or unaffected.
Select Genome
The Select Genome button will open the Select Genome for Family Member dialog box.
Save
Click Save to launch this report.
Cancel
Click Cancel to cancel this report.

Select Genome for Family Member

The Select Genome for Family Member dialog box allows you to choose a genome from any project in the workspace for the family member you added to the test. 

Choose Project
Select the Project containing the genome you want to add to the test. Once the project is selected the Genome selection will be display the list of available genomes in that project.
Genome
The list of all available genomes with a completed Variant Report are displayed excluding those already selected for other family members. If the Sex was already selected before opening the Select Genome for Family Member dialog box only genomes of that gender or genomes with unspecified gender are displayed.
Select
Click Select to confirm the genome selection for the family member.
Cancel
Click Cancel to cancel selecting a genome for the family member.

 

 

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