Navigating to samples in Congenica¶
Routinely, samples should be accessed via the link provided in the Interpretation Portal. To find samples without the Interpretation Portal link, or review samples belonging to other GLHs as part of a WGS specialist interpretation service, select the appropriate project by clicking on the GLH name. The project names reflect the interpreting GLH, and cases are organised accordingly. Users can filter the list of projects by entering some or all of the project name in the free-text filter (Figure 3).
Info
In the GMS, it is possible to view all patient data, genetic data, patient reports and clinical background information, for patients belonging to other GLHs. Unrestricted GLH access is offered to facilitate the provision of WGS specialist interpretation services.
When a user has selected their project, they can scroll down to see the list of patients in this project. Users can search the list by entering text into the free text box (Figure 4). This filters the list by the entered text in any of the fields in the table. For example, a user could enter ‘Ready’ to show cases with status ‘Ready for review’. Refer to Sample Status Table for the list of relevant statuses.
Users can also search by SAP-ID, or Family / Referral ID (see Abbreviations for further details).
Users should click on the patient they wish to view. This will open the patient overview (Figure 5).
Note
Only samples with Lab IDs starting “LP” have been sequenced. Samples with ID starting “NR” have no sequence data available; only clinical data were provided for these individuals.
The Family Identifiers screen¶
When you click on a patient from the Project Page, this will open the Family Identifiers screen. This tab (not illustrated here) shows personally identifiable information about this patient from TOMs (Test Order and Management system), so that you can confirm the identity of the patient associated with the sample.
The Patient overview tab¶
The patient overview tab contains the patient data including clinical indication and panels applied to the case – this information is populated from the interpretation request sent to Congenica by Genomics England. This page will also contain the referral and patient ids.
The Family tab¶
In the “Family” tab, a pedigree is generated from the information in the Interpretation Request (Figure 6).
As per standard pedigree nomenclature, the proband is indicated with an arrow. The currently viewed patient is highlighted with a blue outline - to view the data for any other family member click on their lab number in the pedigree. The pedigree is constructed using Reported Sex.
For further information about the “Family tab”, please refer to the full Congenica user manual