Clinical Genomicist Workstation
Clinical Genomicist Workstation
Clinical Genomicist Workstation (CGW) is a secure, n-tiered application where web browser submits requests to application servers that persist the data in a relational database. CGW is used by Washington University Genomic and Pathology Services for clinical genomic testing of many cancers. CGW is a 'soup-to-nuts' solution to track, analyze, interpret, and report clinical genomic diagnostic tests.
Sharma MK, Phillips J, Agarwal S, Wiggins WS, Shrivastava S, Koul SB, Bhattacharjee M, Houchins CD, Kalakota RR, George B, Meyer RR, Spencer DH, Lockwood CM, Nguyen TT, Duncavage EJ, Al-Kateb H, Cottrell CE, Godala S, Lokineni R, Sawant SM, Chatti V, Surampudi S, Sunkishala RR, Darbha R, Macharla S, Milbrandt JD, Virgin HW, Mitra RD, Head RD, Kulkarni S, Bredemeyer A, Pfeifer JD, Seibert K, Nagarajan R.
AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:156-7. eCollection 2013.
Per the request of our customers, Labii ELN & LIMS has developed many widgets to perform CGW analysis directly with Labii interface. CGW widgets is developed to create accessions for new cases, create new sequencing runs for cases, upload appropriate data files (VCF/BAM files) for a given sequencing run, begin bioinformatics jobs for generating a pharmacogenomic report, and retrieve reports in pdf format after they have been signed off on by an accredited individual.
Widgets can take full advantages of Labii LIMS (Laboratory Information Management System) to provide sample specific metadata. Labii widgets simplified the usage of CGW with just a few clicks and enabled the documentation of all analysis process.
Notes: These widgets are private to a certain customer(s) only.
Labii ELN & LIMS currently provides these widgets:
Here are some settings needed to be configured before starting using the widgets.
These metadata is required:
- CGW_INSTITUTION: your account username
- CGW_EMAIL: your email address to login
- CGW_PASSWORD: your password
- CGW_VERSION: v2.0.0
The samples and patients are stored in the tables. These tables are required:
- samples, to store specimen information
- patients, to store the patient information
- disease, to store disease code
- mass, to store the sample type code
Please create the tables with these settings:
The columns are used to store the attribution of a table.
No specific columns are required. However, the name field have to be:
[First Name] [Last Name]
Add a default section so that all new records will have the same section. The default section is only needed for samples:
- Job, use the widget of CGWJob
CGWCase is a widget to create or update a Case.
Click the edit icon and the widget shall collect all necessary information to create a case. Error message will be provided if certain data is missing.
Create a CGW Case
Click Create Case button to create a case. If successful, a case id will be stored for the column.
CGW Case ID
The detail of a case can be updated via update a case. To do that, click the edit icon, and then click the Update Case button.
If for some reason, you want to discard the case and redo the analysis. You can click Clear Case button and then create a new case.
A *.vcf file needs to be uploaded to initial the jobs. Use this widget to upload a *.vcf file. A case needs to be created first for this widget to work.
One or more CGW jobs can be created for one sample. Each section of CGWJob can create one job.
Before creating a CGW job, a CGW case need to be created and a *.vcf file need to be uploaded first.
Click Create a job button to create a job.
Create a CGW job
Once a job is created, the job id will be assigned to the job id.
Once a job is created, it can be canceled by clicking Cancel Job button.
Note: Currently, the CGW API to cancel job is not working.
Once a job is generated, the job will start running immediately. It will take around two hours to finish the CGW scripts.
You can use the button Check report to check if the report is complete. If it is complete, a report id will be assigned and you will have the option to download the report.
Once a report is completed, the report can be downloaded via clicking Download report button.
The report is generated in PDF format, and zipped in a package [Report Id].pdf.gz.
- 1.Add a new sample, fill in all necessary information.