Clinical Genomicist Workstation

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Overview
​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. 
​Clinical genomicist workstation.​
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.
PMID: 24303327
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:
Widget
Type
Description
​CGWCase​
Column
Create a CGW case
​CGWUploadFile​
Column
Upload analysis-related files
​CGWJob​
Section
Generate a job and report
Before starting
Here are some settings needed to be configured before starting using the widgets.
Metadata
CGW is account specific, your CGW authentication information needs to be provided and configured in the organization metadata (Settings -> Organization Detail -> Metadata).
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
Tables
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:
Name singular
Name plural
Description
Unique code
sample
samples
Specimen information
SP
patient
patients
Patient information
PA
disease
diseases
Disease code
DS
mass
masses
Sample type code
MS
Columns
The columns are used to store the attribution of a table. 
Samples:
Name
Description
Widget
Default Value
Is Required
dateAccessioned
​
Date
​
false
firstName
​
Text
​
false
lastName
​
Text
​
false
dateOfBirth
​
Date
​
false
datecollected
​
Date
​
false
dateReceived
​
Date
​
false
gender
​
Select
unknown
male
female
unspecified
other
ambiguous
not_applicable
false
race
​
Select
american_indian_or_alaska_native
asian
black_or_african_american
native_hawaiian_or_other_pacific_islander
not_reported
unknown
white
false
ethnicity
​
Select
hispanic_or_latino
not_hispanic_or_latino
not_reported
unknown
false
externalSpecimenId
​
Text
​
false
hl7SpecimenId
​
Text
​
false
studyIdentifier
​
Text
​
false
studySubjectIdentifier
​
Text
​
false
type
Sample Type
ForeignKey
MS
true
panelName
​
Text
​
false
sampleType
​
Select
patientcare
true
indication
​
Text
​
false
identified
​
Boolean
1
false
disease
​
ForeignKey
DS
false
Patients:
No specific columns are required. However, the name field have to be:
[First Name] [Last Name]
Disease:
Name
Widget
Default value
Is required
code
Number
​
TRUE
code_system
Text
SNOMED-CT
TRUE
Mass:
Name
Widget
Default value
Is required
code
Number
​
TRUE
code_system
Text
SNOMED-CT
TRUE
Default Sections
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
Import data
If you already have some data for samples, patients, disease, and/or mass, use Import function to import them first.
CGWCase
CGWCase is a widget to create or update a Case. 
Create 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
Update a case
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.
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Clear case data
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.
CGWUploadFile
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.
CGWUploadFile Interface
CGWJob
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.
Create a job
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.
Cancel a job
Once a job is created, it can be canceled by clicking Cancel Job button. 
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Note: Currently, the CGW API to cancel job is not working.
Check report
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.
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Download 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.
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CGW Workflow
To start a CGW analysis, please follow these steps. This workflow assumes you have configured everything in Before starting.
1.Add a new sample, fill in all necessary information.
2.​Create a new case from Case column.
3.​Upload a *.vcf file from Analysis related files column.
4.Add a new section with widget CGWJob (optional, such section will be created automatically if correctly configured in the default sections). 
5.​Create a new job.
6.​Check the report.
7.​Download the report.