Clinical Genomicist Workstation

Clinical Genomicist Workstation

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
physicians		ForeignKeys	PA	false
accessionNumber		Text		false
case		CGWCase		false
lane		Number	1	false
barcode		Text		false
runType	This identifies whether the sequencing was done using paired end or single end.	Select	pairedEnd	false
analysis_related_files		CGWUploadFile		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.

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.

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.

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.

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.