# Presentation: 405262

## Laboratory Workflow Automation at Virginia Commonwealth University

- Andrea Ferreira-Gonzalez, Ph.D.
- Professor of Pathology
- Director, Molecular Diagnostics Laboratory
- Virginia Commonwealth University

## Admissions 	 	 > 31,000

**Patient Days****	****	****   171,751**
**Ave Daily Census        500**
-      ***Tertiary Care/ Level I Trauma****  *
**Outpatient Visits****	****> 500,000**
**Home Visits****	****  ****	****    19,760**
**ED Visits****	****	**** > 82,000**
**Faculty physicians       600**
**Medical Specialties  >  200**
**Staff members              >    6,000**
_**www.vcuhealth.org/about**_**/**

## Slide 3

## Molecular Diagnostics, VCU – October 2006

| Faculty | Administration | Techs |
| --- | --- | --- |
| Dr Richard McPherson, MD
Chair, Clinical Pathology | Edward William Payne
Lab Manager | Lidia Epp
L&R Specialist II |
| Dr. Andrea Ferreira-Gonzalez,  Ph.D.
Director | Maria Mikenna
Program Support Tech | Ming Lu
Med Tech Sr. |
| Dr. Catherine Dumur, Ph.D.
Assistant Professor
 | Irene Gonzalez
Database Manager
 | Luival Mulder
Med Tech, FISH |
|  | TDAC Cancer Genomics Project | Paula Anderson
Med Tech Sr. |
| Post Docs, Fellows, Residents | Julia Schuwn
Tissue Bank Coordinator | Mark Volkner
Med Tech Sr. |
| Fernanda Sabato, MS
Post Doc Associate | Tricia Beich
Tissue Bank Coordinator | Pam Morris
Med Tech Sr. |
| Dr. Amy Ladd, Ph.D.
Post Doc Associate |  | Claudester Miller
Med Tech Sr. |
| Sanghita Redy, M.D.
MGP Fellow | Practicum | Amy Jones
Med Tech Sr. |
| Patrik Vistaka, MD, PhD | Dhia McCarvage
L&R Specialist II | Ming Lu
Med Tech Sr |
| Space – 6,400 sq ft Total=> 4,000 sq ft Labs(2) + 2,400 sq ft Admin |  |  |

## Test Menu (VCU)

**FDA-Approved**
- HIV-1 Viral Load (Roche, MagnaPure-COBAS)
- HIV-1 Genotyping for Drug Resistance
- Her2-neu-  Fish
- Factor V Leiden  (Roche Diagnostics, MagnaPure- Lightcycler)
- FII Polymorphism (Roche Diagnostics MagnaPure- Lightcycler)
**Non FDA-approved**
**Manufacturer kit (RUO)**
- HCV viral load (Roche-MagnaPure-COBASTaq48 Real Time)
- HBV viral load (Roche-MagnaPure- COBAS Taq48 Real Time)
- HCV Genotyping (Third Wave)

## In house developed and ASRs
Infectious Disease
Quantitative BKV- Real Time PCR
Quantitative EBV- Real Time PCR
Quantitative CMV-Real Time PCR
HSV in CSF
Oncology/Hematology:
Quantitative t(9;22) Major Break Point Region- Real Time RT-PCR
Quantitative t(9;22) Minor Break Point Region- Real Time RT-PCR
Quantitative t(15;17)- Real Time RT-PCR
t(14;18) Nested PCR
B and T cell Gene Rearrangement: Southern-PCR
Bone Marrow Engraphment
Bone Marrow Engraphment- T cell enrichment
Human Genetics 
FRX: Southern and PCR-Fragment analysis in ABI 310
Beta 2 Adrenergic Receptor Genotyping (MagnaPure-Lightcycler)
Prader Willi/Angelman Syndrome: Met sensitive PCR
Conx 26  ( Sequencing) ABI 3100
Cystic Fibrosis (MagnaPure- ABI3100)
Human Identity (PCR Fragment analysis in ABI 3100)
Specimen Mix up
Paternity 

**Infectious Disease**
**Quantitative BKV- Real Time PCR**
**Quantitative EBV- Real Time PCR**
**Quantitative CMV-Real Time PCR**
**HSV in CSF**
**Oncology/Hematology:**
**Quantitative t(9;22) Major Break Point Region- Real Time RT-PCR**
**Quantitative t(9;22) Minor Break Point Region- Real Time RT-PCR**
**Quantitative t(15;17)- Real Time RT-PCR**
**t(14;18) Nested PCR**
**B and T cell Gene Rearrangement: Southern-PCR**
**Bone Marrow Engraphment**
**Bone Marrow Engraphment- T cell enrichment**
**Human Genetics**** **
**FRX: Southern and PCR-Fragment analysis in ABI 310**
**Beta 2 Adrenergic Receptor Genotyping (MagnaPure-Lightcycler)**
**Prader Willi/Angelman Syndrome: Met sensitive PCR**
**Conx 26  ( Sequencing) ABI 3100**
**Cystic Fibrosis (MagnaPure- ABI3100)**
**Human Identity (PCR Fragment analysis in ABI 3100)**
**Specimen Mix up**
**Paternity **

- Test Menu

## Molecular Diagnostics Test Volume/ Year

## Multi step process

**Multi step process**
**Need to keep track of specimen **
**through process **

- Flat file

- Flat file

**Macros-Excel**

**MDx Access **
**DBase**

**MDx Access **
**DBase**

**CERNER **
**PathNet**

**Cerner**
**Interface**

**CERNER **
**PathNet**

**Cerner**
**Interface**

- Flat file

- Flat File

- Flat File

## Factor V Leiden- SNP- Melting Curve Analysis

## Data Management: Access System with HL7 interface 

- Data Management: **Access System with HL7 interface **
** ****with Cerner Millenium for test order and blob text result**

## Slide 12

## Slide 13

## Millennium Helix

- Molecular Diagnostics Module
- Helix implementation
- -          Design
- o        Order catalog
- o        CBO content mapping
- -          New features:
**o**        **Scientific notation**
**o****        ****Flat file interfaces**

## Millennium HelixTM - 2007 Release

**CBO**
**Database w/ concepts**

**Enter Genetic**
**Findings**

**Protocols**

**Case **
**Integration**

**Cerner EMR**

**Millennium HelixTM**
**Laboratory**

**Worklist**

**Results**

**Instrument**

**Report**

**AP**

**Micro**

**Radiology**

**FSIs**

**Process**
**documentation**

**Discrete results**
**Numeric**
**Text**
**Interps**

**Template-based**
**Reporting**
**Import discrete**
**results**

**MDI (very**
**few devices **
**are enabled for MDIs)**

**Flat file**
**Export / import**

**Report**

- Helix Module
- Tools
- Protocol
- EGF
- Case Integration

## Clinical Bioinformatics OntologyTM (CBO)

- CBO is an ontology of biomedical concepts that catalogs human genes, gene variants, cytogenetic findings, and genomic concepts related to infectious organisms.
- Controlled medical terminology in computer-based systems to support clinical care through structured documentation and decision support.
- It provides a common representation for observations obtained in current clinical practice, and uses definitional relationships to reflect biological context.
- Opportunity to integrate data from research databases, clinical databases and to index content for information retrieval.

## CBO

- Inserted in Helix

## Slide 18

## Slide 19

## Slide 20

## Slide 21

## Slide 22

## Slide 23

## Slide 24

## Factor V Leiden

**CERNER **

- Flat File

- Flat File

**Millennium Helix**

**CERNER **

- Flat File

## Nomenclature

- Need for standardization of nomenclature
- CAP Mol Path Checklist and  JACHO
- _“__Include”_ standard nomenclature- HUGO
- both common and official names
- COX2 vs PTGS2
- HER2 vs ERBB2
- PubMed typed ERB2 got 8939 references.
- typed HER2  actually got 8240.
- When refined search to include "ERBB2 and Press", only 32 references.
- But, typed "HER2 and Press", got 132 references.
- all major journals should have a policy that HUGO official gene name be listed when the gene is first mentioned in the article, e.g. HER2 (ERBB2), E-cadherin (CDH1), beta-catenin (CTNNB1)

## Slide 27

## Acknowledgements

- VCU
- Greg Miller, PhD
- Mary Jo Taylor
- Irene Gonzalez
- Eddie Payne
- Mark Volkner
- Paula Anderson
- Pam Morris

- Cerner
- Mark Hoffman, PhD
- Rhea Osborn
- Kevin Power
- Scott Haven
- Ginger Kuhns
- Maki Moussavi