megan schmidt vice president of product management ... · compugroup medical . description: ... 10%...
Post on 04-Jun-2020
5 Views
Preview:
TRANSCRIPT
A01
COLA Resources, Inc. and COLA do not endorse, directly or indirectly, the presentations given at this conference or the products or services provided by the exhibiting vendors. Presentations are intended to be free of bias. The use of any particular product is for demonstration purposes only, and does not imply an endorsement of the product by the presenter or the sponsors of the symposium. © 2017 CRI
Molecular and Genetic Testing: How to Position your Laboratory for New Technology
Megan Schmidt Vice President of Product Management,
CompuGroup Medical
DESCRIPTION:
Molecular testing is transitioning from research to clinical laboratories. With this change, clinical laboratories are faced with new requirements and challenges to standardize, document and follow test procedures. Laboratories must also demonstrate end to end sample traceability and comply with CLIA and other accreditation organizations. This presentation will provide a basic background for clinical molecular testing, key examples of some of the challenges facing laboratories and the support provided by laboratory information systems with the management of data.
OBJECTIVES:
At the end of the session, participants will be able to:
Define molecular testing and its transition into the clinical laboratory.
Describe key examples of some of the challenges encountered in the clinical laboratory.
Recognize the functionality that Laboratory Information Systems provide to support molecular testing
Thursday April 6, 2017
Molecular and Genetic Testing:How to Position Your Laboratory for New Technology
Megan SchmidtVP Product Management CGM
This Presentation
DescriptionMolecular testing is transitioning from research to clinical laboratories. With this change, clinical laboratories are faced with new requirements and challenges to standardize, document and follow test procedures. Laboratories must also demonstrate end to end sample traceability and comply with CLIA and other accreditation organizations. This presentation will provide a basic background for clinical molecular testing, key examples of some of the challenges facing laboratories and the support provided by laboratory information systems with the management of data.
ObjectivesAt the end of the session participants will be able to:
Define molecular testing and its transition into the clinical laboratory
Describe key challenges encountered in the clinical laboratory
Recognize the functionality that LIS provides to support molecular testing
Agenda
Market
Definitions and Core Technology
Common Applications
Workflow
Challenges
LIS functionality
MARKET CHANGESTesting
Labs Opening
Oversight
Our Reality
U.S. healthcare organizations are coping with increasing pressure to contain costs
The laboratory must optimize testing, leverage information technology and improve productivity
Automation helps to achieve these goals, as does making the best use of your available laboratory resources
The Molecular Era
1980s
Assays for bacterial
ribosomal RNA
Adaptation of research
amplification assays for use in
clinical laboratories
Automated testing platforms and detection of amplified targets in “real‐time”
Today
Multiplex assays, partial/whole
genome sequencing assays and microarray
Molecular Market
Molecular testing is expanding…
• Molecular testing for Infectious Disease has been highly adopted in hospital clinical labs for years
• 2015 marketplace revenue estimates range from $9.1 billion ‐$9.7B 1
• In 2016, estimated 600 independent (non‐hospital) clinical laboratories offered some molecular testing 1
• In 2016, estimated 550‐800 clinical laboratories, hospital or independent, offer some next generation sequencing (NGS) 1
• Molecular Diagnostics testing market has estimated CAGR of 9‐10% through 2020 1
• NGS market is expected to grow at a CAGR of 20.8% 2
1. G2 US Clinical Laboratory and Pathology 2013‐20152. RNCOS
Oversight Interests
FDA
CLIA ‘88
Joint Commission (JCAHO/JCI)
College of American Pathologists
ISO15189
State Health Departments
Payers
DEFINITIONSDNA
PCR
Sequencing
The Double Helix
DNA is the hereditary material that is in humans and most other organisms.
Most of our DNA is located in the nucleus of our cells, packaged in chromosomes.
DNA consists of 4 nucleotides (A, T, C, G) repeated millions of times.
Specific sequences of those nucleotides are our genes.
Terminology‐ Genomics, Genetics, huh?
Genomics deals with entirety of an individual’s genetic infoGenetics can include the genome, but can also be more narrowly focused on a specific gene or mutation“Molecular”‐ is the term most often used to describe this work in a laboratory, as in Molecular Genetics or Molecular Pathology; testing leverages molecular attributes of DNA or RNA, such as electric charge, bonding affinity, size, etc.Cytogenetics and FISH are sometimes incorporated into Molecular laboratories and sometimes operate independently, but still rely on genetic principles for testing
Molecular Diagnostics (MDx)
An assay which works by detecting and classifying genetic material (DNA or RNA)
as opposed to:
• Immunological testing
• Chemistry testing
• Biochemical phenotype testing
• MDx market includes testing for genetic sequences using a variety of methodologies
• Nucleic acid assays —polymerase chain reactions (PCR), sequencing,
in site hybridization (FISH), microarrays, cytogenetics
• Genomic immunohistochemistry (IHC)— oncology
immunohistochemistry tests like estrogen receptor amplifications
We started with one copy and ended with 8 !!!
PCR‐ Exponential Duplication
C
A
C
G
A
C
G
A
C
G
A
C
C
G
A
C
C
G
A
C
C
Sequencing by Capillary Electrophoresis
Massive Parallel sequencing (high throughput)Next‐generation sequencing of partial or whole genomes is achieved by parallelizing the sequencing process, yielding thousands or even millions of overlapping sequences
An extremely sensitive pH meter to identify which nucleic acids are passing through the instrument
Next Generation Sequencing
COMMON APPLICATIONSPathogen Detection
Tumor Typing
Inherited Disorders
Applications for Molecular Diagnostics
Pathogen detection
Targeted genotyping• Inherited metabolic disorders
• Pharmacogenomics / Drug responsiveness
Cytogenetics
Oncology• Tumor classification
• Treatment monitoring
Identity tracking• Forensics
Human leukocyte antigen• Transplant matching
Detection of Targets by Multiplex PCR
Multiplex PCR involves amplification of many targets simultaneously in one reactionThe Luminex xTAG® assay detects the amplified targets by hybridization with probes bound to dyed microspheres
The microspheres are interrogated in a flow cytometer with dual lasers to identify the color dyes in each particle and the reporter dye attached to amplified targets
http://www.pri.wur.nl
Pathogen Detection by Microarray Testing
Thousands of DNA oligomer “capture probes” of known specificity are immobilized on the solid surface of a silicon chip Fluorescent dye‐labeled amplified targets hybridize to the “capture probes”, are washed, and then scanned with UV light to detect the resultant fluorescence
Infectious disease microarray testing is a molecular analog of culture in that hundreds or even thousands of pathogens can be sought simultaneously in a specimen
http://www.tessarae.com
Sequencing to Recognize Genes and Mutations
Targeted sequencing of single genes is used for phylogenetic studies and for detection of mutationsPathogenic microorganisms can be identified, virulence factors recognized and antibiotic resistance detected
http://upload.wikimedia.org
Cytogenetics
If our Genome was a set of encyclopedias
Each chromosomewould be a different volume or book
Cytogenetics testing assesses if you have all the necessary books and if you in fact got one copy of each book from each parent
Molecular versus Other Diagnostics
Traditional assays are being replaced with molecular techniques • PCR dominates market technology
• Sequencing expected to have most growth
Advantages:• High sensitivity
• High specificity
• Rapid assay design
• Easy automation
Disadvantages: • Risk of contamination
• Genotypic data /= phenotype
• Costs
WORKFLOWSPCR
NGS
Complex Workflows
Most Molecular‐based assays are heavily regulated and rely heavily on paper‐driven systems
Small volumes, small containers, and batching require calculations, tracking, and tray maps
Data often requires multiple interpretive steps
The industry is often research‐driven, which means instruments and assays are not initially suited for LIS incorporation
The Molecular Workflow
1. Build Tray Maps and Worklists 2. Perform Extractions 3. Prepare MasterMix in Clean Room
4. Add Patient Sample to MasterMix 5. Run PCR Amplification 6. Process Results
Workflow Example‐ PCR
LIS
Instrument Interface
Automation in Molecular Diagnostics
While automated testing is common in clinical chemistry and hematology, molecular testing remains primarily manual
A small number of automated “sample‐to‐result” testing platforms exist, but they are restricted primarily to diagnosis of a limited number of infectious diseases
What are lacking and are currently under development are integrated automated approaches to molecular diagnostic testing as we know it today
Genetics Workflow
Provider
Laboratory
Order Entry
Wet BenchWork
BioinformaticsAnnotation
Filtration andVariant Assessment
Reporting
Clinical Management/
Decision Support
CHALLENGESComplex Workflows
Regulatory Compliance
The Transition of Molecular Testing
From Research …
We determine what works best.
Each tech can change steps or reagents as needed.
What is a QC reagent and why would we need it?
We keep all records on paper.
… To Clinical Testing
Need to standardize, document and follow test procedures.
Should comply with regulatory performance standards.
Be prepared to demonstrate end‐to‐end sample traceability to an auditor.
Challenges Facing Genetics Labs
Complex workflows• Current molecular testing is manual, laborious and essentially non‐
standardized, interspersed with sophisticated instrumentation, leading to errors that impact patient safety
Shortages of highly‐skilled molecular diagnostics technologists exist in many parts of the world – there is a “graying” of the laboratory
workforce
• Big Data
• Large data sets that require bioinformatics
Interpretation• Results need interpretation, required acquisition and application of knowledge
• Multiple layers of result and report review
• CLIA / CAP compliance
• Lab‐developed tests are not provided by a manufacturer = more ownership of risk to lab
Challenges Facing Molecular Labs
Lack of integration• QC/QA performed outside of LIS
• Heavy dependence on paper records and Excel
• Instruments lack ASTM specifications > not interfaced > manual transcription of data
Inventory Management
• Multiple reagents and controls, some created in‐house
Multi‐well Plate Formats
• Many patients and controls in small containers
Areas for Concern or Failure
People do NOT do well working in multiple systems to do tasks they view as non‐essential
Preparing for inspection by backtracking through reports, sending piles of documents for signatures, etc.
Other issues• Slow workflow
• Opportunity for error
• Limits capacity from expanding to meet the projected demand for molecular testing
Goals
Reduce paper dependent systems
Incorporate daily tasks into standard workflow
Provide systems that track key performance indicators in real time and according to requirements
Lean strategies for laboratory testing call for greater reliance on automation to streamline this testing workflow
Strategies Being Employed
Not fully leveraging the power of the LIS
• Paper‐based Systems – Well thought out, but not scalable
• Homegrown Systems – High risk for supportability
• Research‐based LIMS – Lack patient‐centric view
• Limited use of the LIS – Orders and results only
Is operating outside the LIS the right solution?
• Stand‐alone orders, inventory or specimen management lacks integration
and analytics
• Molecular‐specific workflow not well supported
• Lack of Instrument interfaces
• Manual result entry is prone to clerical errors
• Use of excel and charts for traymap layout and calculations is laborious
• Non‐integrated reporting is inefficient
• Disparate documentation created from pre‐ to post‐ analytics
36
Concerns With Non‐LIS Solutions
LIS SUPPORTTraceability
Automation
Integration
Solution
Bring the molecular lab workflow into the clinical setting and into your LIS• Fully integrate your molecular workflow with the LIS
• Take advantage of existing LIS features and maintenance
• Integrate with HIS and other systems
Core LIS CapabilityBarcoding
Order interfaces to integrate lab work to reduce paper and manual transcription
Robust rules to drive actions ‐ combine or delete tests or orders; order additional tests; check for appropriateness of test; route orders based on patient insurance
Results review screen to make previous patient results available in tabular or graphical format
QC features to protect result quality: delta and normal range checking; highlight abnormal results; QC failures can block resulting from filing
Interface instrumentation to accept instrument outputs in various formats including Excel, ASCII, CSV
Biomarker and genetic results handled as discrete results
Use of panels and reflex testing ‐ each step with its own result, QC and decisions
Management Review of results and reports
Molecular LaboratoriesManage Complexity…
Reagent Management
Workflow Management
Plate Maps
Tracking
Workflow Management
Reagent Management
Workflow Management
Plate maps
Tracking
Inventory
Example: Inventory
Labs need to:
Track reagents
• Controls & non‐control inventory items
• Lots and shipments
• Receive/Expiration dates
Check availability
• Uses on hand
• Low balance alerts
• Quality Control Definitions
CONCLUSIONMolecular is a reality
Are you ready?
Leverage your LIS
Forecast
Careful thought must be given to the future when considering the expenditure of large amounts of money on technology
The laboratory of tomorrow will become increasingly dependent upon molecular approaches for diagnosing and managing patients with infectious and genetic diseases
Traditional testing will not disappear, but will become minor activities of the laboratory in the future
Projections for the Future
Automation of molecular testing will enable increasing numbers of laboratories
Molecular testing will become more standardized and amenable to Lean‐based improvement
LIS vendors will add the processing power, storage capacity and system flexibility to handle increasingly complex molecular testing
Considerations in Implementing Molecular
Ask Yourself…• Is molecular really needed for this purpose?
• Does the intended platform meet the need?
• What other assays of use could share this platform?
• What other platforms could also meet this need, and what are the pros and cons of each?
• Is there a likely soon emerging ‘disruptive technology’ in this space?
• Is it desirable to go with today’s technology, or can it wait a year?
• How can I leverage LIS to support my goals?
Conclusion
Molecular Diagnostics tools are powerful and increasingly essential
Molecular clinical diagnostics contribute to better health management
Many platforms and approaches can be used – due diligence to get best value and impact
Leverage your LIS
Questions?
Thank you for your time
top related