Innovation in the LIS:
Implications for Design, Procurement and Management
Ulysses J. Balis, M.D.
Director, Division of Pathology Informatics &
Director, Pathology Informatics Fellowship Program
Department of Pathology
University of Michigan
ulysses@med.umich.edu
Pathology Informatics 2012 Meeting:
October 9, 2012 Chicago Illinois
An Evolving Tension:
EHR vs. LIS
•
Thesis Statement:
– The contemporary stand-alone LIS model is being challenged by the reality of fullyintegrated primary vendor EHR solutions, which promise to provide functional
equivalence of the stand-alone LIS with the added benefits of:
•
•
•
•
•
•
Simplified enterprise complexity
Simplified deployment logistics
Reduced total cost of ownership
Simplified long-term stewardship of both software, hardware and data
Enhanced patient safety
Simplified Meaningful Use certification
• Justification:
– If the pathology -owned LIS can be justified as the correct place to house data
and workflow in the overall enterprise data model, Pathology will be allowed
to continue in its role of being elector and steward of such systems
Key LIS Innovation Areas to
Consider
• Enterprise Data Models and Support for High Dimensional
Data
• Shared Stewardship of Knowledge Management Systems
• Reverse federation in support of personalized medicine (bidirectional data feeds)
• Intrinsic support for customized workflow
– “Workflow Engines”
• Transition to zero knowledge interfaces (XML)
• LIS interoperability
• Digital Pathology Workflow
Lee Hood, IOM February 27, 2012
Challenge: Evolving the contemporary LIS will be critical to
staying current with the anticipated deluge of knowledge
management challenges facing the clinical laboratory
Population(s)
From: Athey and Omenn, 2010
The Clinical Laboratory Information System holds the potential to
be the “Information Commons” for all aspects of P4-assoicated
patient data.
George Poste,
IOM Feb. 28, 2012
Lee Hood IOM February 27, 2012
Five _____
Education
and Training
View
‘Omics Enhanced
William S. Dalton; Moffitt Cancer Center; IOM Feb. 27, 2012
Whole Genome Mapping and Variant Annotation Pipeline:
an EHR or LIS functional component?
Genome Mapping and Raw Output Pre-Processing
Input
Map
Algorithm 1
Output
Result 1
Output
Custom
Conversion
Script
Map
Algorithm 2
Output
Result 2
Output
Custom
Conversion
Script
Mapping
Algorithms
Pre-Processed
Variant Data
D. Wall, CBMI, HMS
PreProcessed
Data Custom
Conversion
Script
Standardization,
Annotation, and Summary
of Results
Standardized
Variant
Output File
Annotate
Variants and
Analyze
Quality and
Coverage
Mapping &
Annotation
Summary
Report
Finalized
Variant
Output
Files
(HGVS)
From WGA to Clinical Annotation: Possible
LIS workflow
Paired-end
WGA workup
sequencing
ordered
RNA-seq
Database
Oncogene/Tumor Suppressor
Detection
Validation
(FISH, RTPCR,
Sanger)
Validation
Gene
Expression
Treatment
Plan Prepared
Amplified CNV
Over-expressed
Deleterious, LOH
Variants Identified
FDA
Approved
On-Label
FDA
Approved
Off-Label
Clinical
Trial
Underway
Medical Impact Report
Generated
D. Wall, CBMI, HMS, Athey & Omenn
Global Presence of an LIS-centric world view at the enterprise level::
Education, Research, & Patient Care
Brian Athey
& ECRIT
1/11/11
Admissions
Clinical Scheduling
& Grading System
Education
IT Security
IT SERCUIRTY
Research Pre,
Post- Award
Bioinformatics
Research
Click
Administration
Commerce
Systems
(IRB)
Research
Proteomics
Core
Metabolomics
Facilities/
‘Omics’
Ctools/Saki 3
eThority
(billing)
Tissue
Biorepositories
Visiting Student
Application Service(VSAS)
M-Pathways
Collexis
ULAM
Education
Knowledge
Repository
Research
Administration
Data Warehouse
RedCAP
Populations
Research
Research &
BioDBX
Individuals
Data
Quality
Diseases
Velos
Management
Metrics
Systems
Data
Marts
Demographics
OpenClinica
Clinical
Quality
Analysis
Metrics
Database
Reporting
(CAD)
&
Peer
Others
Review
Others …
Registries
Research Data Warehouse
CareLink/
Eclipsys
Emergency Med.
Pharmacy
Cycle
Patient Care Revenue
Systems
Pathology
Legacy+/Epic EHR
Radiology
Scheduling
HIM/
Documentation
Others…
CDR
Epic Clarity
HSDW
Enterprise Federated Data Warehouse
CAD
Historical
SPORES
i2b2
Ambulatory
Data
Biomedical
Engineering
HIPAA/IRB Services (Honest Broker, DE-ID Consent Management, …)
Common Identifier Services
(Patient, Provider, Information
Research, Specimens,
Service-Oriented
BusExternal Mappings)
Vocabulary & Terminology Mapping Services (ICD-9/10 SNOMED, IMO, caDSR, ...)
Security
ITITSecurity
Campus Systems
Curriculum Eval.
System
Next-Gen
Sequencing
Portals / Providers, Payors, P. Health Databases / HIEs / NHIN
Comprehensive
Clinical Assessment Exam
Messaging Bus, ETL & External Collaboration Services (SOA, caGRID, SHRINE, ...)
Health
Sciences
Library
Resources
NIH-Specific &
External Data
Resources
(PubMed, GenBank,
KEGG, GO, etc.)
High
Performance
Cloud
Computing &
Data Storage
Bioinformatics and Systems
Biology Workbenches
• Reporting
• Visualization
• Analysis &
• Data Mining
Data Sharing
with External
Collaborators
International
Industry:
Pharma/
caBIG
I2b2/ CTSAs Biotech
TCGA SHRINE
Global Presence of an LIS-centric world view at the enterprise level::
Education, Research, & Patient Care
Education
Admissions
Clinical Scheduling
Metabolomics
BioDBX
Individuals
M-Pathways
Tissue
Biorepositories
Diseases
eThority
(billing)
Velos
Others…
Collexis
ULAM
CTools/Sakai 3
IT Security
IT SERCUIRTY
Campus Systems
Curriculum
Evaluation System
Education
Knowledge
Repository
Research
Administration
Data Warehouse
Populations
CIDSS
Analytics
& Reporting
Tools
OpenClinica
Demographics
Registries
Others …
Research Data Warehouse
i2b2
Historical
Data
Ambulatory
Emergency Med.
Pharmacy
Pathology
Revenue Cycle
Radiology
Scheduling
Centricity
Documentation
Others…
CDR
HSDW
CAD
SPORES
Others
CareLink/
Eclipsys
HIM
Security
ITITSecurity
Click
Commerce
(IRB)
Proteomics
RedCAP
Patient Care Systems
Legacy + Epic Epic EHR
Epic Clarity
Biomedical
Engineering
HIPAA/IRB Services (Honest Broker, De-ID Consent Management, …)
Common Identifier Services (Patient, Provider, Research, Specimens, External Mappings)
Vocabulary & Terminology Mapping Services (ICD-9/10 SNOMED, IMO, caDSR, ...)
Portals / Providers, Payors, P. Health Databases / HIEs / NHIN
Comprehensive
Clinical Assessment
Exam
Research
Research Core
AdministrationFacilities/‘Omics’
Quality
Systems
Metrics
Research &
Research
Reporting
Quality
Metrics
Data
Next-Gen
&
Management Data Marts
Sequencing
Research Pre,
Peer
Systems
Post- Award
Bioinformatics
Review
Brian Athey
& ECRIT
1/11/11
Messaging Bus, ETL & External Collaboration Services (SOA, caGRID, SHRINE, ...)
Health
Sciences
Library
Resources
NIH-Specific &
External Data
Resources
(PubMed, GenBank,
KEGG, GO, etc.)
High
Performance
Cloud
Computing &
Data Storage
Bioinformatics and Systems
Biology Workbenches
• Reporting
• Visualization
• Analysis &
• Data Mining
Data Sharing
with External
Collaborators
International
Industry:
Pharma/
caBIG
I2b2/ CTSAs Biotech
TCGA SHRINE
Concept: Reverse Federation
• Not only does the LIS serve the greater EHR
connectivity ecosystem, so to should the greater
plurality of EHR repositories serve the LIS and its
emerging workflow needs, in the capacity of decision
support data feeds assisting in report generation.
– Increasingly essential for:
• Molecular reporting
• Personalized medicine
• Synoptic cancer checklist reporting of correlation of
histopathology staging in concert with clinical stage and
longitudinal reporting (AJCC Cancer Staging Manual, 7th edition
and later…)
Concept: Complex data & Thiopurine Metabolite testing:
The emergence of Encoded Data
from primary lab test data
Comparing MLA to 6-TGN
Summary
• The future LIS will leverage:
– Enterprise Data Models and Support for High Dimensional
Data
– Shared Stewardship of Knowledge Management Systems
– Reverse federation in support of personalized medicine
(bi-directional data feeds)
– Intrinsic support for customized workflow
• “Workflow Engines”
– Transition to zero knowledge interfaces (XML)
– LIS interoperability
– Digital Pathology Workflow