Transcript Terminology for Personalized

Clinical terminology for
personalized medicine:
Deploying a common concept model for
SNOMED CT and LOINC Observables in
service of genomic medicine
James R. Campbell MD
W. Scott Campbell PhD
Departments of Internal Medicine and Pathology
University of Nebraska Medical Center
Observables Project Group and iPALM SIG; IHTSDO
Outline
 ONC terminology model for clinical Interoperability
 Terminology challenges created by Personalized
Medicine
 LOINC – SNOMED CT harmonized model for
observable entities
 Application of harmonized model to genomic
observables/findings
 Anatomic and molecular pathology project at
UNMC
 Deploying observables model extensions for
AP/MP:
 Ontology model application
 Content development
 Publication for comment and evaluation
ONC Terminology Model for Semantic
Interoperability
 Demographics: LOINC, HL7/OMB code set
 Social and medical history: SNOMED CT
 Problem list/encounter diagnoses: SNOMED CT /
ICD-10-CM
 Lab results (observables): Lab LOINC
 Physical findings: LOINC, SNOMED CT observables
 Medication orders: RxNORM, SNOMED CT
 Laboratory Orders: LOINC
 Immunizations: CVX, MVX
 Procedures: CPT, HCPCS
 Documents: LOINC
Office National Coordinator :
Objectives of Interoperability
Facilitate transitions of care
Promote free flow of results data
Engage patients and families in
managing their EHR
Support Public Health
Enhance clinical research within
Learning Healthcare Environment
Interoperable Learning Health
Ecosystem
Revolution in healthcare
 Sequencing of human genome has led to flood of
new observational data appearing in scientific
literature and now…clinical records
 Majority of this clinical data is unstructured and
not useful for decision support in the EHR or
clinical research
 NLP is a second best approach to re-use of this
data
 Understanding of genetic and molecular basis of
human disease now having impact on therapy
 Challenge for precision medicine - to have
sufficiently detailed molecular genetics
observations and diagnostic data for clinical care
and research
Limitations of ONC terminologies
Research community
 NCBI: Gene Ontology; HGNC; OMIM; Orphanet; Protein Ontology;
Cell ontology
Clinical community
 SNOMED CT:
– No concept model for subcellular anatomy or molecular
structure
– No concept model for Observable entity or molecular basis of
disease in Clinical findings
– Little content, all primitives
 LOINC 2.54:
– 1275 PCR; 1406 MOLGEN; 116 FISH; 1502 CELL MARKERS
– Concept model inadequate to fully define what is being result
– Provides only tag-level interoperability of molecular data
 No meaningful bridge joining genetic research findings with clinical
concept models
LOINC – SNOMED CT
Harmonization of
Observable entities
 2008 agreement between Regenstrief (RI) and
IHTSDO
https://loinc.org/collaboration/ihtsdo/agreement.pdf
– Extend and harmonize a shared concept model for
363787002|Observable entity|
– Map and instantiate LOINC parts in SNOMED CT
content
– Jointly publish expression data set defining (lab)
LOINC concepts within the harmonized concept
model
– Technology preview alpha January 2016
 What is needed to support clinical decision making and
research in molecular genetics is a unified domain
ontology for Observable entities spanning clinical and
research content including genomics
UNMC: Project for structured
encoding of AP/MP cancer reports
Objective: Detailed structured reporting of all
anatomic and molecular pathology
observations for all CAP synoptic cancer
worksheets (82 types of malignancies)
Proposal: Analyze detailed semantics of CAP
worksheets; apply harmonized concept model
to develop terminology requirements; deploy
as real-time structured reporting from
COPATH system interfaced to tissue biobank
and EPIC
Tooling: Nebraska Lexicon© extension
namespace; SNOWOWL authoring platform;
SNOMED CT International + US Extension +
Technology preview; ELK 0.4.1 DL classifier
Penciled into IHTSDO workplan for 2017
Observables Project:
Concept model draft
Development for AP:
Techniques and Properties
Expanded Techniques
272394005|Technique(qualifier value)|
extend the value set of LOINC parts for the
(optional) LOINC attribute of Method
Measurement properties
118598001|Measurement Property (qualifier
value)| extend the value set of LOINC parts for
attribute Property
Developments for MP:
Genes and proteins
Application to MP:
Genes and proteins
MP: Immunohistochemistry
Development for MP:
Datatypes requirements
Molecular Pathology Finding
Fully defining observations of sequence variants
Patient Condition
Terminology summary:
Colorectal and Breast Cancer
Observable Entity:
Domain Ontology Development
Issues with DL classification
across Lab Tech Preview
Testing of model has not extended to
permission to define existing grouper
concepts in SNOMED CT, ergo DL
classification not yet useful across all
subsets
LOINC often does not uniformly specify
methods and so techniques are sparsely
populated in tech preview; clinically useful
& understandable Domain Ontology
probably requires them
Domain Ontology:
Terminology Use Cases
Retrieve all colon cancer tissue specimens
which had BRAF gene testing (IHC or
sequencing)
Retrieve all breast cancer cases that
tested ER-, PR- and Her2/NeuIdentify all colon cancer cases with high
degree microsatellite instability by PCR or
absence of mismatch repair protein by IHC
Identify all cases with Stage IIIa non-small
cell lung cancer that had EGFR mutation
testing by any method
Questions:
What other use cases for clinical genomics
should drive the development or
application of the observables convergent
model?
Requirements for binding the evolving
science of genomics to the SNOMED CT /
LOINC clinical ontologies?