Information Model Requirements of Post-Coordinated SNOMED CT Expressions for Structured Pathology Reports

Information Model Requirements of Post-Coordinated SNOMED CT Expressions for Structured Pathology Reports W. Scott Campbell, Ph.D., MBA James R. Campbell, MD

Acknowledgements Steven H. Hinrichs, MD Chairman of UNMC Department of Pathology/Microbiology William W. West, MD Surgical Pathologist breast specialist, UNMC James C. McClay, MD Biomedical Informatics - UNMC

Overview Anatomic Pathology Process and Background Encoding the Microscopic Exam using SNOMED CT Management of Microscopic Exam Data

Anatomic Pathology Process Background

Anatomic Pathology Report Pre and Post Operative Information Gross Description Microscopic Exam Report Diagnostic Assessment Synoptic Report

Information Capture during the Microscopic Exam Fundamental point of information capture Primary point of cognition Frequently omitted in current pathology documentation practice Items recorded are not computable Loss of knowledge capture Lost opportunity for CDSS and administrative efficiency

The Need There is a need to capture microscopic exam findings in computable form Capture descriptive information of specimens for prognoses and discovery Terminology standards for Surgical Pathology. (C. Daniel and M. Garcia-Rojo)

SNOMED CT for Encoding the Microscopic Examination Investigated in Breast Needle Biopsies 24 Cases (13 Malignant and 11 Benign) Two pathologists reviewed cases by Whole Slide Imaging Areas of diagnostic importance outlined and annotated in pathologists own words Original pathology report reviewed and clinical statements extracted, inventoried

Microscopic Clinical Statements Documented Inventory of 95 lexically unique statements Attempted to encode each statement using SNOMED CT 2012 International Release Searched for pre-coordinated terms Developed post-coordinated terms when no precoordinated terms found Clinical Finding Definitional Expression Strict adherence to 2012 editorial rules Each definitional expression validated by examining pathologists for semantic correctness

Results Statement classification 69 conclusive or probabilistic in nature 26 descriptive in nature 73 unique post-coordinated expressions 1 pre-coordinated expression No valid SNOMED CT expression found for 34 statements 11 statements involved discrete, linear measurements. Conflated to a single coding deficiency Example: 385405004 linear extent of involvement of carcinoma in specimen obtained by needle biopsy 75% of stated expressions could be encoded

Clinical Finding Attribute-Value Hierarchies Used FINDING SITE ASSOCIATED MORPHOLOGY ASSOCIATED WITH CLINICAL FINDING SEVERITY FINDING METHOD SITUATION WITH EXPLICIT CONTEXT

Example Epithelial Hyperplasia

Role Groups - Atypical Hyperplasia

Example of Malignant Finding with Histologic Grade

Probability and Negation Situation with Explicit Context Focal Epithelial Hyperplasia without atypia

Storage and Utilization of Structured Microscopic Examination Data Specificity of data: Case, Specimen, Block, Slide, Stain, Method Management of CLINICAL FINDING Attribute-Value Pairs using postcoordination Bind findings to Digital Images and specific Regions of Interest (Annotations)

CLINICAL FINDING by Tissue Level Case Specimen A Specimen B Block A Block B Slide A1 Slide A2 Slide B1 Slide B2

Finding Attribute-Value Model

Slide Annotations

Information Model

Example Final Diagnosis: PROCEDURE: 432157003 Vacuum assisted biopsy of breast using ultrasound guidance (procedure) FINDING SITE: 73056007 Right breast structure (body structure) FINDING: DCIS solid growth pattern and high nuclear grade FINDING SITE: 31737007 structure of small lactiferous ducts ABNL MORPH: 128880009 ductal carcinoma in situ, solid type (morphologic abnormality) ASSOCIATED WITH: 369783007 ductal carcinoma in situ (DCIS) nuclear pleomorphism, grade 3: Markedly pleomorphic nuclei, usually >2.5 red blood cells diameters, with coarse chromatin and multiple nucleoli (finding) FINDING METHOD 1: 104210008 H&E stain method FINDING METHOD 2: 104157003 light microscopy FINDING METHOD 3: 52416005 histopathology test OTHER FINDINGS: Necrosis Microscopic Report Nodular Focus noted on slide A1 Initial H&E Abnormal epithelial cells and necrosis noted on slide A1 Initial H&E DCIS with possible invasion noted on slide A1 Initial H&E, high grade, solid growth pattern Microcalcifications noted on slide A1 Initial H&E Abnormal epithelial cells equivocal on p63 block A1 Abnormal epithelial cells equivocal on AE1/AE3 block A1

Data Tables for Exemplar - Necrosis

Conclusions SNOMED CT is a viable mechanism for documented the Microscopic Exam Additional concept definitions are needed Model of meaning enhancements: representation of numbers Data Model to support structured annotations Must handle SITUATIONS Role Groups Multiple attribute-value pairings Many-to-many relationship between findings and tissue level Contextual value sets

Future Directions Develop microscopic examination SNOMED CT local extension defining subset of anatomic pathology Bind Whole Slide Imaging modality with structured annotation data structure Development of contextual value set in a subset of anatomic pathology Bind structured microscopic exam information to structured anatomic pathology report and subsequent synoptic reports

Thank you