Patologian tietosisältöjen yhtenäistäminen Suomessa. SNOMED CT Pathology project in Finland. Pekka Laurila, HUSLAB and Paula Kujala, THL SNOMED CT 2019 -seminaari (28.3.2019)

1. PATOLOGIAN TIETOSISÄLTÖJEN
YHTENÄISTÄMINEN SUOMESSA.
SNOMED CT PATHOLOGY PROJECT
IN FINLAND
Paula Kujala and Pekka Laurila
28.3.2019

2. PATHOLOGY
▪ Pathology is the study of disease
▪ Pathologist is a consultant to clinician
▪ Surgical pathology and cytopathology specimen make
over 99 % of the specimen in Finland, autopsies make
less than 1 %
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3. PATHOLOGY
▪ Process of specimen
▪ Reporting
▪ Snomed use at present
▪ SNOMED CT project
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4. PROCESS OF TISSUE SPECIMEN AND
INFORMATION IN PATHOLOGY LABS IN
FINLAND
▪ Request is transferred from patient reporting system to
pathology systems (Qpati, C5Lims)
▪ National classification for lab orders since 1980’s
(about 70 codes for pathology specimen):
6144 Ts-PDBrea (rinnan paksuneulabiopsian
histologinen tutkimus) for breast biopsy
6146 Br-PAD-4 (rinnan histologinen tutkimus, laaja
leikkauspreparaatti) for breast cancer specimen
removed in surgery (see next slide)
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5. Dissection of breast cancer specimen 6146 Br-PAD-4
Histologiaa blokista
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6. Histology from breast cancer specimen, scanned slide
tuumoripeti
ä

7. Breast cancer report in structured form (=”Synoptic Reporting”)

8. BREAST CANCER, REPORTING PROGNOSTIC
FACTORS IN STRUCTURED FORM
▪ Positiivisten ER-solujen prosenttiosuus: 0
▪ Positiivisten PgR-solujen prosenttiosuus: 0
▪ Proliferaatioindeksi (Ki-67 prosenttiosuus): 4
▪ HER2-IHC: 1+
▪ HER2 ISH-signaalisuhde: 1,12
▪ HER2-analyysin tulkinta (ISH): Negatiivinen
▪ Analyysiin käytetty blokki: 6
▪ → all this information is essential for selecting right patient treatment
AND in quality registers
▪ → not covered by traditoinal SNOMED II

9. SNOMED USE
▪ 1965 SNOP
▪ 1974 SNOMED
▪ 1979 SNOMED II
▪ 1993 SNOMED International 3.0
▪ 1995 SNOMED Microglossary of Signs and Symptoms
▪ 1993-98 SNOMED International versions 3.1-3.5
▪ 2002 First release of SNOMED CT
▪ 2007 All versions of SNOMED acquired by IHTSDO
▪ 2017 All SNOMED versions except SNOMED CT have been
formally deprecated by IHTSDO
Version used today

10. REPORTING DIAGNOSES USING
SNOMED II
Topography and Morphology: fairly uniform coding in laboratories
• Female breast, left (T04030): Carcinoma, infiltrating duct (M85003)
Prognostic factors: no uniform coding, even if some of the codes exist in
SNOMED II
• Female breast, left: ER neg/PR neg (M69901)
• Female breast, left: Her2 negative (DDISH) (M69900)
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11. PATHOLOGY REPORTING TO NATIONAL
CANCER REGISTRY AND QUALITY REGISTRIES
▪ All pathology labs send cancer case reports to National
Cancer Registry using electronic data exchange
▪ Some hospital districts send detailed cancer case reports to
regional quality registries (e.g. Helsinki)
▪ National quality register initiative aims to consolidate regional
quality registers
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12. NEED FOR SNOMED CT IN PATHOLOGY
▪ Harmonization of SNOMED use in pathology labs to be able
to compare the quality of diagnostics and treatment, both
nationally and internationally
▪ Need for syncronized update of codes in all laboratories
▪ Need for uniform data for research
▪ Need for uniform data for cancer registry, quality registries,
biobanks
▪ In 2017 all traditional SNOMED versions except SNOMED
CT were formally deprecated by IHTSDO
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13. SNOMED CT IN PATHOLOGY
▪ Pathology defined to be one of two applications in the Finnish
SNOMED CT launch
▪ Pathology SNOMED CT project started in August 2018
▪ Finland was accepted as IHTSDO member in November
2018
▪ Pathology SNOMED CT feasibility study (phase 1) will be
completed by the end of March 2019
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14. SNOMED CT IN PATHOLOGY,
WHAT WAS DONE DURING PHASE 1
▪ Analysis of present use of SNOMED II in 5 university hospitals
▪ Mapping Snomed II to SNOMED CT using NHS SNOMED II to SNOMED
CT mapping tables and SNOMED CT to ICD-O-3 mapping tables
▪ Initial plan was to find a ”ready-and tested” reference set from one of the
member countries – finally came up with NHS reference set for
histopathology (to be used as ”reference” – not directly copying it)
▪ Evaluating the needs for SNOMED CT coding for secondary use (National
Cancer Registry, biobank (cooperative), national and regional quality
registers
▪ Designing the structure and use of the SNOMED CT based reference set –
aiming also to maintain some level of backward ”compatibility”
▪ Work plan for the introduction of reference set to be used in Finland
▪ Collaboration with Swedish pathologists and SNOMED CT NRC in
Socialstyrelsen
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15. SNOMED CT IN PATHOLOGY,
RESULTS OF PHASE 1
▪ SNOMED II usage in the five university hospitals is fairly stable for general
codes of common diagnoses and topographies (M, T, D)
▪ Number of codes in active use is fairly low (3 241 / year 2017)
▪ Use of own/local codes for new terms, and use of synonyms and “non-
standard” attributes within the term are common
▪ The granularity of codes (e.g. the subtypes and/or grades of cancer,
specific locations) varies
▪ Languages used in terms are Finnish, Swedish, English, Latin
▪ NHS reference set was also evaluated, probably parts will be used as part
of the Finnish reference set
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16. SNOMED CT IN PATHOLOGY,
RESULTS OF PHASE 1
▪ Algorithmic mapping using NHS SNOMED II to SNOMED CT and “reverse mapping”
using IHTSDO to SNOMED CT produced “promising” results:
▪ Some errors in existing mappings, some cancer forms are not included in
ICD-O-3 mapping etc.
▪ In addition, there are quite a lot of agreeing on granularity of coding, how to
code certain concepts so that the data is truly harmonized between labs
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NO CT MAP YES CT MAP TOTAL
SNOMED II
AXIS N % N % N
D 26 14 % 162 86 % 188
M 545 28 % 1372 72 % 1917
T 85 7 % 1051 93 % 1136
TOTAL 656 20 % 2585 80 % 3241

17. SNOMED CT IN PATHOLOGY,
PLAN FOR PHASE 2
▪ Focus on M (morphologic abnormality), T (body structure), D (disorder)
categories
▪ Further evaluation of initial reference set including comparison with NHS
Reference set for histopathology
▪ Start with one university hospital, then continue to other four (lab by lab)
▪ Terms in English – may be later in Finnish incl other synonyms
▪ By-product: SNOMED CT coding of 1-3 synoptic reports (to be used as
templates for other patient groups)
▪ ICD-O-3 mapping from SNOMED CT Finnish Pathology refset
▪ Preparation of delivery package for SNOMED NRC FI
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18. SNOMED CT IN PATHOLOGY,
PLAN FOR PHASE 2
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TMD INPUTID SNOMED
CONCEPTID
SNOMED CT FULLY SPECIFIED NAME
M M80000 3898006Neoplasm, benign (morphologic abnormality)
M M80001 86251006Neoplasm, uncertain whether benign or malignant (morphologic abnormality)
M M80003 86049000Malignant neoplasm, primary (morphologic abnormality)
M M80006 14799000Neoplasm, metastatic (morphologic abnormality)
M M80009 6219000Neoplasm, malignant, uncertain whether primary or metastatic (morphologic abnormality)
M M80011 39577004Tumor cells, uncertain whether benign or malignant (morphologic abnormality)
M M80013 88400008Tumor cells, malignant (morphologic abnormality)
M M80102 68956006Carcinoma in situ, no International Classification of Diseases for Oncology subtype (morphologic abnormality)
M M80103 68453008Carcinoma, no subtype (morphologic abnormality)
M M80106 79282002Carcinoma, metastatic (morphologic abnormality)
M M80109 7010000Carcinomatosis (morphologic abnormality)
M M80123 22687000Large cell carcinoma (morphologic abnormality)
M M80133 128628002Large cell neuroendocrine carcinoma (morphologic abnormality)
M M80203 38549000Carcinoma, undifferentiated (morphologic abnormality)
M M80213 58248003Carcinoma, anaplastic (morphologic abnormality)
M M80223 16741004Pleomorphic carcinoma (morphologic abnormality)
M M80313 42596004Giant cell carcinoma (morphologic abnormality)
M M80323 65692009Spindle cell carcinoma (morphologic abnormality)
M M80400 128876004Tumorlet, benign (morphologic abnormality)
M M80401 72938002Tumorlet (morphologic abnormality)
M M80413 74364000Small cell carcinoma (morphologic abnormality)
Note: Table is for illustratory purposes only – algorithm generated from existing
SNOMED II usage data using mapping tables

19. THANK YOU!
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