WG 2 Informatics Standards in Pathology. Dr Christel DANIEL (IHE Anatomic Pathology co-chair) Jacques KLOSSA (DICOM WG26 co-chair) Bernd BLOBEL

Transcription

1 WG 2 Informatics Standards in Pathology Dr Christel DANIEL (IHE Anatomic Pathology co-chair) Jacques KLOSSA (DICOM WG26 co-chair) Bernd BLOBEL

2 Agenda Progress report of WG2 IHE/HL7 Anatomic Pathology DCIOM WG26 WG 2 Informatics Standards in Pathology meeting IHE Anatomic Pathology Structured Reports Extending the scope? Mapping PathLex to SNOMED CT Joint IHE AP/DICOM WG26 initiative Better use of DICOM in Anatomic Pathology workflow (DICOM Modality Work list)

3 Progress report of WG2 IHE AP : Overview Intra hospital integration profiles Anatomic Pathology Workflow (APW) Ordering and performing anatomic pathology examinations Community Anatomic Reporting for Public Health (ARPH) Sending anatomic pathology reports to public health organizations Anatomic Pathology Structured Report (APSR) Sharing/exchanging structured anatomic pathology reports as CDA documents

4 Organization of Anatomic Pathology Technical Framework Revision 2.0 July 23, 2010 Draft for Trial Implementation 2010 & 2011 Supplements for Trial Implementation

5 Anatomic Pathology Workflow (APW) Establishes the integrity of basic pathology data acquired for examinations being ordered for an identified patient Defines the actors and transactions involved in Ordering and reporting aspects of the workflow Order entry, report creation and transmission. Imaging aspects of the workflow Image acquisition, storage and distribution among multiple systems.

6 Anatomic Pathology Workflow (APW) Hospital Care Ward Anatomic Pathology Laboratory Image Mgmt Image Archive/ Image Manager (PACS) Order Placer Order Mgmt Acquisition Modality Order Filler Report Mgmt Order result tracker

7 APW actors & transactions

8 Anatomic Pathology Reporting to Public Health (ARPH) Joint initiative : IHE AP, HL7 AP, NAACCR (North American Association of Central Cancer Registries), CDC (Centers for Disease Control). Defines the actors and transactions involved in anatomic pathology reporting to public health organizations. Global Perspective of Cancer Surveillance International Association of Cancer Registries 241 Registries (Voting Member) from all 6 continents North American Association of Central Cancer Registries All Canadian Provinces All US States All US Territories and Jurisdictions

9 Anatomic Pathology Reporting to Public Health (ARPH) Hospital Care Ward Anatomic Pathology Laboratory Healthcare community Report Receiver Order Filler Report Sender Public Health Report Mgmt Clinics Report Sender Anatomic Pathology Laboratory

10 ARPH actors & transactions

11 Anatomic Pathology Structured Report (APSR) Just published for Trial implementation! Joint IHE and HL7 anatomic pathology initiative Content integration profile standardizing Anatomic Pathology Structured Report (APSR) using HL7 CDA APSR as CDA documents including Anatomic Pathology observations bound to images or regions of interest Shared or exchanged within a community of care providers using existing integration profiles defined by IHE Information Technology Infrastructure Unique opportunity to share/exchange Anatomic Pathology Structured Reports that are semantically interoperable at an international level

12 Scope APSR for surgical pathology 21 CDA templates Generic APSR template All fields of anatomic pathology (inflammatory, vascular, traumatic, metabolic diseases as well as cancer) 20 organ-specific cancer APSR templates Traditional anatomic pathology observation using light microscopy (including immunohistochemistry, FISH, etc) Further cycles Forensic (autopsy, toxicology) Special ancillary techniques (flow cytometry, cytogenetics, electronic microscopy) Research (TMA, etc)

13 Background From clinical document models Recent recommendations for required, preferred, and optional elements for any APR of surgical pathology, regardless of report types [Goldsmith 08] National initiatives Anatomic Pathology SR (Netherlands, Germany, Australasia) Cancer APSR US - CAP (College of American Pathologists) 67 cancer checklists and protocols (October 2009) France - SFP (French society of pathology) INCa (French National Cancer Institute) Minimum data sets for cancer APSR in 20 locations (85% of new cancers in France) (required by accrediting bodies) Australasia 6 templates for cancer APSR UK Royal college Goldsmith, J.D., et al., Reporting guidelines for clinical laboratory reports in surgical pathology. Arch Pathol Lab Med, (10): p

14 Background to IT templates Non healthcare IT standard CAP electronic Cancer Checklist Healthcare IT standard CEN archetypes Australia HL7 CDA Most reliable standard for clinical document templates Existing implementation guides for the APSR? Netherlands, Germany

15 Anatomic Pathology Structured Report (APSR) Hospital Care Ward Anatomic Pathology Laboratory Healthcare community Document Repository Order Filler Document Source Document sharing Clinics Document Source Anatomic Pathology Laboratory

16 APSR actors & transactions Content (Anatomic Pathology Structured Report) is created by a Content Creator consumed by a Content Consumer. Sharing or transmission of content from one actor to the other XDS, XDM and XDR Integration Profiles, described in Volume 3 of the Anatomic Pathology Technical Framework.

17 CDA Document Content Module (n=21) Any APSR CDA document content module is composed of a header and a structured body. 2 types of CDA Document Content Modules Generic APSR ( ) 20 organ-specific cancer APSR

18 CDA Section Content Modules (n=6)

19 CDA Entry Content Module (n=5) e.g Diagnosis entry Diagnoses on all specimens that are delivered to the pathology reported separatly Additional pathologic finding(s), results of ancillary studi(es) & images In case of cancer, this section includes the cancer checklists

20 Anatomic Pathology Observation [0..*] <value> (zero to many response) coded (code, coding system, version, display name) [0..*] <qualifier> (post coordinated expression) numeric (integer or real, unit) textual

21 The CDA Iceberg Pathologist/clinician sees Machine sees

22 The pathologist/clinician sees

23 The pathologist/clinician sees

24 The machine sees <ClinicalDocument xmlns='urn:hl7-org:v3'> <typeid extension="pocd_hd000040" root=" "/> <!-- conformance to a generic APSR content module --> <templateid root=' '/> <!-- conformance to a cancer APSR content module --> <templateid root=' '/> <!-- conformance to a breast cancer content module --> <templateid root=' '/>...remainder of the header not shown... <component> <structuredbody> <component> <section> <templateid root=' '/> <code code=' ' displayname= Pathology report relevant history' codesystem=' ' codesystemname='loinc'/> <title>relevant information provided by the ordering physician</title> <text> Tissue submitted: left breast biopsy and apical axillary tissue </text> <entry>... </entry> <component> <section> <templateid root=' '/> <code code=' ' displayname= Reason for referral codesystem=' ' codesystemname='loinc'/> <title>reason for anatomic pathology procedure</title> <text>breast mass - left breast</text> <entry>... </entry> </section> </component> <component>

25 Agenda Progress report of WG2 IHE/HL7 Anatomic Pathology DCIOM WG26 WG 2 Informatics Standards in Pathology meeting IHE Anatomic Pathology Structured Reports Extending the scope? Mapping PathLex to SNOMED CT Joint IHE AP/DICOM WG26 initiative Better use of DICOM in Anatomic Pathology workflow (DICOM Modality Work list)

26 Extending the scope of APSR?

27 Example of templates IHE-HL7 AP joint initiative 20 organ-specific AP structured reports templates (85% of incident cancers) 488 observations & procedure templates 27

28 IHTSDO

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30 IHTSDO Arbeitsgruppen Anesthesia Concept Model Education IHTSDO Workbench Developers Implementation International Family Practice/General Practice International Pathology & Laboratory Medicine Mapping Nursing Pharmacy Translation IHTSDO Projektgruppen Anatomy Model Collaborative Editing Roadmap Content Product Development Planning Event, Condition and Episode Model Family/General Practice Refset and ICPC Mapping IHTSDO Translation Tooling Machine & Human Readable Concept Model Mapping SNOMED CT to ICD-10 Migration Observable and Investigation Model Organism & Infectious Disease Model Request Submission Substance Hierarchy Redesign COST Translation Action IC0604 Quality -Assessment Belgrade, April 1st, 2011

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32 Mapping PathLex to SNOMED CT

33 AP observation (Coded Descriptor) Specific value set Breast-Specimen Collection Procedure (OID ) Value set OID: displayname Breast excision without wire-guided localization Breast excision with wire-guided localization Total mastectomy (including nipple and skin) CodeSystem: PathLex OID: Admitted exceptions : Unknown, Asked but unknown, Other

34 Mapping PathLex to SNOMED CT (using UMLS) PathLex Short label TNM No TNM UMLS Search EM/NM 1349 CUI Exact match SNOMED CT No CUI No SNOMED CT Split label No new tokens New tokens Partial match No CUI CUI SNOMED CT 3 4 Metamap SNOMED CT To be explored No SNOMED CT

35 Results of the automatic mapping process Matching situations Number of labels Percenta ges of labels Labels mapped to SNOMED CT through exact match (EM) or normalized match (NM) to UMLS % Labels mapped to another terminology through exact match (EM) or normalized match (NM) to UMLS 79 6% Tokens mapped to SNOMED CT through exact match (EM) or normalized match (NM) to UMLS % Tokens mapped to another terminology through exact match (EM) or normalized match (NM) to UMLS 25 2% Tokens without any match 80 6% Labels without any match and that cannot be split in tokens % TOTAL %

36 Examples of PathLex labels/expressions with automatic mappings Categories of observations PathLex label CUI SNOMED CT code Examples of AP macroscopic observation types related to the specimen Examples of AP microscopic observation types related to a lesion related to a lesion Specimen size, largest dimension C Specimen size, additional dimension C Lesion size, largest dimension C Lesion site C Histologic type C Histologic grade C Margins involvement C

37 No automatic match Types of ancillary techniques Types of histologic grades Extension Label HER2/neu (FISH method) Mismatch Repair Proteins-MLH1 (Immunohistochemistry Study) Histologic grade (Clark) Histologic grade (Gleason-Primary (Predominant) Pattern) Histologic grade (Gleason-Total Gleason Score) Number of lymph nodes with isolated tumor cells (< = 0.2 mm and < = 200 cells)

38 No automatic match Anatomic location Histologic types Label Anterior floor of mouth (qualifier : right, left, medial) Distal esophagus Atelectasis Extends to the hilar region but does not involve entire lung Atypical squamous cells for which a high-grade lesion cannot be excluded (ASC-H) Cirrhosis/severe fibrosis (Ishak score 5-6) (F1) Combined small cell carcinoma (small cell carcinoma and non-small cell component) Complex hyperplasia without cytologic atypia DCIS Comedo Ductal carcinoma in situ involving nipple skin (Paget disease) with microinvasion

39 No automatic match 3 9 Label Histologic grades FIGO grade 1 G1: Nuclei round, uniform, approximately 10 mm; nucleoli inconspicuous or absent Low-grade squamous intraepithelial lesion encompassing HPV infection or mild dysplasia (CIN 1) Score 2: 10% to 75% of tumor area forming glandular/tubular structures Extension <50% myometrial invasion Results of AP ancillary techniques Amplified (HER2 gene copy >6.0 or ratio >2.2) Equivocal (HER2 gene copy 4.0 to 6.0 or ratio 1.8 to 2.2) Immunoreactive tumor cells present (> = 1%) (Specify Quantitation) Mild to moderate (0-2 per high-power [X400] field) Intratumoral Lymphocytic Response (tumor-infiltrating lymphocytes)

40 Shall we map TNM to SNOMED CT? TNM values Label pm1c: Metastasis to all other visceral sites or distant metastasis at any site associated with an elevated serum lactic dehydrogenase (LDH) pn2: Metastasis in a single ipsilateral lymph node, more than 3 cm but not more than 6 cm in greatest dimension, or in multiple ipsilateral lymph nodes, none more than 6 cm in greatest dimension, or in bilateral or contralateral lymph nodes, none more than 6 cm in greatest dimension pt2a: Tumor greater than 3 cm, but 5 cm or less in greatest dimension surrounded by lung or visceral pleura, without bronchoscopic evidence of invasion more proximal than the lobar bronchus (ie, not in the main bronchus); or Tumor 5 cm or less in greatest dimension with any of the following features of extent: involves main bronchus, 2 cm or more distal to the carina; invades the visceral pleura; associated with atelectasi or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung

41 Better use of DICOM in Anatomic Pathology workflow DICOM Modality Work list

42 What is anatomic pathology? It is not radiology Order => report Imaging procedure step is optional Specimen-driven One study = one or more specimen (one or more patients) Slides always available Order => imaging procedure => report Patient driven One study = one patient

43 Modality Work list: Requested procedure, accession number & Study Order & Requested procedure The Order Filler translates the received Orders into Requested Procedure(s) identified by Order Filler Numbers and automatically assigns Study Accession Numbers Accession number <-> Order Filler Number The unique identifier assigned by the Pathology Information System of an Anatomic Pathology laboratory to an imaging Study. As expressed in DICOM Supplement 122: The concept of accession in Anatomic Pathology has been determined to be sufficiently equivalent to an accession in Radiology so that the existing Accession Number at the Study level may be reused for the same purpose and with essentially the existing definition. For Anatomic Pathology, like in Radiology, the Accession Number may correspond to the Order Filler Number, as specified in HL7 v2.x.

44 Modality Work list Procedure step & Series Procedure Step A Procedure Step ( Work Order Step ) is an atomic operation belonging to Requested Procedure, to be performed on one specimen by a single type of device (e.g. immune-histo-chemistry automaton, staining automaton, image acquisition modality). Some Procedure Steps are dedicated to image acquisition Series A subset of an imaging Study acquired from a single specimen by a single acquisition modality. Whenever an image is acquired from a new specimen or involves a new acquisition modality a new Series is created. A new series is also created when an image is acquired for an existing study after the original order has been fulfilled.

45 Modality Work list Requested procedures & procedure steps OR123: Lungectomy Study Case OrderFiller ID Accession Number = One Requested procedure DP07110: Lungectomy DP07110-A: Left upper lobe (gross image) DP07110-A-1: Frozen section, mass DP07110-A-1-1: FS DP07110-A-1-2: H&E DP07110-A-2: Entire mass DP07110-A-2-1: H&E (WSI) Order Series Two Two (imaging) procedure procedure steps steps

46 Modality Work list Requested procedures & procedure steps Order : AP examination of Breast biopsy Requested procedure : Imaging of AP examination of Breast biopsy (at the patient level) = ACCESSION NUMBER = OrderFiller ID (Imaging) procedure step: scanning Slide DP07110-A-5-1 (at the specimen/derived specimen level) Order : Mammography Requested (imaging) procedure : mammography (at the patient level) = ACCESSION NUMBER = OrderFiller ID

47 Modality Work list A mechanism defined to support the imaging workflow, by which the Pathology Information System provides the attributes of the imaging subject to modalities. In anatomic pathology, the imaging subject is a specimen derived from the patient. Query Modality Worklist: Based on a query entered at the Acquisition Modality, a modality worklist is generated listing all the items that satisfy the query. This list of Scheduled Procedure Steps with selected demographic information and information about specimen is returned to the Acquisition Modality. The Modality Worklist provides patient, order (study) and specimen identification and description to be included in the acquired images. The attributes of the Specimen Module have been defined in a Macro construct, and added to the Scheduled Procedure Step Module of Modality Worklist.

48 Modality Work list Requested procedures & procedure steps Order : AP examination of Breast biopsy Requested procedure Procedure step: scanning Slide DP07110-A-5-1 Worklist (attributes of the imaging subject) List of requested procedures (patient/study level) List of procedure steps (specimen/series level) Order : Mammography Requested (imaging) procedure : mammography Worklist (attributes of the imaging subject) List of requested procedures (patient/study level)

49 Modality Work list Specimen description DICOM Supp 122 : Robust new Specimen Module at image level of hierarchy Specimen short/detailed textual description Including specimen ancestry description in case of derived specimen In conformance with DICOM supp122, the short textual description of a specimen retrieved from the Order Filler is a concatenation of the short description of the specimen and all the short descriptions of the specimen ancestry Example : Whole Slide Image of DP07110-A-5-1 DP07110-A: Left upper lobe DP07110-A-5: Left upper lobe/tumor DP07110-A-5-1:H&E DP07110-A-5-1: Left upper lobe/tumor/h&e

50 More information Googlegroup : ihe-anatomic-pathologycommittee@googlegroups.com Road map logy