CP-2194 Add Specimen and Container Type to Preparation Template Status Letter Ballot Date of Last Update 2022/06/23 Person Assigned David Clunie Submitter Name IDC Submission Date 2021/11/20 Correction Number CP-2194 Log Summary: Add Specimen and Container Type to Preparation Template Name of Standard PS3.16, PS3.17 Rationale for Correction: The Specimen Preparation template does not specify either the Container Type or the Specimen Type of the sample, though the included Specimen Sampling template does specify the Parent Specimen Type. This information is useful to understand the scope of the Specimen Identifier. Add Container Type and Specimen Type as optional, specify the appropriate Context Groups for values, and update the example to include the new concepts. [Ed.Note: Incorporates changes from CP 2143 Correct code for microscope slide (final text incoprorated in 2022a).] Correction Wording: <informaltable rules="all" frame="box"> <tr> <td> <para><emphasis role="italic">Amend PS3.16 as follows, according to this pattern:</emphasis></para> </td> </tr> </informaltable> <section label="TID 8001" status="3" xml:id="sect_TID_8001"> <title>Specimen Preparation This Template describes a single specimen preparation step. Type: Extensible Order: Significant Root: No
Specimen Preparation
VT Concept Name VM Req Type Condition Value Set Constraint
1 TEXT EV (121041, DCM, "Specimen Identifier") 1 M
2 TEXT EV (111724, DCM, "Issuer of Specimen Identifier") 1 U
2a CODE DT (434711009, SCT, "Specimen container") 1 U B
2b CODE DT (371439000, SCT, "Specimen type") 1 U B
3 CODE EV (111701, DCM, "Processing type") 1 M D
4 DATETIME DT (111702, DCM, "DateTime of processing") 1 U
5 TEXT DT (111703, DCM, "Processing step description") 1 U
6 CODE DT (111703, DCM, "Processing step description") 1 U D
7 CODE DT (17636008, SCT, "Specimen Collection") 1 MC IFF Row 3 Processing Type value is (17636008, SCT, "Specimen Collection") B
8 INCLUDE D 1 MC IFF Row 3 Processing Type value is (433465004, SCT, "Specimen Sampling")
9 INCLUDE D 1 MC IFF Row 3 Processing type value is (127790008, SCT, "Staining")
10 CODE DT (430864009, SCT, "Tissue Fixative") 1 U B
11 CODE DT (430863003, SCT, "Embedding medium") 1 U B
Content Item Descriptions Row 1 For sampling steps (which create a child specimen from a parent), the ID is that of the child specimen. For other preparation steps, the ID of a specimen does not change during the processing. Row 2 The issuer shall be formatted in accordance with the HL7v2 Hierarchic Designator Data Type. That format is [ Namespace ID]^[ Universal ID^ Universal ID Type], where Namespace IDidentifies an entity within the local namespace or domain, Universal IDis a universal or unique identifier for an entity, and Universal ID Typespecifies the standard format of the Universal ID (see HL7 v2 Section 2.A.33).
Specimen Sampling Type: Extensible Order: Significant Root: No
Specimen Sampling
VT Concept Name VM Req Type Condition Value Set Constraint
1 CODE DT (111704, DCM, "Sampling Method") 1 M B
2 TEXT DT (111705, DCM, "Parent Specimen Identifier") 1 M
3 TEXT DT (111706, DCM, "Issuer of Parent Specimen Identifier") 1 U
4 CODE DT (111707, DCM, "Parent specimen type") 1 M B
5 TEXT DT (111708, DCM, "Position Frame of Reference") 1 U
6 TEXT DT (111709, DCM, "Location of sampling site") 1 U
7 NUMERIC DT (111710, DCM, "Location of sampling site X offset") 1 U
8 NUMERIC DT (111711, DCM, "Location of sampling site Y offset") 1 U
9 NUMERIC DT (111712, DCM, "Location of sampling site Z offset") 1 U
10 IMAGE DT (111709, DCM, "Location of sampling site") 1 U
Content Item Descriptions Row 3 The Issuer of Specimen Identifier shall be formatted in accordance with the HL7 v2 Hierarchic Designator data type (see HL7 v2.6 Section 2.A.33), i.e., [ Namespace ID]^[ Universal ID^Universal ID Type] Row 5 Description of coordinate system and origin reference point on parent specimen or parent specimen container used for localizing the sampling site Rows 7-9 The X, Y and Z locations are used as needed to describe the sampling site; not all may be needed. E.g., resection from 10 cm along the colon may be described as only a Y dimension location. Row 10 Reference to image of parent specimen localizing the sampling site; may include referenced Presentation State object
Container Types Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20080626 UID: 1.2.840.10008.6.1.1043
Container Types
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 434464009 Tissue cassette A-0101E C0183953
SCT 434708008 Tissue microarray cassette A-01022 C2315967
SCT 434746001 Specimen vial A-01024 C2316421
SCT 433466003 Microscope slide A-0101B C0026017
SCT 434711009 Specimen container A-01023 C0183391
SCT 434533009 Electron microscopy grid A-01021 C2316945
SCT 434822004 Specimen well A-01025 C2316030
Anatomic Pathology Specimen Types Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20220115 UID: 1.2.840.10008.6.1.1045
Anatomic Pathology Specimen Types
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 38266002 Entire body T-D0010 C0229960
SCT 309050000 Body substance sample G-80A5 C0586522
SCT 309051001 Body fluid sample G-80A6 C1292527
SCT 119376003 Tissue specimen G-8300 C1292533
SCT 430861001 Gross specimen G-843A C2316367
SCT 430856003 Tissue section G-8439 C2316368
SCT 430970004 Core sample of tissue block G-843B C2316369
SCT 431196006 Tissue spot G-843C C2316370
SCT 1179252003 Slide
SCT 258433009 Smear sample G-803C C0444086
SCT 430855004 Touch preparation cytologic material T-1A404 C2316942
SCT 430346005 Liquid based cytologic material T-1A403 C2315942
SCT 119295008 Aspirate G-8003 C0370199
SCT 258562007 Genetic sample G-81A0 C0444241
Include
The SNOMED CT concepts for specimens rather than corresponding concepts for physical objects are used in this Context Group. (258661006, SCT, "Slide (specimen)") has been inactivated by SNOMED and replaced with (1179252003, SCT, "Slide submitted as specimen (specimen)".
Amend DICOM PS3.17 as follows:
One Specimen Per Container In normal clinical practice, when there is one specimen per container, the value of the specimen identifier and the value of the container identifier will be the same. In , each slide is prepared from a single tissue sample from a single block (cassette).
Sampling for one specimen per container
The example Specimen Preparation Sequence first describes the most recent processing of the slide (staining), then goes back to show its provenance. Notice that there is no sampling process for the slide described here; the LIS did not record the step of slicing of blocks into slides.
Specimen Preparation Sequence for Slide
Specimen Preparation Sequence - Item # Specimen Prep. Step Content Item Sequence - Item # Template / Row Value Type (0040,A040) Concept Name Code Sequence (0040,A043) Example Value Comments
1 1 8001 / 1 TEXT (121041, DCM, "Specimen Identifier") S07-100 A Part Collection in OR.
2 8001 / 2 TEXT (111724, DCM, "Issuer of Specimen Identifier") Case Medical Center
2a 8001 / 2a CODE (434711009, SCT, "Specimen container") (434711009, SCT, "Specimen container")
2b 8001 / 2b CODE (371439000, SCT, "Specimen type") (38866009, SCT, "Anatomic part")
3 8001 / 3 CODE (111701, DCM, "Processing type") (17636008, SCT, "Specimen collection")
4 8001 / 4 DATETIME (111702, DCM, "DateTime of processing") 200703230827
5 8001 / 5 TEXT (111703, DCM, "Processing step description") Taken
6 8001 / 8 8002 / 1 CODE (111704, DCM, "Sampling Method") (65801008, SCT, "Excision")
2 1 8001 / 1 TEXT (121041, DCM, "Specimen Identifier") S07-100 A Specimen received in Pathology department
2 8001 / 2 TEXT (111724, DCM, "Issuer of Specimen Identifier") Case Medical Center
2a 8001 / 2a CODE (434711009, SCT, "Specimen container") (434711009, SCT, "Specimen container")
2b 8001 / 2b CODE (371439000, SCT, "Specimen type") (38866009, SCT, "Anatomic part")
3 8001 / 3 CODE (111701, DCM, "Processing type") (428995007, SCT, "Specimen Receiving")
4 8001 / 4 DATETIME (111702, DCM, "DateTime of processing") 200703230943
3 1 8001 / 1 TEXT (121041, DCM, "Specimen Identifier") S07-100 A 5 Sampling to block
2 8001 / 2 TEXT (111724, DCM, "Issuer of Specimen Identifier") Case Medical Center
2a 8001 / 2a CODE (434711009, SCT, "Specimen container") (434464009, SCT, "Tissue cassette")
2b 8001 / 2b CODE (371439000, SCT, "Specimen type") (430861001, SCT, "Gross specimen")
3 8001 / 3 CODE (111701, DCM, "Processing type") (433465004, SCT, "Sampling of tissue specimen")
4 8001 / 5 TEXT (111703, DCM, "Processing step description") Block Creation
5 8001 / 8 8002 / 1 CODE (111704, DCM, "Sampling Method") (122459003, SCT, "Dissection")
6 8001 / 8 8002 / 2 TEXT (111705, DCM, "Parent Specimen Identifier") S07-100 A
7 8001 / 8 8002 / 3 TEXT (111706, DCM, "Issuer of Parent Specimen Identifier") Case Medical Center
8 8001 / 8 8002 / 4 CODE (111707, DCM, "Parent specimen type") (38866009, SCT, "Anatomic part")
9 8001 / 8 8002 / 6 TEXT (111709, DCM, "Location of sampling site") Mass This is coming from the summary of blocks field in the LIS
4 1 8001 / 1 TEXT (121041, DCM, "Specimen Identifier") S07-100 A 5 Block Processing
2 8001 / 2 TEXT (111724, DCM, "Issuer of Specimen Identifier") Case Medical Center
2a 8001 / 2a CODE (434711009, SCT, "Specimen container") (434464009, SCT, "Tissue cassette")
2b 8001 / 2b CODE (371439000, SCT, "Specimen type") (430861001, SCT, "Gross specimen")
3 8001 / 3 CODE (111701, DCM, "Processing type") (9265001, SCT, "Specimen Processing")
4 8001 / 4 DATETIME (111702, DCM, "DateTime of processing") 200703231900
5 8001 / 5 TEXT (111703, DCM, "Processing step description") Standard Block Processing (Formalin)
6 8001 / 10 CODE (430864009, SCT, "Tissue Fixative") (111095003, SCT, "Formalin")
5 1 8001 / 1 TEXT (121041, DCM, "Specimen Identifier") S07-100 A 5 Block embedding
2 8001 / 2 TEXT (111724, DCM, "Issuer of Specimen Identifier") Case Medical Center
2a 8001 / 2a CODE (434711009, SCT, "Specimen container") (434464009, SCT, "Tissue cassette")
2b 8001 / 2b CODE (371439000, SCT, "Specimen type") (430861001, SCT, "Gross specimen")
3 8001 / 3 CODE (111701, DCM, "Processing type") (9265001, SCT, "Specimen Processing")
4 8001 / 4 DATETIME (111702, DCM, "DateTime of processing") 200703240500
5 8001 / 5 TEXT (111703, DCM, "Processing step description") Embedding (paraffin)
6 8001 / 11 CODE (430863003, SCT, "Embedding medium") (255667006, SCT, "Paraffin")
6 1 8001 / 1 TEXT (121041, DCM, "Specimen Identifier") S07-100 A 5 1 Slide Staining
1a 8001 / 2a CODE (434711009, SCT, "Specimen container") (433466003, SCT, "Microscope slide")
1b 8001 / 2b CODE (371439000, SCT, "Specimen type") (1179252003, SCT, "Slide")
2 8001 / 3 CODE (111701, DCM, "Processing type") (127790008, SCT, "Staining")
3 8001 / 4 DATETIME (111702, DCM, "DateTime of processing") 200703240700
4 8001 / 9 8003 / 1 CODE (424361007, SCT, "Using substance") (12710003, SCT, "hematoxylin stain")
5 8001 / 9 8003 / 1 CODE (424361007, SCT, "Using substance") (36879007, SCT, "water soluble eosin stain")