Pathology Specimen Use Case (Dav and Jim)
What is a Pathology specimen? How is Pathology specimen processed?
Some Pathology specimens are large. Some Pathology specimens are small.
A bowel is a large organ. Large specimens arriving at the Pathology laboratory are dissected into manageable parts and held in a variety of containers all of which need identifiers. Much of the bowel organ will eventually be discarded. What typically happens to a large tissue follows:
A large organ will be dissected into one or more sub-specimens that will be distributed into one or several cassettes. Each cassette will contain tissue part(s) from an identified location of the gross specimen (organ). The contents of each cassette are processed (dehydrated) and subsequently infused with paraffin to preserve the tissue structure and morphology. The processed tissues are then imbedded in a paraffin block for sectioning. The block is placed in a microtome and cut into ribbons or sections (generally 2-5 microns thick). The sections are placed on slides and fixed. The slides are then processed with a variety of stains or other procedures and are examined and classified by pathologists.
The processing steps described above require multiple tissue dissections, multiple containers, and separate processing and staining before the pathologists can begin to examine and classify the tissue. The tissue processing steps are summarized are:
- A case is created. A case (or accession) number is an identifier for the event of specimen(s) collection.
- Specimens received (example: 3 floating objects in one container, one with a tissue clip) (JTC: specimens may be fresh, fixed [in formalin] or in transport medium)
- Specimen gross observations recorded
- Specimen dissected into sub-specimens and placed in cassettes. (if fresh, typically placed in formalin at this step: preservative)
- Cassettes are processed in tissue processor (for several hours)
- Cassettes contents are embedded in paraffin (an additive? preservative)
- Paraffin blocks are microtomed into sections (ribbons or slices)
- Sections are fixed to microscope slides
- Microscope slides are processed by a variety of staining procedures
- Microscope slides are presented to Pathologists to interpret the tissue
The process of tissue sub-division is complicated. Tissues are subdivided onto multiple media or containers. Maintaining the relationships from patient to organ to tissues to part to slide requires detailed annotations and descriptions.
Smaller biopsies or tissues can be processed differently from large tissues. Several parts from small tissues are often are placed into a single cassette. This is because processing times are shorted for small biopsies. Different techniques are used to locate and identify the multiple parts of a small biopsy in a single cassette or block.
There are also occasions when staining of fresh (i.e. not processed) tissue is required. In these instances the tissues are quick frozen and imbedded in a special imbedding media and then sectioned at very low temperature (refrigerated microtome). The slides are then fixed in alcohol and stained.
The HL7 specimen model needs to accommodate multiple container types that may hold one or more parts of a biopsy specimen. Specimen and container identifiers need to be verified in the use case. The specimen use case also needs to accommodate multiple procedures performed on the dissected part of a single pathology specimen. Specimen archival requires persistent container identifiers. Both cassette blocks and liquid based cytology vials can be subsequently assayed by PCR and DNA procedures and the needs to find these specimens is emerging in the clinical laboratory.
