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Pathology Report Use Case (John Gilbertson)

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HL-7 Anatomic Pathology SIG Use Case

Version 20061110 John Gilbertson MD

This storyboard documents the main components of a typical (and ideal) surgical pathology report. The purpose of the storyboard is to guide development of the CDA based anatomic pathology report model recently proposed by the Anatomic Pathology SIG.

Because the subject of is storyboard is a document, not a process, its structure will be different than most HL-7 storyboards.


During an office visit, Danny Dermatologist removed two suspicious looking moles from left arm and right upper back of Patty Patient. The resulting tissue were placed in two, formalin filled containers. One container was labeled with the patient’s name, her medical record number and the words “lesion, left arm” while the other was labeled with the patient’s name, her medical record number and the words “lesion, right upper back”. These (as well as a filled out requisition slip) were sent by courier to the Burning River Hospital Pathology Department’s Specimen Receiving desk.

At the Receiving Desk, Terry Technician accepted the containers and slip. Realizing the containers and requisition involved the same patient, surgeon and encounter, the two containers (and by extension their contents) were Accessioned into the Laboratory Information System as a single case or “Accession” with two different “Parts” (Part A for the “lesion, left arm” and Part B for the “lesion, right upper back”)

Terry Technician writes the accession number and the appropriate part letter on each container.

  • S06-1000 A
  • S06-1000 B

At the same time, Terry Technician (using the data on there requisition) entered into the LIS following information:

  • Surgeon’s name (Danny Dermatologist in our case)
  • Date and Time of receipt (of Sample/Containers)
  • Date and Time of surgical procedure (when Danny Dermatologist removed two moles)
  • Name of the Patient (Patty Patient)

Because Danny Dermatologist’s practice was at Burning River Hospital and because Patty Patient had previously registered in the hospital, Lab's LIS (through HL-7 interfaces with ADT system) was able to access more information about the physician (for example, Danny’s contact information) and the patient (for example, Patty’s address, insurance and primary care physician).

Finally, Terry Technician chose a “case type” and two “part types” from LIS dictionaries. These “types” are used by the LIS to define a wide range of processing, billing and reporting workflow parameters.

From the Receiving Desk, the two specimens in containers are passed to a Grossing Bench were they are examined by Roberta Resident. Roberta examines the requisition and each container (and contents). At this point, the Resident dictates a short clinical history (usually taken directly from the requisition): “During routine dermatology examination, two new, flat, hyper-pigmented lesions were identified on the arm and back. The patient has a history of “melanoma” five years prior. Lesions were removed by excisions biopsy”

In addition, the Roberta Resident documents the Pre and Post Operative Diagnosis (from the surgeon and taken from the requisition):

  • Pre operative Diagnosis: Rule out melanoma
  • Post operative Diagnosis: Rule out melanoma

Then the Roberta Resident:

  • Documents the gross appearance each “Part” of the case by (dictated) description and possibly by photography,
  • Dissects each specimen (Part) as necessary
  • As part of the dissection, some or all (or none) of each “Part” may be placed into containers for further (microscopic) examination. This may include 1) placing small sections into cassettes (labeled with the case number, part letter and cassette (or “block” ) letter, 2) creation of “touch preps” (slides touched against the specimen tissue so that cells adhere to the slide, 3) aspirations, 4) etc.

In this case, Roberta Resident dictates a description of Part A as follows: “Received in formalin and labeled with the patients name, medical record number and ‘lesion, left arm’ is an ellipse of tan skin measuring 2.0 x 1.0 x 0.3 cm. In the center of the ellipse, and not grossing involving any margins, is an irregular, dark, flat lesion. The specimen in bread loaved. The tips of the ellipse are submitted for histology in Block 1, the remainder of the specimen is submitted in five sections in Block 2.

Part B is handled in a similar way: “Received in formalin and labeled with the patients name, medical record number and ‘lesion, right upper back’ is an ellipse of tan skin measuring 2.2 x 1.0 x 0.3 cm. In the center of the ellipse, and not grossing involving any margins, is an irregular, dark, flat lesion measuring approximately 0.5 cm in greatest dimension. The specimen in bread loaved. The tips of the ellipse are submitted for histology in Block 1, the remainder of the specimen is submitted in six sections in Block 2.

Several things happen at this point:

The “gross dictation” is sent to transcription. The transcribed text is entered into the LIS, usually in a large free text field known as the “Gross Description Field” and the cassettes:

  • S06-1000 A 1
  • S06-1000 A 2
  • S06-1000 B 1
  • S00-1000 B 2

are sent to the histology lab where they are processed and made into paraffin blocks (one block per cassette). From each block one or more slides are cut, stained and labeled. The number of slides made per block, the type of stain used and other parameters are usually defined by the LIS “part type” (previously selected by Terry Technician), but this can changed by the resident or the histology techs. In this three slides are cut from each block and all are stained with H&E:

  • S06-1000 A 1 1 (H&E)
  • S06-1000 A 1 2 (H&E)
  • S06-1000 A 1 3 (H&E)
  • S06-1000 A 2 1 (H&E)
  • S06-1000 A 2 2 (H&E)
  • S06-1000 A 2 3 (H&E)
  • S06-1000 B 1 1 (H&E)
  • S06-1000 B 1 2 (H&E)
  • S06-1000 B 1 3 (H&E)
  • S06-1000 B 2 1 (H&E)
  • S06-1000 B 2 2 (H&E)
  • S06-1000 B 2 3 (H&E)

The next morning, Peter Pathologist is presented with a “preliminary” or “working” report on Case S06-1000 from the LIS system. The working report includes the “header” Information entered by Terry Technician (or taken from the ADT system), the Clinical History and Gross Description dictated by Roberta Resident, (any gross images available) and the “Histology Log” which documents the blocks, slides and stains that have been created on the case to the current point. Peter Pathologist is also presented with 12 slides (3 slides per block, 2 blocks per part, 2 parts in Case S06-1000).

Peter Pathology has many options when examining a case. He can ask for a consultation, he ask fo more slides or different stains, he could ask for molecular studies, etc. In this case, he simply writes his diagnosis:

Part A: Skin, Left Arm, Excisional Biopsy:
Compound melanocytic nevus with architectural disorder and mild to focally moderate cytologic atypia
Margins are free of nevus
Part B: Skin, Right Upper Back, Excisional Biopsy:
Malignant Melanoma, superficially invasive
Breslow’s Thickness: 0.33 mm
Clark’s Level: II
Superficial Spreading Type, Radial Growth Phase Present
Vertical Growth Phase Not Present
Surface Ulcer Not Present
Lymphoid Response at Base is Non-Brisk
Lymphoid Infiltration of Tumor is Mild/Minimal
Mitotic Rate: 0/10 HPF
Margins are Free of Melanoma
TNM Stage (AJCC 2002) = pT1a Nx Mx
“Comment: The lesion consists of an asymmetrical, poorly circumscribed lesion with pagetoid spread and horizontal bridging. While the lesion is predominantly in-situ disease, one focal area appears to be invasive. The lesion is completely excised. Dr Donna Dermatopathologist reviewed this case and concurs with the diagnosis.

There are some things to notice:

1. The diagnosis is presented by Part. The pathologist is communicating back to the surgeon using the one ‘structure’ that the two share – the original specimens presented to pathology by the surgeon.

2. In Part A, the report is written in free text, however in Part B, the report appears to be created through some type of structured data program. This particular program does not externalize the options and “valid values” available in the program, but other might (and should).

3. The diagnostic “Comment” is a common structure in pathology reports, it is a way for pathologists to expand on or temper the points made in the diagnostic text. Notice that the documentation of a second opinion is buried within the diagnostic comment.

After the diagnosis is written up, it is entered into the LIS, usually into a single “Final Diagnosis Field”.

Finally the pathologist reviews the report in the LIS and “signs the case out”, usually through a electronic signout option. In most cases, the final report would include:

  • A header region that state the case number, patient name, patient MRN, surgeon, primary MD, signout pathologist, procedure date, signout date, etc.
  • A Clinical History Field (vide supra)
  • A Gross Description Field (vide supra)
  • A Microscopic Description Field (not discussed in this use case, but essentially a free text description of the microscopic anatomy of each Part. Microscopic Descriptions are becoming less common
  • Histology Summary of Log (listing all slides and all Stains on all Parts)
  • A Final Diagnosis Field

That said, the numerous other fields that are possible in surgical pathology.

After signout, a report can still be changed. Minor changes are usually considered “addended” reports (for example, final confirmation of a special stain that does not change the clinical implications of the diagnosis). Major changes (such as from benign to malignant) which has clinical implications tend to be referred to as “amended” reports. While amended reports are rare, addended reports are becoming more common more auxiliary studies are being performed and there is increased pressure for lower reporting turn around times.


Case S06-1000 was a very simple case as far as reporting in concerned. However, it does demonstrate some basic principles of pathology reports including:

1. Like all medical documents, the pathology report has a header that included information on the patient, provider, encounter, etc.

2. Surgical Pathology Reports are “written” on a single case (which is based primarily on a single surgical encounter. However, pathology reports are “about” one or more primary specimens (called “parts”).

3. Surgical Pathology Reports are made up of multiple sections. These sections tend to relate to specific parts of the work flow (i.e. Clinical History, Grossing, Final Diagnosis, Frozen Section Diagnosis (Frozen section was not included in this case study). Different reports might use different sections depending on how the case was worked up (for example, S06-1000 did not have a Frozen Section section). Each section includes information on all of the primary specimens in the case, but the distinction between the primary specimens is vital in understand the report, but the distinction is not done structural, it is done largely in free text.

4. Each Section may observations made in Free Text and/or Structured Text (or both)

5. Each Surgical Pathology Cases are made up of one or more “Parts”. A Part corresponds to a discrete, labeled specimen received by pathology from surgery. As a case is worked up, a “Part” is often sub-sampled in to blocks, slides, etc. Pathology reports seldom discuss all of the process steps involved in processing a case, but they often include a section in which all the sub-sampling, processing and staining is summarized (for billing and interpretation purposes). However, in most systems today, this summation often fails to include important information. For example, a Histology Log section of a report may include the following line: Part A: Block 1: Slide 1 (Stain H&E), but it may not include the surgical description of the part (in this case “lesion, left arm”). To find that description, one needs to look at a different section of the pathology report (the Gross Description).

6. Reports have a life cycle and versions (working draft, final non-signed out, final signed out, addended, amended, etc)

7. Reports have multiple authors (in this case signed out pathologist and resident both contributed text to different sections of the report).

8. Different sections of the report have different value and power. The final diagnosis field is much more important than the gross description.

9. Important information is often “stuck” in free text. For example, the opinion of the dermatopathologist (in this case) was placed almost as a side note in the comment field.

Most importantly, the pathology report is a complex document:

1. The report is basically case (or encounter) centric

2. Like all medical documents, it identifies the patient, doctors, encounter, etc (usually in the headers).

3. However, the report really isn’t about the patient (or the encounter). It is about the analysis of one or more primary specimens (Parts).

4. However, the structure of the report (the way the report is handled in the LIS) is not on the basis of primary specimens but rather on the basis of “workflow based” sections like gross description, microscopic description and final diagnosis. There is only one “gross description” field in a pathology report no matter how many “parts” there are. The distinction between “parts” in a report field is done in free text. This is a major problem.

The CDA based needs to be able to handle all of above issues.