Difference between revisions of "Starting pathology (entire handbook)"

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The goal of this curriculum is to make a pathology trainee able to properly handle at least 95% of cases that are expected at an average general pathology department.  
 
The goal of this curriculum is to make a pathology trainee able to properly handle at least 95% of cases that are expected at an average general pathology department.  
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'''FROZEN SECTION CHAPTER'''
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'''Surprise frozen sections'''
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While most frozen sections can be predicted from schedules of the operating room and thereby be looked up beforehand, this chapter deals with the most common ones that do not offer such preparation time, thus indicating memorization of how to handle them.
 +
 +
(Gather most common situations.)
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 +
'''Other frozen sections'''
 +
 +
Although these are generally given on schedules of the operating room, any pathologist may end up suddenly covering for another one, and subsequently be presented with the frozen section case without having had the time to look it up beforehand.
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'''NON-EMERGENT PATHOLOGY'''
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Also largely a directory of external guidelines and databases.
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'''Non-emergent pathology questions'''
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FINDING GUIDELINES
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Which of the following situations does not have comprehensive guidelines available online?
 +
 +
INFECTIOUS DISEASES
 +
 +
Ask what are the main locations to look for infection in a specific autopsy case.
 +
 +
Provide algorithm of gram stain etc. and table of main bacteria by various locations.
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 +
'''Where to find information'''
 +
 +
INFORMATICS QUESTION
 +
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Provide genetic variant in long format.
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- Which database is the best to use to look up the pathogenicity of this variant?
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 +
 - ClinVar (correct)
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 +
 - gnomAD (population frequencies)
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 +
 - PolyPhen (likelihood of protein damaging)
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 +
 - PharmGKP (associated treatments)
 +
 +
- In ClinVar, what would you enter
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 +
 - A1708V (then BRCA1)
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'''Dealing with Internet denialists and their exams'''
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They take '''pride''' in for example memorizing the chromosome locations of even rare mutations, but when being called in for a frozen section of even relatively common specimens such as brain, lung or skin tissues, they may not know how to differentiate even the most common 90% of diagnoses.
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An Internet denialist who has memorized something may '''assume''' that pathology trainees should memorize it as well, and entire lectures may largely consist of rants of such items. In reality, when something is encountered and looked up something enough times, it will generally get memorized. It is generally more efficient to let time tell which situations will be common versus uncommon, rather than trying to memorize knowledge for even uncommon situations.
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Exam studying (as per Art of Procreation)
  
 
=Fixation=
 
=Fixation=

Revision as of 12:57, 15 May 2021

Contents

This curriculum contains the pertinent things a pathologist need to memorize, which can broadly be categorized into:

  • Emergent pathology, mostly relating to intraoperative or frozen section consultations. This includes information that usually cannot be timely looked up on the Internet when needed.
  • Main pitfalls: Most common and dangerous situations where a pathologist may not recognize the need to look something up further or ask a senior colleague.
  • Patterns and signs which can be seen grossly or under the microscope. It confers the ability to translate visuals into words that can be looked up if needed.
  • Knowledge of where to find information for various situations. It includes which person or which search engine is most useful for various clinical situations. Google is generally an appropriate search engine, but sometimes more specific or comprehensive databases are necessary, such as for example ClinVar to look up the pathogenicity of specific genetic variants. The chapter will include a directory of major databases and external guidelines, and how to use them.
  • Proficiency in diagnosing equivocal or borderline cases where readily available sources and evidence usually deal with discrete and specific disease entities and subcategories thereof.  Thus, in the question sections, many questions will be in the format of displaying readily available facts about diseases, including their typical immunohistochemistry patterns, but with equivocal or borderline case presentations.
  • Having an idea of one’s unknowns; being aware of unfamiliar fields. For example, a pathologist generally does not need in depth knowledge about cases that are generally sent out to specialized centers (such as pediatric musculoskeletal oncology), as long as that pathologist is aware of lack of knowledge in that field.
What you need to memorize.jpg
  • Dealing with Internet denialists and their exams. With the ease of access to pathology information on the Internet through smartphones and computers, those studying to for everyday practice as a pathologists should not spend time memorizing what can essentially always be conveniently and timely be looked up in times of need. The topics listed above are already immense enough to cover a lifetime of learning. Nevertheless, the path to pathology certification includes one or more exams, whose questions are largely made up of people who still do not acknowledge the access to the Internet in everyday pathology practice, and therefore this curriculum also includes this chapter.

Aim

Other doctors and even laypersons can look up diseases and conditions themselves, including pathology characteristics, without the need for a pathologist consultation, so the expertise of memorizing such readily available information is expendable.

In a world where diseases and conditions can readily be looked up, a major skill that distinguishes a pathologist from any person with Internet access is

Also, unusual or equivocal presentation of very common diseases and conditions are still generally more common than rare diseases, and constitutes a major workload in everyday pathology practice. Most textbooks still give disproportionately large room for rare diseases compared to such presentations. However, strive to master the common conditions (including the most common pitfalls) before diving into the uncommon. Specialists and subspecialists may already have learned the common conditions, at least in their subspecialty, and they will often distract you from this pursuit by presenting rare conditions to you, because that is now interesting to them, but do not spend excessive time or mental effort on such rare conditions.

The goal of this curriculum is to make a pathology trainee able to properly handle at least 95% of cases that are expected at an average general pathology department.

FROZEN SECTION CHAPTER

Surprise frozen sections

While most frozen sections can be predicted from schedules of the operating room and thereby be looked up beforehand, this chapter deals with the most common ones that do not offer such preparation time, thus indicating memorization of how to handle them.

(Gather most common situations.)

Other frozen sections

Although these are generally given on schedules of the operating room, any pathologist may end up suddenly covering for another one, and subsequently be presented with the frozen section case without having had the time to look it up beforehand.

NON-EMERGENT PATHOLOGY

Also largely a directory of external guidelines and databases.

Non-emergent pathology questions

FINDING GUIDELINES

Which of the following situations does not have comprehensive guidelines available online?

INFECTIOUS DISEASES

Ask what are the main locations to look for infection in a specific autopsy case.

Provide algorithm of gram stain etc. and table of main bacteria by various locations.

Where to find information

INFORMATICS QUESTION

Provide genetic variant in long format.

- Which database is the best to use to look up the pathogenicity of this variant?

 - ClinVar (correct)

 - gnomAD (population frequencies)

 - PolyPhen (likelihood of protein damaging)

 - PharmGKP (associated treatments)

- In ClinVar, what would you enter

 - A1708V (then BRCA1)

Dealing with Internet denialists and their exams

They take pride in for example memorizing the chromosome locations of even rare mutations, but when being called in for a frozen section of even relatively common specimens such as brain, lung or skin tissues, they may not know how to differentiate even the most common 90% of diagnoses.

An Internet denialist who has memorized something may assume that pathology trainees should memorize it as well, and entire lectures may largely consist of rants of such items. In reality, when something is encountered and looked up something enough times, it will generally get memorized. It is generally more efficient to let time tell which situations will be common versus uncommon, rather than trying to memorize knowledge for even uncommon situations.

Exam studying (as per Art of Procreation)

Fixation

Immersion

Adipose tissue with crumpling artifact due to insufficient fixation.

Within an hour after removal from the body,[1] tissue samples should generally be placed in vessels with enough fixative to allow them to lie freely in the solution.[2] The standard fixation fluid is generally 10% neutral buffered formalin, which is roughly equivalent to 4% formaldehyde.[3] The ratio of tissue:formalin should be 1:5[4] to 1:10[5].[5]

Duration

The duration depends on tissue thickness, where formalin will penetrate and fix the tissue at ~1 mm/hour.[6]

When not to use formalin

The main exceptions to using formalin are mainly: edit

  • Intraoperative consultation.  
  • Suspected crystals, such as a tophus or other specimen suspicious for gout versus pseudogout. These should be sent in alcohol or dry, since formalin will dissolve the crystals.
  • Suspected lymphoproliferative disorders, such as lymph nodes (or other lymphoid aggregates) with a suspicion of lymphoma, where samples are generally put in a special solution for flow cytometry.
  • Need for genetic testing, such as some cases of products of conception.
  • Cytology specimens, which are preferably sent fresh (such as in red top tubes) to be processed within a few hours. If processing may be after a few hours, put tubes on ice, or add 50% alcohol.[7]
  • Need for microbiology evaluation, mainly bacterial culture. For potentially infectious workups, check with the microbiology lab if they have the tissue they need before putting the specimen in formalin.
  • Need for immunofluorescence, such as immune complex-mediated disease, where specific preservation will give better test sensitivity.[8]

If you don't know, and if you cannot soon get in touch with anyone who can guide you, specimens can generally be stored in a fridge in the meantime, even overnight if it is late (but make sure to follow-up as soon as possible in the morning). Until then, don't put the specimen in formalin and don't freeze the specimen.


Selection and trimming

  1. REDIRECT Gross processing

Evaluation of tumors

  1. REDIRECT Evaluation of suspected malignancies

Reporting

Following are general notes on reporting in pathology.

  • Save your digital work frequently, and also before you leave a computer, even if you think you'll be back shortly. If you have many small specimens to write up in the same report, you may want to save every 2 to 3 specimens. It doesn't matter how much time and effort you spend on something if you're just going to let it disappear in the next glitch.
  • Double-check your report, especially if you copy-pasted and adapted a previous report rather than using a template with blank fields or making your report from scratch.

Components

Selection and trimming

From the stage of selection and trimming, a histopathology report should preferably include:

  • Case:
  • Patient identification and/or sample number
  • Type of tissue sample as described on container
  • Dimensions of original tissue[9]
  • Directions or other features of any inked surfaces.
  • Generally the weight of larger samples[9]
  • Dimensions of pathologic components[9]
  • Whether the entire specimen or representative sections were submitted.

Microscopic evaluation

  • Specimen chronology, often A, B, C, etc., at least where there are multiple specimens from the same case. With multiple specimens, preferably write out the chronology for all of them first, so that you don't miss reporting any of them later.
  • Specimen type and/or surgery type, such as "appendix, appendectomy", for clarification. This is not necessary at all departments. For the procedure, use the same term as the operating report whenever possible.
  • Microscopic description. This is not always necessary, but should be included if the diagnosis is uncertain. One systematic approach is to describe findings from largest to smallest ones. For example, a description of a tumor can start with the demarcation of the tumor, followed by texture, cell shapes, nucleus shapes and chromatin appearance.
  • Diagnosis or most probable diagnoses.
  • If the diagnosis does not clearly account for all conditions that were requested, suspected or asked to be ruled out by the referring clinician (such as stated on the requisition form), you need to classify the specimen as "positive for" versus "negative for" for each such condition, or give a reason for why an evaluation thereof could not be made.
  • In case of malignancy or suspected malignancy:
  • Depth or most distant invasion of malignant findings.[9] Depending on location, it may need to exclude important pathways, such as vascular, neural and/or through capsules or other layers.
  • Whether the resection is radical or not.

Depth

Factors supporting a relatively more comprehensive report, particularly in the inclusion of negated findings:

  • Lack of explanation from existing evidence. For example, an inflamed appendix that fits the medical history does not need detailed mention of harmless incidental findings.
  • Prospective review: If your report is likely to undergo double-reading by another pathologist before sign-out, it should either be more detailed, because the doctor who will do the double-reading then gets an idea of your thought process, including what you have looked for versus what may still need to be evaluated. If you know who will do the prospective review for a report of yours, you may alternatively convey your thought process by other means such as directly talking to that person.
  • Highly suspected locations, such as given from the referral.
  • Difficulty in obtaining the specimen, such as a CT-guided biopsy versus a skin shave.
  • Defensive precautions, which appears to be more common among doctors in the Unites States compared to for example Europe.[10][11]

Multiple instances of the same type of pathology (such as lung nodules) can often simply be reported as such, at least with a particular mention of the largest or the most severe example thereof.

Uncertainty

Words, from
most likely to
least likely
  • (is)
  • positive for
probably
likely
suggesting
suspicious for
possibly
(benign condition)
cannot be excluded
not likely
(malignant condition)
cannot be excluded
  • negative for
  • effectively ruling out

When something looks very much like a specific entity but you are not sure, preferably use "-like" (or when feasible, "-oid" such as squamoid for squamous-like cells).

When the clinical picture strongly favors a certain condition, and the pathology favors it as well, findings are generally described as "consistent with". Sometimes, "bordering on" can be described when the picture almost fits specified criteria of a specific diagnosis.

It is alright to consider the diagnosis of a pathology report to be a combination of the clinical picture and what can be seen on the specimen. For example, if the microscopy picture is uncertain, you may to a certain degree tend towards the diagnosis that best fits the clinical picture. However, mention differential diagnoses if they are still significantly possible, and would confer a different treatment or another substantially different consequence.

For both findings and diagnoses, is preferable to write "negative for..." rather than "no..." to emphasize the possibility of false negative findings.

Synoptic reports

For cancers, generally include a synoptic report, such as per College of American Pathologists (CAP) protocols at cap.org/protocols-and-guidelines. However, synoptic reports are generally not needed for tumor metastases.

Sizes

Whenever possible, give numerical quantities of sizes, rather than descriptions that are subjective (such as "small" or "large") or variable (such as "apple-sized").

Tailoring

The information contained in the reporting sections in this resource assume that the clinician has requested the exam for the topic at hand, but should still be tailored to any particular questions or requests by the clinician. Any relevant findings beyond the issues or questions raised by the clinician should also be mentioned.

As there are generally local practices about how to write reports, it is recommended to have either a personal or practice-specific repository of report templates that you can copy-paste for various cases. When doing so, however, use marks or empty spaces for relevant findings that are frequently changed in the template. Such marks should be conspicuous, so that the report clearly looks unfinished if you haven't tailored it to the case at hand (such as "...measuring _____."). Thereby, you avoid omissions or even wrongly entered information from templates.

The most important findings are preferably moved to near the top of the report if feasible.

Example of report format:

A. Organ, side/site, procedure:
  • Diagnosis 1.
  • Diagnosis 2.

Wording

If a certain grammatical rule has a risk of making the report less clear to the reader, ignore that rule in that situation.

Restrict acronyms/abbreviations to those who are certainly well known among all doctors, such as "cm".[note 1]

Generally describe what can be seen rather than processes (such as preferring "an abundance of" rather than "proliferation of").

If using a dictation device, avoid "no", and instead use "negative for" (and "positive for" in opposite cases), since there's a risk of "no" not being transcribed and thereby creating the opposite meaning.

Avoid "evidence of" unless you feel comfortable with the legal implications of its meaning in the report.

Whenever there is text needing formatting (text size, font type and/or UPPER vs lower case), it is generally most efficient to do it all at once after all the text is written.

Skin excisions

In skin cancers, use "peripheral" or "radial" margins (whereas "lateral" margin should be reserved for the margin opposite to the medial margin).[12]


Notes


References

  1. . Breast pathology grossing guidelines. UCLA Health. Retrieved on 2021-09-09.
  2. Katarzyna Lundmark, Krynitz, Ismini Vassilaki, Lena Mölne, Annika Ternesten Bratel. Handläggning av hudprover – provtagningsanvisningar, utskärningsprinciper och snittning (Handling of skin samples - Instructions for sampling, cutting and incision. KVAST (Swedish Society of Pathology). Retrieved on 2019-09-09.
  3. . Paraformaldehyde, Formadehyde and Formalin. Duke University. Retrieved on 2019-12-17.
  4. . Fixation of Tissues. Approval Date: August 2016, August 2020. Review Date: August 2024|website=Royal College of Pathologists of Australia
  5. 5.0 5.1 Buesa RJ, Peshkov MV (2012). "How much formalin is enough to fix tissues? ". Ann Diagn Pathol 16 (3): 202-9. doi:10.1016/j.anndiagpath.2011.12.003. PMID 22483550. Archived from the original. . 
  6. . How to Submit Tissues for Embedding. University of Pittsburgh, Starzl Transplantation Institute. Revised 04/19/21
  7. . How to send fluid and make good cytology slides. Tufts University.
  8. Mubarak M, Kazi Javed I, Kulsoom U, Ishaque M (2012). "Detection of immunoglobulins and complement components in formalin fixed and paraffin embedded renal biopsy material by immunoflourescence technique. ". J Nephropathol 1 (2): 91-100. doi:10.5812/nephropathol.7518. PMID 24475396. PMC: 3886135. Archived from the original. . 
  9. 9.0 9.1 9.2 9.3 . An Example of a Melanoma Pathology Report. Melanoma Foundation. Retrieved on 2019-09-24.
  10. Studdert D. M.; Mello M. M.; Sage W. M.; DesRoches C. M.; Peugh J.; Zapert K.; Brennan T. A. (2005). "Defensive medicine among high-risk specialist physicians in a volatile malpractice environment ". JAMA 293 (21): 2609–2617. doi:10.1001/jama.293.21.2609. PMID 15928282. 
  11. Steurer J.; Held U.; Schmidt M.; Gigerenzer G.; Tag B.; Bachmann L. M. (2009). "Legal concerns trigger PSA testing ". Journal of Evaluation in Clinical Practice 15 (2): 390–392. doi:10.1111/j.1365-2753.2008.01024.x. PMID 19335502. 
  12. David Slater, Paul Barrett. Standards and datasets for reporting cancers - Dataset for histopathological reporting of primary cutaneous basal cell carcinoma. The Royal College of Pathologists. February 2019


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