Starting pathology (entire handbook)

Author: Mikael Häggström

This is a handbook directed at new pathology trainees (mainly residents or trainees with medical doctor degrees or similar).

To get a printable version of this handbook, go to patholines.org, click Starting pathology (handbook), and click Printable version in the left hand menu. For best print results, use a color printer and color printer paper (or google a "copy shop" for a color print delivery or in-store pickup).

Contact

To contact the page creator/author, write a message to mikaelFile:Dot.svghaeggstroemFile:Arobaze.svgnuvancehealthFile:Dot.svgorg.

Please give feedback on any errors that you encounter in this resource, as well as pertinent omissions that you feel should be there. Preferably, contribute yourself: See the Contribute page at Patholines.org.

Learning pathology

The goal of this resource is to make a new pathology trainee able to properly handle at least 70% of cases that are expected at an average general pathology department, including the exclusion of the most pertinent differential diagnoses thereof. Its aim is to present you at least one way of doing things that is at least adequate for a particular situation. Still, there may be various routines at various locations, but adherence to these methods should not result in a worse reprimand from a senior than "although that was adequate, that is not how we do it here". Still ask for help whenever needed, such as first time you are doing something, or whenever you are not sure about what to do, especially when doing something potentially irreversible. When confronted with a question, until you are certain what to answer, rather say something in the line of "I'm not sure, but I'll find out and get back to you".

What a pathologist needs to memorize

The best method for memorization is generally through repeated exposure in everyday practice, and the scope thereof will depend on your eventual location and subspecialty, and you will eventually forget everything else, more or less. Yet, the following things are most important for a pathologist trainee to focus on memorizing:

• Emergency 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: The most common and dangerous situations where a pathologist may not recognize the need to look something up further or ask a senior colleague, or where a significant risk of diagnosis error remains after doing so.
• Interpretation of non-written results, including patterns and signs which can be seen grossly or under the microscope. It confers the ability to translate visuals and other more or less non-verbalizable information into words that can be looked up if needed, and conceive the most likely diagnoses based on both describable and more abstract appearances.
• Proficiency in diagnosing equivocal or borderline cases where readily available sources and evidence usually deal with discrete and specific disease entities and subcategories thereof. Unusual or equivocal presentations of very common diseases and conditions are still generally more common than rare diseases, and constitutes a major workload in everyday pathology practice. However, most textbooks still give disproportionately large room for rare diseases compared to such presentations. Nevertheless, strive to master the common conditions (including the most common pitfalls) first, and skip the uncommon in the meantime. After all, you will get by with effectively handling the regular cases wherever you work, so that when unfamiliar cases appear, you will have time to study or ask others for how to handle them, as long as you know your pitfalls, and have an idea about your unknowns:
• Having an idea of one’s unknowns; being aware of a lack of knowledge in unfamiliar fields. For example, a pathologist generally does not need in depth knowledge about diseases that are generally sent out to specialized centers (such as pediatric musculoskeletal oncology), but just enough to be able to suspect such diseases. In the same manner, a pathologist needs to have an idea of the optimal limits of practice, between what should optimally be handled personally by the pathologist and what is better handled by others, including senior colleagues, technicians, pathology assistants, junior colleagues and artificial intelligence.
• Where to find information for various situations. It includes which person or which search engine is most useful for various clinical situations. See the Using resources section below for further information. Similarly, a pathologist often needs to be efficient at finding what is relevant among a large amount of information, and be able to integrate it into a decision or a relatively short report. Experience in looking up information will eventually give you an idea of where to locate specifics that you haven't even seen before. For questions where a look-up does not readily give the answer, a new trainee usually gets satisfactory replies even from senior trainees, but the more experienced you get, the more you need to establish contacts with particular people, such as certain subspecialties, who are most likely to be able to answer your questions when needed.

The areas of these figures are not exact, but aim to give a rough overview of all information relating to pathology. This resource aims to cover the most important things you need to memorize as a first year pathology trainee.

• How to distinguish memorization-worthy versus look-up versus practically useless information. With the ease of access to pathology information on the Internet through smartphones and computers, those studying for the everyday practice as a pathologist should not waste time memorizing what can essentially always be conveniently and timely looked up when needed. This includes most of the content of books and web pages that are sorted by names of diseases and conditions, because if the name of a disease is already known, then it can relatively quickly be looked up when needed in such sources. When finding relevant look-up information on the Internet or local repositories, it is generally enough to remember enough of its related words in order to find it again. After all, other doctors and even laypersons can look up diseases and conditions themselves, without the need for a pathologist consultation, so the expertise of memorizing such readily available information is expendable. Similarly, electronic systems are better suited than the human brain for the storage and rapid retrieval of databases of for example immunohistochemistry and genetics results of various diseases. The topics listed in this section are already immense enough to cover a lifetime of learning. Learning pathology therefore optimally involves the memorization of where and how to find look-up information, rather than directly memorizing such information. Therefore, if you need to choose a textbook to study, then choose one that you will always be able to quickly reach through your smartphone whenever you need its look-up information. Accordingly, the final aim of this resource is to help pathology trainees to give accurate and clinically useful reports to clinicians, in synergy with the resources that are available in everyday pathology practice, and to establish routines to continue such practices. The intended end result is to help clinicians to improve the lives as much as possible to as many people as possible, even if it means forgoing the prestige of becoming a walking encyclopedia. After all, life is not a Trivial Pursuit game; Don't fill your brain with random facts, even pathology-related ones. Rather, use high-yield learning sources, for even if they may take longer time to find, you will be better prepared for real life than when you study low-yield knowledge. For instance, the optimal studying is generally not of diseases individually, but rather of patterns of signs and other findings and the likelihoods of each differential diagnosis thereof. Arguably the best method of acquiring such knowledge is to be involved in many real cases at a pathology department, making your own diagnostic thinking of them, and correcting your thinking based on how you differed from a senior's decision on the case. Real life experience also gives you a better idea of what is memorization-worthy versus look-up information in various resources. After real life experience, the next best resource is arguably to solve virtual cases such as found in pathology qbanks.
  As a general rule, the following factors makes a piece of information a look-up one:

File:Histopathology of fibromatosis-like metaplastic carcinoma.png

A potential pitfall: Fibromatosis-like metaplastic carcinoma of the breast (pictured) may look like benign fibromatosis. The gland-like components are a clue that it's in fact metaplastic carcinoma.

• The probability of realizing that you don't know it in situations where it makes a difference. For example, when being presented with a numerical test result and you do not know the normal reference range for it, you at least realize that there are reference ranges out there that you can look up to help you. Thus, reference ranges are generally look-up information. It is generally the opposite for pitfalls. For example, if a person thinks a breast nodule looks like benign fibromatosis but does not know (or does not consider) that fibromatosis-like metaplastic carcinoma (FLMBC) looks similar, the probability is relatively low that the person will look that up.
• The ease and speed of looking it up in reliable sources. Decisions with higher patient impact require more reliable sources. For example, the first forum answer from an anonymous user can be sufficient for an inconsequential decision, whereas information that may make a diagnosis benign versus malignant generally needs to be found on credible and peer reviewed sites.

• How to efficiently study for exams that contain questions that require direct memorization of look-up (or even practically useless) information, as long as such exams are in the way of practicing pathology. The best approach is arguably to spend enough time and effort on memorizing what is memorization-worthy, to the point where you will pass an exam even if you will fail multiple questions that require memorization of look-up or practically useless information. However, when starting pathology training, do not focus on studying for any final exams that are years away, because the content on such exams is systematically very different from what you need to know initially. For instance, you initially need to know how to handle the common types of cases, but exam makers on the other hand, in their effort to distinguish those who have studied more extensively than others, will systematically choose presentations that are not commonly encountered. Further information: Secrets Further exam advice is found in the Secrets chapter at patholines.org.

Type of information	Examples (usually)	Learning approach
Memorization-worthy	Emergent matters Pitfalls Interpretation of non-written results	Directly memorizing it.
Look-up	Textbooks and websites organized by names of diseases and conditions Immunohistochemistry results Associations between genetic mutations and diseases, and related molecular biology. Classifications such as cancer staging Large tables and diagrams Long lists	Knowing where to find it when needed, and how to use it.
Low-yield	Diseases individually	Instead studying patterns of findings and signs, and how they support various differential diagnoses.
Practically useless	History Most of scholarly articles Most clinical management	Avoiding, or skipping to potentially useful parts.

File:Cover to cover reading versus problem or project based learning.png

Example of problem/project based learning versus reading cover to cover. The problem/project based learner may memorize a smaller amount of total information due to spending time searching for the optimal material across various sources, but will likely learn more useful items for real world scenarios, and will likely be better at knowing where to find information when needed.

Whether any piece of information is useful versus useless depend mainly on:

• The likelihood of a situation where the information is useful.
• The benefit versus detriment of having versus not having the information at hand in such a situation.

The clinical management aspects that can be useful for pathologists to learn are the thresholds for pathologic findings that substantially change the clinical management, such as a cancer stage that determines whether clinicians will try to completely remove all tumors versus treat palliatively. With such knowledge, pathologists can put relatively more effort on the cases and parts thereof that make the most difference to the patient. Otherwise, clinical management knowledge is generally useless to a pathologist.

Lectures may be memorization-worthy depending on the content, but a lecture of look-up-information is practically useless unless you maintain a system to quickly retrieve the information when needed. Thus, sometimes, it is better to study something more memorization-worthy while pretending to listen to a lecturer.

Also keep in mind that pathology in our look-up era is mainly a processing work rather than a memorization one, since your most important skills are to interpret findings, and sometimes involve a vast amount of information in order to suggest the most likely diagnoses. Again, arguably the best method fur such purposes is solving real or virtual cases.

Using resources

This resource is written with the intention to teach you what to do in the most common situations you are expected to encounter during your first years of pathology training, at least until the point that you are usually fairly confident about what disease or condition you have at hand, because then you know what words to use to look it up in the vast literature out there. At that point, the fastest way to get more information is generally by Googling the disease or condition name, followed by pathology outlines (which is generally the most likely to quickly give you the information you need), since Internet will always be readily available in pathology. The most efficient method of studying to solve a case at hand is to not read articles in their entirety, but to scroll directly to the parts that are most likely to give you the information you need (generally past the first half of Pathology Outlines articles). A major skill of a pathologist is to have a good idea of what pages and texts can be skipped by only a quick glance.

Specific search methods for some specific purposes include the following (and the author has no financial or other conflicts of interests in mentioning any of these):

• Google, and then clicking the Images tab, if you just want to see more micrographs of the disease or condition. Even when you don't have a clue what condition you are looking at, you may find something that looks similar to your case by entering words you would use for the microscopic findings that you see.

• Adding cancer.net staging in Google searches for definitions of cancer stages, for example Googling prostate cancer cancer.net staging. The first search will then generally be the one from the American Society of Clinical Oncology.

• Googling "CAP synoptics" for guidelines for the most common cancer locations and types [1]. Don't google individual protocols, bypassing the overview list of protocols, as it may cause you to click on an outdated protocol.
• Considering a subscription for ImmunoQuery (or equivalent database if you find one) in order to generate the most pertinent immunohistochemistry stains when you have two or more differential diagnoses for a case at hand. It is not sufficient to just memorize a few usually positive or negative immunostains for each disease and condition, because what you need in reality is to figure out what immunostains to order so that you can pinpoint one diagnosis among your multiple differentials. To master that, you will need to memorize a vast amount of immunostains and at what percentages they are positive for a vast amount of diseases and conditions, or you can have an online service like ImmunoQuery do that work for you. After all, in pathology there is essentially no immunohistochemistry that is so emergent that you do not have the time to use a computer or smartphone to look it up.
• ClinVar to look up the pathogenicity of specific genetic variants/mutations.

If the above resources do not provide a sufficient answer, more general search tools are mainly:

• Googling what you are looking for. You may add the word pathology or equivalent if results are too clinical or layman-oriented. Before even reading the title of results, first look at the URL. If it is from a reputable organization then you may proceed to check if the title is pertinent to what you are looking for, but if it is from an unfamiliar site then you should only proceed if you don't find a better source among your search results. On such unfamiliar sites, you will need to look for additional proof of reliability such as authorship of the content in order to use it as part of any diagnostic decisions.
• ChatGPT is useful in answering specific questions, or generating texts with particular content or format. However, don't make significant diagnostic decisions based on its answers without first verifying it with reliable sources, as it might give a false answer despite appearing confident.

You can generally rely on online articles for presumably well-established topics (such as anatomy, and relatively common diseases). However, for potentially controversial and experimental topics, you generally need to ask yourself if the author has a conflict of interest before using its information for important decisions. In such cases, seek highly reliable sources, such as peer reviewed review articles, or professional organizations and societies. In contrast, beware of sites with flashy images, as it indicates a financial interest.

Ask a colleague at least whenever your own memory or a resource search is not enough, and there is a significant risk that you may do something irreversible that will negatively affect a patient.

Regarding lectures and knowledge your colleagues will tell you, make a judgment for each piece of information if it fits a criterion for memorization, or if it merits being written down somewhere you can find it so that you can look it up when needed.

Wikipedia often shows up among top Google results, and is generally accurate.

Whenever possible, use textbooks and other sources that you can quickly access online, because you will likely always be close to the Internet, but not always close to your collections of physical material. Keep in mind that for the vast majority of content, you only need to have a hunch of where to find it again when needed, or what search terms to use. If something may be difficult to find again, you may add it to a personal digital collection to be readily available in times you need it.

Strive for sources that, taken together, are comprehensive enough for the presentation at hand. For example, if you first look in a resource on only benign conditions that may cause your presentation, you generally need to look for another source that includes malignant conditions as well.

Generally skip any part that tries to explain a microscopic appearance using only words, since a Google image search is generally more useful.

Test question A 4 year old girl with a renal mass File:Histopathology of Wilms' tumor, original.jpg File:Histopathology of Wilms' tumor, annotated.jpg You are a new resident at a community hospital that is closely affiliated with a university hospital. The attending gives you a couple of slides from a case that is not yet signed out to preview and then come back with what you think would be the next steps. You are also told to share them with a med student who rotates at the department. One of the cases is from a kidney of a 4 year old girl. You look up the patient's history and she was admitted for orthopedic care for multiple fractures, and CT incidentally found a kidney tumor where workup was initiated as an inpatient. Microscopy shows the image at right. The med student has a smartphone and by googling "common kidney tumors in children", Wilms' tumor (also known as nephroblastoma) shows up as one of the top choices. You look up the condition on Pathology Outlines and the case seems to fit the microscopic description with its 3 typical components (second image at right). On the same web page you also quickly see the following pieces of look-up information: Risk classification systems, where for example "COG intermediate risk" requires favorable histology and no evidence of anaplasia. That there are no specific/diagnostic laboratory findings. A bunch of associated genetic changes (WT1 (11p13), CTNNB1 (3p22), IGF2 (11p15), TP53 (17p13), MYCN (2p24), and 1q gain). A bunch of associated immunohistochemistry results in the tumor, related non-neoplastic tissue, as well as in notable differential diagnoses (WT1, PAX8, vimentin, CD56, CD57, cytokeratins, EMA, desmin, cyclin D1, BCL2, CD34, myogenin, MyoD1, INI1, Glypican 3, AMACR, CK7, melanocytic markers (MelanA, HMB45), BRAF V600E, TFE3, TFEB, BCOR, and FLI1) Which of the following would be the best next step if you were to decide yourself? Diagnosing Wilms' tumor, COG intermediate risk, based on the shown microscopic view alone. Look at the complete blood count for diagnostic findings. Order genetic testing for WT1 (11p13), CTNNB1 (3p22), IGF2 (11p15), TP53 (17p13), MYCN (2p24), and 1q gain. Order immunohistochemistry for WT1, PAX8, vimentin, CD56, CD57, cytokeratins, EMA, desmin, cyclin D1, BCL2, CD34, myogenin, MyoD1, INI1, Glypican 3, AMACR, CK7, MelanA, HMB45, BRAF V600E, TFE3, TFEB, BCOR, and FLI1. Say "I don't know" and ask for help. Correct answer A major skill of a pathologist is having an idea of one’s unknowns. Furthermore, pediatric oncology is generally outside the limits of independent practice of any individual pathologist, generally requiring at least consultation with a colleague before diagnosis, classification and decisions about further workup (which in this case may be made at a pediatric oncology center). Thus, even if you though you knew how to proceed on your own, saying "I don't know" and asking for help is still the most correct as a new resident for a case like this. Incorrect answers You can skip reading these if you are already agree with the explanation above. Although the microscopic view that is shown is enough to diagnose Wilms' tumor, it is not enough to classify it as COG intermediate risk without first having looked at the entirety of the microscopy slides to exclude evidence of anaplasia. There are no specific/diagnostic laboratory findings of Wilms' tumor. A senior or specialist consultation would be needed in order to find out which genetic tests would actually be worth performing in this case, even after reviewing the history or asking a clinician for any suspected syndrome associated with Wilms' tumor. The choice of immunohistochemistry panels should be based on which ones most efficiently distinguish the possible differential diagnoses of the case at hand, and not just which ones are associated with the lead diagnosis. As with genetic testing, a senior or specialist consultation would be needed in order to find out which immunohistochemistry tests would actually be worth performing in this case. Further information: Immunohistochemistry

Using this resource

In this resource, it is recommended to read attentively until the end of the emergent pathology section. That part can be regarded as mainly describing concepts, which are relevant to read through and understand or at least consider. The rest will mainly provide guidelines for various situations, such as when you are presented with a biopsy of the gastrointestinal tract. Memorization-worthy information will generally be highlighted by: Memorization-worthy:, otherwise it is recommended to scroll quickly through such situation-based chapters, just to get an idea of what kind of information is available there, and then keeping this resource at a known location for whenever you are in that situation.

• Memorization-worthy: This resource is available open-access and ad-free by googling patholines and then Starting pathology (handbook).

This resource is aimed at presenting the most important knowledge that you will need when starting pathology. For further knowledge that you will need as a pathologist and any subspecialization, the best way is to learn from reality, by solving the cases and problems that get presented to you, and thereby look specifically for the information that you will need among the immense literature and other information that is out there.

Also, this resource assumes that you use additional sources when needed (such as The WHO Classification of Tumors or others in the Using resources above). Therefore, it will not simply repeat such information, but may display external links to further information.

This resource also assumes that you will ask a colleague for advise if you see an unfamiliar presentation, and any literature lookup thereof still does not explain it. Therefore, this resource will focus on the most common presentations and the main differential diagnoses thereof, which may include rare conditions if the clinical management thereof would be significantly different. On the other hand, this resource omits rare conditions that rarely look similar to common presentations. Therefore, keep in mind that there are many such rare conditions that you do not know about, so keep asking colleagues whenever a presentation remains strange to you, and choose initial workplaces where you have experienced people to ask if needed.

Be tolerant to encountering many repetitions of the same content in related articles, since for example a cervical biopsy and a cervical cone have similar microscopic evaluation.

Using AI "chatbots"

For AI "chatbots" (such as ChatGPT, Gemini or Copilot), you can generally trust a simple answer to a simple and presumably common question. More complex answers generally require you to provide more details together with your question. For example, a question of "what is the risk that this patient has..." would require you to provide a patient summary for a better answer, while avoiding identifiable information. Avoid leading prompts (such as "these features indicate invasiveness, right?") but rather keep them neutral and open-minded.

Using question banks

To test your knowledge on memorization-worthy information, seek questions that present you with a possible real life situation, as well as all pertinent information you can readily look up before needing to answer the question, so to ensure that it tests you on pertinent information as per the items earlier in this chapter. On the other hand, don't waste time on questions whose answer requires memorization of look-up or practically useless information (except if you want to practice looking up the answers online). There are about 5700 questions in PathPrimer, PathDojo, BoardVitals, and the ASCP Question Bank combined, so you can be picky about which questions to take and which ones to skip.

Consider the usefulness of each question before spending significant time memorizing its answers or explanations, in order to maximize the useful knowledge you will learn overall. Generally, skip questions that test you on look-up information and practically useless information. Whenever you have a question where you can not picture in what real life situation it would be relevant to remember, then you can generally assume that it never will be. For questions that consists of a useful item combined with a more useless one, only learn the the useful part and move on. The typical example of that combination is a memorization-worthy appearance of a disease, but then the question asks about a rather random fact that you can easily look up if you know the disease name. If you can, flag/mark questions on memorization-worthy information that you did not know, and move on fairly quick on those as well, and later revisit those questions specifically if you have the time, as repetition is generally more efficient than lingering.

A common sign that a question will deal with look-up or practically useless information is where it asks which of the alternatives is false or correct for one particular condition, and the alternatives are relatively heterogenous (such as one dealing with diagnosis and another one dealing with prognosis). The high prevalence of such questions is mainly because they are easy and quick create, because the question creator can simply look up a condition, choose some more or less random facts, and then change small details to create alternatives. It requires no real life experience in everyday pathology practice, and learning from such a question is hence generally not useful for that purpose either. The thought processes of real life pathology is generally the opposite of this, because you are generally presented with a specific location, gross appearance and microscopic appearance, and you need to practice on finding the most likely causative condition thereof among many differential diagnoses. Even other kinds of memorization-worthy pieces of information generally have a more limited scope among alternatives (like knowing the optimal staining duration in hematoxylin for a frozen section among alternative durations (see Emergent pathology). Thus, to practice your knowledge in memorization-worthy pathology, it is generally most efficient to skip false-versus-correct questions, in order to spend your limited time on something more worthwhile. Similarly, questions are in general rather low-yield whenever they deviate from the realistic direction.

Also, prefer succinct questions, that give you only the most relevant information in order to test the key learning point, without having to spend effort finding the most relevant information in long patient presentations, because you will get enough practice of that in everyday scrolling through patient charts.

If you have gone through all 5000 questions of the main question banks, and still have plenty of time for a second round, then you may work on lower yield questions as well. For example, you may practice on looking up answers for look-up questions, unless the presentation makes it clear that you cannot timely and conveniently do so (such as being in a rush during a frozen section).

Test question A question on a question You want to practice your memorization-worthy knowledge in real life pathology and not for exams (Further information: Secrets 'as per the Secrets chapter at patholines.org.). You find the following multiple choice question: "Which of the following statements for squamous cell carcinoma (SCC) of the skin is false?" For staging of SCC of the of the head and neck, pT1 corresponds to a diameter ≥ 2 cm and < 4 cm (this is the false alternative, as this defines pT2, whereas pT1 is defined as ≤ 2 cm) Most patients have a favorable outcome after surgical resection. It occurs most often in sun exposed areas. It often presents as a hyperkeratotic scaly plaque. Microscopy typically shows carcinoma of keratinocytes that infiltrates the dermis. What is the most efficient way of dealing with this question for real-life pathology practice? Choosing an answer, then thoroughly reviewing each alternative, as well as the question explanation. Like the first alternative, but only if you answered the question wrong. Only carefully review the single association you need to answer the question correctly (in this case, that for SCC of the skin, pT1 is defined as ≤ 2 cm). Skip this question and move on. Correct answer The answer alternatives of this question are all over the place (a mix of prognosis, location, staging, gross description and microscopic description), which usually means that it was created by just looking up the condition in a resource and picking information from there, resulting in a collection of what is usually just look-up information. Incorrect answers You can skip reading these if you are already agree with the explanation above. 1 and 2. These are waste of time. 3. If this was a question of memorization-worthy information, or if you were studying for an exam, this would generally be the correct answer. However, staging of cancers can essentially always conveniently and timely be looked up when needed, so this is not memorization-worthy for everyday pathology practice.

Other indications for skipping a question include:

• Unrealistically withholding information, such as mentioning what kind of test identified the condition without giving you the test result (such as a case presentation that includes "Serology identified the organism").
• Unrealistic chronology, that is, not following the order of actual processes. It may include giving you the diagnosis and asking you what would be the expected clinical history.
• Showing you a molecular structure and asking you to identify the substance or its category, which is extremely unlikely to be a task in real life, and which can generally quickly be looked up (such as googling search by image and clicking the camera icon, followed by uploading the image of the structure, such as a photo or screenshot thereof).
• Unpractical statistics that is very unlikely to be used diagnostically, mainly because their calculations would be so complex that it is not worth it. For example, in reality you generally have a pattern of signs and other findings and you want to know the likelihood of each differential diagnosis, and for this purpose you only get limited help by knowing the reverse likelihood of what percentage each individual condition is to display the finding, because it would still be necessary to also know the epidemiology of each disease to calculate its likelihood.

Learning clinical pathology

For learning hematopathology, unless you plan on specializing in that field: focus on the aspects of it that you may be expected to handle rather independently, mainly including peripheral blood smears and general screening of lymph nodes. Also learn how to suspect an incidental hematopathologic disease for specimens submitted for other reasons. Otherwise, a hematopathology workup is generally a very complex matter that should be performed by subspecialists thereof. In the unlikely event that you will end up at a workplace without an internal arrangement for how to consult a hematopathologist, make such arrangement yourself, since it will save you a lot of time compared to even trying to learn yourself how to perform a modern hematology workup.

For molecular pathology, focus on learning the situations in which molecular workup is needed, rather than the specific derangement. The latter can generally easily be looked up when needed, whereas the former can easily be missed.

Microbiology:
Put substantial effort on identifying what is actually memorization-worthy before starting to memorize microbiology-related content. For example, have an idea of the main workflows in a typical microbiology lab, but do not waste much time memorizing bench tests (negative/positive for indole, lactose/sucrose fermentation etc. etc.). In everyday practice there are only a limited number of bacteria that are identified by such testing, whereas the rest are generally identified by multitarget assays and/or MALDI-TOF. For exams where the passing score is an average of multiple topics (including the American Board of Pathology Certification Exams), focus on more useful topics instead.

General advice

• When making a mistake, admit that you did it and learn from it so as to focus on not repeating it. Also learn from the mistakes of others.
• Say "I don't know" instead of making up answers for what you do not know.
• Ask for help whenever needed, such as first time you are doing something, or whenever you are not sure about what to do, especially when doing something potentially irreversible. Also ask for help in moments whenever there is a high risk that you will not achieve what you need to do within a clinically acceptable time. Still, before asking, try to do as much as you can, as long as you do not do anything potentially irreversible, so that you can evaluate how you did it compared to the standard, and thereby know better how you will do it next time.
• Try to fit findings with the clinical picture so that the report makes sense, but do not make up findings that you do not see, especially in cases where you copy-paste words from a previous report or template. At the same time, do not omit relevant features just to fit an expected story.
• Do not wait for the whole pile. Whenever you can, do not be idle or do less urgent work while there is a pile of more urgent work gathering for you elsewhere. Instead, be familiar with where such piles are forming, and go there and grab whatever you may start working on right away.
• For larger specimens that need fixation before final grossing, you can still start writing a report of measurements and other externally visible findings to save time for later.
• Save your digital reports frequently.
• Focus on learning pitfalls and the interpretation of visual patterns and other non-written results, and do not waste much time memorizing information that can essentially always be conveniently and timely looked up when needed (but have an idea of where to find it). Further information: Learning pathology

Emergent pathology

Author: Mikael Häggström
Memorization-worthy: Information relating to emergent pathology is often not conveniently and timely looked up when needed because of the urgency in reaching a report.

Comprehensiveness

On this resource, the following formatting is used for comprehensiveness:

• Minimal depth
• (Moderate depth)
• ((Comprehensive))

Frozen sections

Even new pathology trainees may end up being the first responders to frozen sections (as well as intraoperative consultations by gross inspection only).

Preparation

Prepare at least the following:

• Finding out which senior to call for help if responding to a frozen section. A fairly new pathology trainee should generally not independently make a report to the referring physician without having at least consulted with a senior, and therefore the diagnostics of frozen section slides is not included in this section. In the meantime, ensure that you have the contact information to relevant seniors and/or attendings, and the means to perform micrography and telepathology if that person may not be able to be physically present within an acceptable time. Also consider calling additional colleagues, even at your own level or below, if there are many specimens coming at once.

File:Metastasis sites for common cancers.svg

Main sites of metastases for some common cancer types. Primary cancers are denoted by "...cancer" and their main metastasis sites are denoted by "...metastases".

• If possible, look up pertinent medical histories of potential cases that may appear as frozen sections or other forms of intraoperative consultations. For example, surgery departments may have schedules of patients for the day that you will cover frozen sections. On such lists, types of surgeries that often come as intraoperative consultations mainly include potentially malignant skin excisions, lung excisions (larger than biopsies), ovarian tumors, and samples from other common metastasis sites (lungs, liver, brain, bone). The most important details to find out are:

• What you may do yourself if you will be alone when you get the specimen, or if you need to wait for particular seniors before doing potentially irreversible steps such as inking and sectioning.
• Previous biopsies. For expected excisions from common metastasis sites, look thoroughly for any past cancer diagnoses. Note the pathologic diagnoses of the biopsies((, as well as the collection dates and accession numbers.)) (Pull out previous slides of the malignancy so that you can compare its appearance with the current case.)
• Tumor sizes where applicable(, and whether the estimation was from imaging or microscopy).

• Make sure you have a working microtome. Switch its blade if you are not certain it has had limited use.
• Prepare at least as many chucks as you think you will need according to any surgery schedule (or at least 3 of preferably various sizes).

• You can theoretically put a specimen directly on the chuck plate, but to reduce the risk of tearing, put embedding medium on empty chucks
  You can theoretically put a specimen directly on the chuck plate, but to reduce the risk of tearing, put embedding medium on empty chucks
• Wait until the embedding medium is frozen at the bottom
  Wait until the embedding medium is frozen at the bottom
• Place the conductor on top of the chuck. You now have a prepared chuck with a smooth surface.
  Place the conductor on top of the chuck. You now have a prepared chuck with a smooth surface.
• Smear some oil on the bottom of the conductor, to avoid it getting stuck to the specimen later.[note 10]
  Smear some oil on the bottom of the conductor, to avoid it getting stuck to the specimen later.

(If you don't have a conductor, or if the embedding medium completely hardened before you applied it, perform cryotomy of the embedding medium to get a larger and smoother top.)

• Inspect the H&E staining containers and refill if necessary.

• Example of material needed for H&E staining of frozen sections: Staining fluids, glass slides, pencil to mark slides (the ink of pens will generally be washed off in the fluids), slide dipper, timer, cover slips and immersion oil.
  Example of material needed for H&E staining of frozen sections: Staining fluids, glass slides, pencil to mark slides (the ink of pens will generally be washed off in the fluids), slide dipper, timer, cover slips and immersion oil.

• Ensure that you have frozen section medium, as well as cover slips and mounting fluid.

Performing frozen sectioning

• Inform relevant seniors.
• Look at any requisition form or otherwise check or confirm what answers the requesting clinician wants. When the histopathologic type of tumor is known from before and its distance to the closest margin is relatively far, a gross intraoperative consultation is generally enough to measure that distance.
• Measure the size of the specimen.
• If you are permitted to proceed with the following steps, which are potentially irreversible, still consider whether there are any surprising aspects that requires you to wait until a senior arrives.
• Ink relevant margins
• 'Section the specimen so as to be able to see relevant pathologies, and closest distances to relevant margins.
• Select tissue to be able to answer the clinician's questions.
• Trim samples to make them equally thick, since you will need to section away more from thick pieces before thinner pieces will appear in cryotomy slices.

• Put specimens on one or more chucks. It's better to put them on a slightly too large chuck than a slightly too small one, but keep the areas of interest within what presumably fits on a microscopy slide.
  Put specimens on one or more chucks. It's better to put them on a slightly too large chuck than a slightly too small one, but keep the areas of interest within what presumably fits on a microscopy slide.
• Cover the specimen with embedding medium
  Cover the specimen with embedding medium
• Apply a conductor (unless it's a thin specimen that needs to stand on its side)
  Apply a conductor (unless it's a thin specimen that needs to stand on its side)
• Use freeze spray to quicken the freezing if available
  Use freeze spray to quicken the freezing if available
• Breaking off any embedding medium that reaches below the chuck's plate
  Breaking off any embedding medium that reaches below the chuck's plate
• Fasten the chuck on the cryotome. Epithelial surfaces should be oriented vertically, like a picket fence.
  Fasten the chuck on the cryotome. Epithelial surfaces should be oriented vertically, like a picket fence.
• Generally set the thickness to 5μm, and advance the specimen over the blade while holding the section down to prevent it from folding onto itself
  Generally set the thickness to 5μm, and advance the specimen over the blade while holding the section down to prevent it from folding onto itself
• Continue until all the tissue of interest is in the section. Leave at least a small part connected to the chuck to avoid folding.
  Continue until all the tissue of interest is in the section. Leave at least a small part connected to the chuck to avoid folding.
• Put a glass slide on the tissue (this case is actually borderline too spread out to fit on one slide). It is now ready to be put in staining solutions:
  Put a glass slide on the tissue (this case is actually borderline too spread out to fit on one slide). It is now ready to be put in staining solutions:

File:Time in solutions for frozen sections.jpg

Minimal time in solutions for frozen sections.

Test question Hematoxylin in frozen sectioning You are put on frozen sectioning duty, and a specimen arrives. You inform the attending over the phone, who will require a moment to reach the room, and therefore tells you to prepare two microscopy slides in the meantime. You make sections, but the note that instructs the number of dips or duration in the hematoxylin solution has become unreadable due to a hematoxylin stain. You don't have any phone signal in the frozen section room, so you don't have time to look it up. To what extent will you put the slide in the hematoxylin solution? A. 1 minute and 30 seconds B. 1 dip C. 10 seconds D. 5 dips Answer Explanation This is generally the minimal time required for proper hematoxylin staining during frozen sections. Yet, if you know the solution is not expired or diluted, and you are really in a rush, then you can possibly have it acceptably stained in 1 minute in hematoxylin.

Troubleshooting

Problem	Cause	Solution
Tissue cracks off in cryotomy	Block too cold	Repair by warming slightly and adding embedding medium
Thick and thin slices	Inconsistent clamping Dull blade Incorrect blade angle	Ensure block holder and blade holder are tight Change blade Correct knife angle
Wrinkled, compressed or puckered sections	Dirty or dull blade Tissue too warm	Clean blade Move or replace blade Cut tissue at colder temperature
Tissue advances but does not cut	Inconsistent clamping	Ensure blade holder is tight
Sections roll up	Anti-roll plate is not adjucted correctly	Readjust anti-roll plate
Sections thaw on the blade	Blade is too warm	Cool the blade
Sections stick to the anti-roll plate or blade	Static in the cryostat	Apply anti-static spray or anti-static gun
Sections split vertically	Dirt or nick on blade	Clean, move or replace blade
Sections have fine cracks parallel to the blade edge	Too cold temperature	Warm the tissue
Sections show signs of vibrations	Specimen too loose Incorrect blade angle	Tighten chuck to the holder Change the blade angle
Stain is dull and muddy	Drying artifact	Put sections on glass slides immediately in fixative

Thawing

• 
  When no more frozen sections are needed for a block, do not use water directly on the sample, as it may get flushed away.
• 
  Rather, apply hot water to the stem of the chuck, while slightly tilting your grip of the top to apply pressure towards making the block slide off the chuck. As soon as you feel it starting to move, move away from the sink and finish sliding the block off the chuck.

Reporting of intra-operative consults

• Call the requesting clinician
• Verify that you are talking to that person, or someone who can immediately convey the diagnosis to that person. You may request to talk directly to the surgeon if a conversation is warranted.
• Tell the patient identity (with at least two different identifiers, such as name and date of birth)
• (Ask for a readback of your diagnosis. This is particularly important in cases with multiple specimens, and when it needs to be stated that a more specific diagnosis is deferred until standard slides have been evaluated.)
• State your diagnosis succinctly. If necessary in cases with limited diagnostic tissue, you may state that additional tissue is required for a more certain report.
• (Make sure the clinician reads the diagnosis back to you.)

Example:

Hello, this is from pathology. I have a frozen section result for Dr. (name of the clinician) This is Dr. ____, and I have a diagnosis on (patient name and date of birth)(, if you could please read back to me after,) the diagnosis is (diagnosis)

Frozen sectioning of suspected malignant skin excisions

While most frozen sections can be predicted from schedules of the operating room and thereby be looked up beforehand, suspected malignant skin excisions often come from outside the main surgery department, even more indicating memorization of how to handle them.

Tissue selection

Tissue selection from suspected malignant skin lesions, by lesion size:

<4 mm	4 - 8 mm	9 - 15 mm
File:Tissue selection from skin excision less than 4 mm with suspected malignant lesion.png	File:Tissue selection from skin excision 4-8 mm with suspected malignant lesion.png	File:Tissue selection from skin excision 9-15 mm with suspected malignant lesion.png

In table above, each top image shows recommended lines for cutting out slices to be submitted for further processing. Bottom image shows which side of the slice that should be put to microtomy. Dashed lines here mean that either side could be used. Further information: Gross processing of skin excisions

Donor kidney biopsy

Gross processing

Prepare a separate slide for right versus left kidney if applicable.

Microscopic evaluation

Generally evaluate as per local protocol, which generally includes the following parameters, given individually for right and left kidney:

• - Number of glomeruli with global sclerosis - Total number of glomeruli. - Percentage of glomeruli with global sclerosis (number of glomeruli with global sclerosis divided by total number of glomeruli).
  - Number of glomeruli with global sclerosis
  - Total number of glomeruli.
  - Percentage of glomeruli with global sclerosis (number of glomeruli with global sclerosis divided by total number of glomeruli).
• Tubular atrophy/tubular interstitial fibrosis, as percentage of tubules. Features of tubular atrophy are shown (of which casts is often not present).[8][image 1]
  Tubular atrophy/tubular interstitial fibrosis, as percentage of tubules. Features of tubular atrophy are shown (of which casts is often not present).
• Arteriosclerosis seen as intimal thickening with an onion skin-like appearance. Arteriosclerosis can be graded as mild, moderate or severe.
  Arteriosclerosis seen as intimal thickening with an onion skin-like appearance. Arteriosclerosis can be graded as mild, moderate or severe.
• Arteriolar hyalinosis, graded as mild, moderate or severe.
  Arteriolar hyalinosis, graded as mild, moderate or severe.

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.

In malignant or suspected malignant cases, surgical margins are generally more important than main tumor diagnosis.

• In lung wedge resection and lobectomy, sample the surgical margin that is presumably closest to a tumor for frozen sectioning. Further information: Lung wedge resection and lobectomy
• In an intestine with tumor, it is generally enough to open the intestine (avoiding cutting through a tumor unless it is corcumferantial, and grossly measuring the distances to the proximal and distal surgical margins, as well as the distances to the radial or mesenteric surgical margins. Further information: Intestine with tumor
• For a donor kidney biopsy, generally evaluate as per local protocol. Further information: Donor kidney biopsy

However, for myocarditis requests (see the heart article), generally have the cardiac biopsy sent in formalin for regular H&E processing (even on weekends) rather than perform frozen sectioning, since good quality slides is the priority.

FOr further learning, focus on learning to triage, gross and sample specimens that may come for frozen sections. Microscopic evaluation is less of a priority as long as you can get assistance from seniors (including telepathology).

Fixation

Immersion

File:Adipose tissue with crumpling artifact due to insufficient fixation.jpg

Adipose tissue with crumpling artifact due to insufficient fixation.

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

Duration

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

When not to use formalin

The main exceptions to using formalin are mainly:

• 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.
• 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.

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.

Gross processing

Following are general notes on selection and trimming in pathology.

Priority

Priority

1. More invasive intraoperative consultations (such as open surgery) 2. Less invasive intraoperative consultations (such as skins) 3. Fresh lymph nodes 4. Fresh breast tissue (should be in formalin within an hour from surgery) 5. Other fresh tissue 6. Tissue in formalin

For prioritizing when you have more than one thing ongoing at the same time, the list at right can be used.

Fresh specimens

The initial processing of fresh specimens is also termed triaging.

• For intraoperative consults including frozen sectioning, see separate article on Emergent pathology.

When triaging a specimen, the measurements are most important as these may change after fixation. Other descriptions can generally be made after the specimen is fixed.

• See also separate article on fixation, including what specimens should not immediately be put in formalin (mostly tophus, lymph nodes and products of conception).

Before cutting

• Confirm that the patient identity on the specimen container matches the identity that will be applied to the gross description and cassettes. {{If the referral or requisition form is available, confirm the patient identity on that one as well.}}

File:Right or left renal stone.jpg

For unclear or potentially ambiguous handwriting (here "Right" or "Left" renal stone), look at the referral or requisition form ((and the medical record if available)).

• (Check for any discrepancy between the specimen description on the container and on the referral or requisition form, such as left versus right.)
• Don't omit any piece in the container, such as ones hidden in wraps.
• Generally measure in 3 dimensions, or in volume, but the greatest dimension is generally enough for specimens less than 0.4 cm.
• Generally weigh entire organs, after having any attached tissue trimmed away if feasible.
• (Note the color of the sample, even when unremarkable, but do not linger on deciding it.)
• Generally, use inking for resection margins where tumor radicality is important. Further information: inking
• (On fatty or greasy surfaces, apply vinegar to emulsify and remove the fat, dry the specimen and then ink. Otherwise, vinegar can be used either before or after inking to "dry" it.)
• (Preferably photograph or make a drawing where slices have been taken.)
• Remove any surgical stitches from samples before microtomy.
• (At least for larger samples, consider looking for medical imaging or biopsy reports in order to better guide the process.)
• Fix bone in formalin prior to decalcification. Use reminders so not to forget bone that is decalcifying.
• Plan in which order to cut different parts so as to be able to take all relevant sections. Generally sample relevant surgical margins and smaller parts first, as these may be harder to find or even be fragmented later on.

Cutting

• When cutting with the longer knives, try to cut in one stroke - do not use like a saw (continuous back and forth)
• Generally, strive to make slices perpendicular to visible interfaces of relevant tissues.
• Generelly dissect and inspect the entire specimen, while keeping relevant parts intact enough for presentation to seniors and/or maintaining orientation.
• Trim tissues for microscopy examination to a thickness of maximum 3-4 mm.

Perpendicular versus en face sections

File:Perpendicular versus en face.jpg

Perpendicular and en face sections

Two major types of sections in gross processing are perpendicular and en face sections:

• Perpendicular sections allow for measurement of the distance between a lesion and the surgical margin.
• En face means that the section is tangential to the region of interest (such as a lesion) of a specimen. It does not in itself specify whether subsequent microtomy of the slice should be performed on the peripheral or proximal surface of the slice (the peripheral surface of an en face section is closer to being the true margin, whereas the proximal surface generally displays more area and therefore generally has greater sensitivity in showing pathology, also compared to perpendicular sections).

• A shaved section is a superficial en face slice that contains the entire surface of the segment.

Tissue selection

When sampling sections to submit for microscopic examination, whenever you sample from something that looks abnormal, generally try to also sample from the same type of tissue that looks normal.

Biopsy wraps, bags and sponges

File:Biopsy wrap, biopsy sponge and biopsy bag.jpg

Items used for submitting specimens: (Biopsy) wrap, (biopsy) sponge, (tissue processing) cassette and (biopsy) bag.

Put the following types of specimens in bags:

• Tiny specimens that need to be poured out from their containers.
• Bloody specimens such as endometrial curettages or products of conception. For products of conception, chorionic villi may otherwise contaminate other specimens. Bloody specimens may stick to wraps, so generally avoid that situation.
• Friable tissue such as urinary bladder biopsies.

Put the following types of specimens in bags, wraps or sponges:

• Other tiny specimens
• ((Any small piece of tissue where there is no leftover specimen to retake sections, since tissues occasionally get lost from cassettes, and the absence of a wrap, sponge or bag in the cassette of such cases points towards a mistake made at gross processing.))

Specimens must be fixed enough to be put on sponges.

H&E staining urgency

(Even in departments where other staff are primarily responsible for determining the urgency of H&E staining of each specimen, still double-check that it is correct if you can, such as by cassette color.) A major indication for rushing cases through H&E staining is a high risk of cancer, especially where immunohistochemistry staining will likely be performed, and the decision and types of staining will be determined by the standard H&E stain. Tissues that are generally rushed are:

• Brain biopsy.
• Lung biopsy.
• Breast needle biopsy.
• Biopsy from known tumor tissue.
• Suspected malignant lymph nodes, including lymphoma. However, these are generally not urgent when submitted together with a tumor, except mainly for the following (which are generally urgent):

• Pelvic sentinel lymph nodes
• Sentinel lymph nodes from known invasive lobular carcinoma (but not invasive ductal carcinoma)

In both these cases, the cases are rushed so that immunohistochemistry can be performed if a metastasis is not readily detected on standard H&E slides, so that it is available by the time the rest of the slides are out. Immunohistochemistry in these cases can detect micrometastases that are not readily visible on H&E stain, but are evident on cytokeratin AE1/AE3. However, if the lab stains such cases regardless of whether H&E stain shows a metastasis or not, then they do not need to be rushed.

Marking cassettes

Use only hard pencil (or specially purchased histology markers), as marks made with pens, Sharpie markers, or scientific freezer-safe markers can get dissolved in tissue processing.

Evaluation of tumors

For evaluation of suspected malignancies such as tumors, the most important aspect is whether it is benign or malignant. If malignant, then staging is necessary. There are generally specific criteria for various forms of tumors, which should be used whenever applicable, but following are some generalizations.

A general approach is to start looking at a slide which seems to contain non-necrotic tumor, and if possible it should also show surrounding non-tumor tissue, so that the interface can be appreciated (and tumors are generally less necrotic at the periphery).

Benign or malignant

	Benign	Malignant
Gross examination	Well demarcated from surrounding tissue	Usually no tumor capsule Possibly: Necrosis Infiltration or invasion into surrounding tissue Bleeding
Microscopy	Almost no irregularities of cellular structures	Nuclear atypia: Enlargement Pleomorphism Nuclear polychromasia, which means variability in nuclear chromatin content. Numerous mitotic figures

• Cellular features of malignant cells versus normal cells.
  Cellular features of malignant cells versus normal cells.
• An increased nucleus-cytoplasm ratio is generally an indication of malignancy.
  An increased nucleus-cytoplasm ratio is generally an indication of malignancy.

Primary tumor versus metastasis

File:Metastasis sites for common cancers.svg

Major metastasis pathways: Main origins and sites of metastases for some common cancer types. Primary cancers are denoted by "...cancer" and their main metastasis sites are denoted by "...metastases".

Indications of a metastasis rather than primary tumor are mainly:

• Tumors that are unlikely to arise at the location at hand.
• Tumors conforming to more likely metastasis pathways.

If a suspected malignancy is present, generally check the patient history for any history of cancer, especially for tumors in more common metastasis sites, which mainly include lung, bone, liver and/or brain. In case of such history, preferably look at the microscopy slides of the past cancer to help determining whether the current case is of the same origin, versus a primary at the current body location, versus a metastasis of yet another location. If there is no known history of cancer, still consider a metastasis of unknown primary origin, especially for suspected malignancies in lymph nodes, liver, lungs, bones, or skin.
Further information: Metastasis

Histopathologic type

For specific diagnoses by organ system, see anatomic diagram on Patholines Main page. This resource will give the main steps towards reaching a diagnosis, but before making a tumor diagnosis, generally be sure that it fulfills the criteria of the condition according to The WHO Classification of tumors, and generally consult an experienced pathologist as well until you feel confident.

Visually, tumors and other suspected malignancies can usually be classified into one of the following groups:

• Gland-like tumors, with tumor cells around clearings
  Gland-like tumors, with tumor cells around clearings
• Squamoid tumors, typically having abundant eosinophilic cytoplasm.[24]
  Squamoid tumors, typically having abundant eosinophilic cytoplasm.
• Spindle-cell tumors, with elongated cells and/or nuclei
  Spindle-cell tumors, with elongated cells and/or nuclei
• Undifferentiated tumors, with few to no visual clues to their origin.
  Undifferentiated tumors, with few to no visual clues to their origin.

Further pinpointing of a specific tumor type is often attained by thinking of one or more possible diagnoses, and looking up their differential diagnoses, followed by comparing their microscopic descriptions and multiple micrographs with the case at hand. When two or more diagnoses seem to fit with the case at hand, consider performing immunohistochemistry. Find relevant target proteins that are expected to stain substantially differently between the possible diagnoses. If it's not evident from initial sources, you may use Immunoquery.com which will generally suggest the most relevant target proteins to distinguish the suspected conditions at hand.

Gland-like tumors

File:Histopathology of adenocarcinoma.png

Typical features of adenocarcinomas. In reality, the appearance varies significantly from case to case. Vacuoles are more prominent in mucinous tumors, but can be seen in serous tumors as well.

Gland-like tumors are mainly evaluated for cellular atypia, architectural dysplasia and invasion, and thereby classified into the following main categories:

• Hyperplastic lesions, lacking significant atypia
• Adenomas, which can range from mild to high-grade dysplastic, yet are generally confined within their anatomic layers, that is, they are not invasive.
• Adenocarcinomas, with the main criterion being invasiveness. Evaluate specifically by location when possible. Some specific locations included in this resource:

• Colorectal adenocarcinoma
• Prostate adenocarcinoma
• Lung adenocarcinoma
• Bladder adenocarcinoma
• Esophageal adenocarcinoma
• Endometrial adenocarcinoma
• Pancreatic ductal adenocarcinoma

File:Well-, moderately and poorly differentiated colorectal adenocarcinoma.png

Degree of differentiation, with example from a colorectal adenocarcinoma.

Generally, adenocarcinomas are categorized by degree of differentiation as follows:

• Well differentiated: > 95% of tumor has glandular formations
• Moderately differentiated: 50 - 95% glandular
• Poorly differentiated: < 50% glandular

If metastatic adenocarcinoma seems to be the case (always consider this in at least lung adenocarcinoma), look at the history and radiology reports for a most likely primary. Generally, perform immunohistochemistry with one or two stains that are most typical for the suspected primary, and optionally add CK7 and CK20 as a broad screening. Further information: Metastasis

Squamoid tumors

These are more or less looking like a squamous-cell carcinoma:

• Main characteristics of squamous-cell carcinoma
  Main characteristics of squamous-cell carcinoma
• Typical well-differentiated nests have cells with abundant eosinophilic cytoplasm. Keratinizing centers are seen as well.
  Typical well-differentiated nests have cells with abundant eosinophilic cytoplasm. Keratinizing centers are seen as well.

Differential diagnoses depend on location, such as:

• Squamous-cell carcinoma of the skin, with multiple differential diagnoses
• Squamous-cell carcinoma of the lung
• Urinary bladder: Urothelial versus squamous-cell carcinoma
• Cervix uteri: Cervical dysplasia

Spindle-cell tumors

For Spindle-cell tumors, the shape of the nuclei is a clue to the diagnosis, with the following tendency:

• Pointed on both ends: True fibroblastic tumors
• Pointed on one end and blunted on the other ("bullet-shaped"): Neural
• Blunted on both ends ("cigar-shaped"): Smooth muscle
• Triangular: Myofibroblastic

Evaluate specifically by location when possible

Further histopathologic subtyping and grading

Beyond determining overall malignancy diagnosis (such as adenocarcinoma), probable origin and staging, classification of tumors into a specific histopathologic type or grade is generally of relatively less value. In cases of clearly non-malignant tumors where it is difficult to determine the specific histopathologic type or grade, it is generally acceptable to conclude the evaluation and report it as such, unless the clinician specifically requests otherwise. For potentially malignant or high-risk tumors, typing and grading often still affects the management, but generally much less so than staging.

Undifferentiated malignancy

File:Histopathology of undifferentiated tumor cells.jpg

Histopathology of a biopsy of a lymph node with cancer of unknown primary origin, showing undifferentiated high-grade tumor cells.

An initial panel of cytokeratin (CK, such as by CK AE1/AE3 cocktail), S100, vimentin and LCA (CD45) can be used (see source article for subsequent work-up).

Alternatively, a more comprehensive panel can be performed upfront, with the most pertinent panel suggested below (with main associated primary origins in parentheses), but it should be tailored to additional clues from each individual case:

File:Histopathology of signet ring cell carcinoma of urinary bladder on mucicarmine stain.jpg

Mucicarmine stain showing signet ring cell carcinoma, with the mucin within tumor cells colored pink/red.

• Mucicarmine or Cytokeratin CAM 5.2 (adenocarcinoma)

• CK7 and CK20 can give a broad indication of the primary site. Still use more specific immunohistochemistry stains instead or in addition where applicable. See image below for main patterns.
• NKX3.1 in males (prostate adenocarcinoma), or PAX-8 or estrogen and progesterone receptor in females (female reproductive tract).
• TTF-1 (thyroid or lung tumor)
• GATA3 (urothelial carcinoma, breast tumor)
• CDX2 (gastrointestinal tumor)
• p63 (squamous cell carcinoma)

• S100 (neural, invasive melanoma)
• LCA (CD45) (hematopoietic)
• Synaptophysin (neuroendocrine)

File:CK7 and CK20 by body location.svg

CK7 and CK20 expression by various body locations.

Non-neoplastic

If a neoplasm has been ruled out for what clinically appeared like a tumor, seek a diagnosis that can be consistent with the clinical findings that caused the suspicion. If no explanation is found on the slides, generally take additional levels on the paraffin block, or more sections from any leftover tissue.

For example, for a breast biopsy of what appeared to look like a mass, and there is no neoplasia, look mainly for dense fibrosis or other fibrous changes, so that you can report it and thereby explain the finding, rather than merely writing "benign breast tissue".

Heterogeneity

After having characterized a suspected malignancy, still screen through it for any significant areas that are different and may need own mentioning, or even change the overall type or grade.

Additional levels or slices

Situations requiring additional material include mainly where tumor is expected but nevertheless not seen on existing slides. Such cases include:

• The gross report or other observation describes a tumor or polyp, but none is seen on microscopy.
• Re-excision does not identify tumor cells in a clearly non-radical primary excision or biopsy.

Also consider more material if the most aggressive pattern is seen in the last available section, in which case more sections are indicated (from the same paraffin block if additional tissue is not available).

Depending on availability and greatest suspicion, additional material is either acquired by taking addition step sections of remaining tissue in a paraffin block, or taking additional slices from the original specimen.

Staging

Staging is generally done by TNM classification. Specific TNM systems should be used whenever applicable, mainly the manual by the American Joint Committee on Cancer (AJCC) if you can access it. Further information: Secrets Otherwise, a general system may be used:

T: size or direct extent of the primary tumor Tx: tumor cannot be assessed Tis: carcinoma in situ T0: no evidence of tumor T1, T2, T3, T4: size and/or extension of the primary tumor N: degree of spread to regional lymph nodes Nx: lymph nodes cannot be assessed N0: no regional lymph node metastasis N1: regional lymph node metastasis present; at some sites, tumor spread to closest or small number of regional lymph nodes N2: tumor spread to an extent between N1 and N3 (N2 is not used at all sites) N3: tumor spread to more distant or numerous regional lymph nodes (N3 is not used at all sites) M: presence of distant metastasis Further information: Metastasis M0: no distant metastasis M1: metastasis to distant organs (beyond regional lymph nodes)

File:Histopathology of a lymph node with metastatic invasive ductal carcinoma from the breast.jpg

For positive lymph nodes, generally also note any extranodal extension, and the size thereof.

Put your main focus on features that will determine the final stage. For example, if you see a lymph node involved by cancer, the presence or absence of lymphatic invasion is no longer critical, but rather the presence or absence of additional involved nodes or distant metastasis. If a stage-defining finding is uncertain, generally fall back to the lower stage.

For the size, the greatest dimension of the tumor is most important. Second and third dimensions (preferably at right angles compared to each other) are optional. Use the largest measure for each dimension. For example if one slide shows a tumor measuring 2.0 x 1.0 cm, and another slide shows the same tumor measuring 1.5 x 1.5 cm, then the tumor can be reported as measuring 2.0 x 1.5 cm. The third dimension can be estimated from gross measurement, or, if the tumor is entirely submitted, adding together the presumed thickness of each slice where tumor is found microscopically. For excisions with less than a centimeter of tumor, and where there has been a previous biopsy, consider looking at the size of tumor on the previous biopsy, which may be the largest measurement, and therefore the measurement of choice for staging.

Nx: lymph nodes cannot be assessed also applies when you only find lymph nodes that are not within the physiologic drainage path of the cancer, and they are benign.

Radicality

File:Histopathology of radically excised basal-cell carcinoma with separation artifact.jpg

If tumor is seen at edge of the sample, but it is not inked, consider confirming the finding with adjacent microtomy levels, especially if no ink is seen on an inked surgical margin. In this case, a separation artifact in top image has removed a surgical margin of connective tissue, seen on adjacent microtomy section in bottom image.

Determine if malignant cells are located close to, or even in, any surgical resection margins.

Lymphovascular invasion

Lymphovascular invasion should always be mentioned. When present at margins, it does not count as tumor extension.

• Endometrial cancer with lymphovascular invasion.
  Endometrial cancer with lymphovascular invasion.
• 
  If unsure whether a case is true lymphovascular invasion or a retraction artifact (imaged), use immunohistochemistry for D2-40 to highlight lymphatic vessels or CD-31 for blood vessels.

Molecular workup

Ensure that any cancer undergoes reflex testing where applicable by local guidelines. When they are not applicable, a rule of thumb is to order individual genetic testing if there is a need to test up to 2 genetic targets, and to order genomic sequencing if more targets need genetic testing (not counting immunohistochemitry or other more easily performed tests).

When needing to send out tissue to an outside laboratory, follow their requirements and guidelines for each test. Generally, choose the tissue block with the greatest amount/area of the highest grade malignancy. For molecular proliferation tests (other than immunohistochemistry) such as Ki67, avoid samples with previous biopsy site or inflammation (as these will cause a false high proliferation rates). On the other hand, for next-generation sequencing, hemorrhage, necrosis and adipose tissue does not need to be minimized, as these contain only little genetic material.

Reporting

File:Histopathology of pancreatic adenocarcinoma with treatment effect.jpg

Also note "treatment effect", seen as fibroelastotic tissue, here with scattered remaining tumor cells.

For cancers, generally include a synoptic report, such as per College of American Pathologists (CAP) protocols at cap.org/protocols-and-guidelines. If there is no CAP synoptic available for the cancer type at hand, attempt to find one in the latest AJCC Cancer Staging Manual (see the Secrets article), but make sure to use pathologic staging (with a p preceding the T, N or M) rather than clinical staging.

If a surgery produces a specimen with cancer, as well as re-excisions from certain directions, you should preferably give the closest distance to margins in each specimen, as well as the closest distance overall in a synoptic, for example:

A. (Specimen with most of the cancer) (...) Invasive carcinoma is present at inked medial margin (see specimen B for final medial margin), and is located 0.3 cm from the lateral margin. B. (Re-excision in the direction of the medial margin) (...) Invasive carcinoma is located 0.5 cm from the new medial margin. Synoptic report (...) Distance from invasive carcinoma to closest margin: 0.3 cm Closest margin(s) to invasive carcinoma: Lateral

If possible, generally include features of any previous biopsies or smaller excisions in synoptic reports and staging. For example, if staging is based on tumor size, and the tumor size in a previous excisional biopsy corresponds to a higher stage than the size of residual tumor in a subsequent wider excision, then the report of the latter should give the higher stage, with a comment thereof, such as:

pT__

- Based on previous excisional biopsy (specimen ID: ______)

  See also: General notes on reporting

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

• Gross processing:

• Dimensions of original tissue
• Directions or other features of any inked surfaces.
• Generally the weight of larger samples
• Dimensions of pathologic components
• 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. 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.

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".

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).