Gastrointestinal Pathology

Goals and Objectives

Level: PGY1, PGY2, PGY3, PGY4, PGY5 

In the CBD cohort, junior residents are considered to be PGY-1 and PGY-2 while senior residents are considered to be PGY-3 and PGY-4.  PGY-5 CBD residents are also considered to be senior residents within the CBD curriculum. The ultimate goal is to allow for independence in the form of independent sign out, intraoperative consultations and supervision of junior residents and pathologist assistants.

For surgical sign out in Anatomical Pathology residency training, there is no separation of cases based on complexity.  Due to the nature of Anatomical Pathology (all cases are ultimately reviewed and finalized by a supervising staff), a resident in any training level can review the glass slides and write up a preliminary report on any surgical pathology case.

  • Ordering of any ancillary studies (histochemical stains, immunohistochemical stains, molecular testing) will initially be done under staff supervision for junior residents.  This is done in order to conserve tissue and prevent tissue waste that may limit the staff pathologist's ability to render a diagnosis. 
    • Based on the resident's experience and abilities they will eventually be permitted to order additional ancillary stains for straightforward, routine cases without consulting the staff pathologist.
    • Regardless of training level, any challenging case for which the resident is unsure of cell lineage or is unable to formulate a differential diagnosis that would be resolved by ancillary testing, the resident must consult the staff pathologist before ordering any ancillary stains.
    • It is expected that senior residents, including PGY-5 residents, would be able to initiate a preliminary panel of ancillary studies for routine cases.  This is ultimately at the discretion of their supervising staff.
  • Grossing of routine specimens can be handled by a resident at any training level.  Complex specimens, which for GI pathology include esophageal & rectal carcinoma resections with neoadjuvant therapy, colectomy for dysplasia arising in the backgrounds of IBD, prophylactic gastrectomy for familial gastric cancer, extrahepatic cholangiocarcinoma, previously treated hepatocellular carcinoma, appendix with mucinous neoplasm and other specimens, should be done by residents that are able to demonstrate a complete understanding of the anatomical and imaging findings as well as the surgical procedure.  Junior residents must obtain staff approval or be supervised by a senior resident for a complex specimen.   

It is expected that the first GI pathology rotation by a junior resident will result in the mastery of normal histology, knowledge of the various surgical procedures encountered and the ability to diagnose common entities.  

It is also expected that the junior residents will review the gross report and correct any typographical errors, assess the completeness of the grossing and correctly report the specimen site, laterality and procedure in the diagnostic section of the surgical pathology report. 

Subsequent GI pathology rotations by senior residents will be built upon the above foundation and include the ability to formulate reasonable differential diagnoses as well as to work up challenging cases.  A senior resident should be able to produce a draft surgical pathology report that includes the elements listed above, along with the appropriate diagnosis, completion of a synoptic report (if indicated) and an appropriately completed microscopic description and/or comment field.  This draft report should also be free of typographical errors. The supervising staff pathologist is expected to provide an appropriate volume of cases for review based on the PGY-1 and PGY-2 resident’s level of training in these areas with the understanding that greater responsibility and workload will be taken on in PGY-3. 

Additionally, while junior residents are expected to attend all interdisciplinary rounds in these major subspecialties, they are not expected to present cases while a more senior resident is on service. If there is no senior resident on service, the junior resident will be responsible for obtaining slides of appropriate cases and working with the staff pathologist in order to present cases which are appropriate for their level of training. 

Staff pathologists are required to be present at all interdisciplinary rounds during which a resident is presenting, particularly for junior residents. 

Senior residents are expected to independently prepare for and present cases at interdisciplinary GI rounds, and, with staff pathologist supervision and guidance, answer questions and take part in discussion during said rounds. 

A senior resident (PGY-3 or PGY-4) is expected to complete an end-of-rotation presentation for the one of their senior GI pathology rotations. 

The PGY-5 year is one of senior leadership and the resident should be able to assume responsibility for organizing the service and supervising junior residents and students. The resident should have mastery of the information contained in standard texts and be prompt in using the literature to solve specific problems. The resident will be responsible for presentations at conferences and for teaching junior residents and students on a routine basis. The PGY-5 should begin to have an understanding of the role of the practitioner in an integrated health care delivery system and to be aware of the issues in health care management facing patients and physicians.   

Based on the Royal College guidelines and recommendations, following the completion of their surgical pathology rotations and EPAs, CBD residents should be ready for independent sign out.

Medical Expert                

  • Demonstrate a working knowledge of the anatomy and histology of the esophagus, stomach, small intestine, appendix, colon, rectum, anus, pancreas, gallbladder, and liver (EPA: F#2). 
  • Demonstrate skill in the gross dissection and sampling of routine specimens, including of upper and lower GI tract biopsies, appendectomy and cholecystectomy specimens, colon – polypectomies & resections, and other specimens (EPAs: TTD# 1A, F#1, C#2). 
  • Demonstrate ability to deal with complex specimens, including i.e. esophageal & rectal carcinoma resections with neoadjuvant therapy, colectomy for dysplasia arising in the background of IBD, prophylactic gastrectomy for familial gastric cancer, extrahepatic cholangiocarcinoma, Whipple and distal pancreatectomy, previously treated hepatocellular carcinoma and appendix with mucinous neoplasm (EPAs: C#2, C#3). 
  • Demonstrate proficiency in the interpretation of liver needle core biopsies as well as adequacy requirements for interpretation for medical liver disease and neoplastic (primary and metastatic) conditions (EPAs: F#2, C#4, C#5, TTP#1). 


  • Obtain a relevant clinical history, including relevant laboratory and imaging results and interpreting this information in light of the clinical information and providing a summary to the supervising staff pathologist (EPA: TTD#2). 
  • Demonstrate the ability to function at a junior staff pathologist level at regular rounds by reviewing cases, presenting cases, and responding to questions regarding the cases (EPAs: C#14, C#18, TTP#1, TTP#5, TTP#6). 
  • Demonstrate the ability to teach aspects of GI, liver & pancreas pathology at multidisciplinary rounds and teaching sessions (EPAs: C#14, C#18, TTP#1, TTP#5, TTP#6). 
  • Gain an understanding of clinical aspects of GI, liver & pancreas, including medical, surgical and clinical oncological management (EPAs: C#14, C#18, TTP#1, TTP#5, TTP#6). 


  • Understand the importance of quality control and quality assurance measures for immunohistochemistry stains (e. gastric Her2/neu), including preanalytical, analytical and postanalytical variables (EPAs: F#1, F#2, C#15, TTP#3). 
  • Understand the value of proficiency testing for immunohistochemistry (EPAs: C#15, TTP#3). 

Health Advocate/Professional 

  • Understand the importance of turn-around-time for diagnostic GI tract, liver & pancreas biopsies due to (1) the high level of stress experienced by patients with symptomatic or image detected lesions and (2) the need to start curative and/or palliative treatments as quickly as possible to reduce morbidity and/or mortality (EPA: TTD#1B). 
  • Understand the implications of a specific diagnosis for patients (EPAs: C#4, C#5) – for example - 
    • Barrett’s esophagus (BE) with dysplasia 
    • H. pylori gastritis 
    • celiac disease 
    • inflammatory bowel disease (IBD) 
    • Neuroendocrine tumor 
    • carcinoid 
    • hepatocellular carcinoma 
    • metastatic liver disease 
  • Know when to appropriately consult an expert in GI, liver & pancreas pathology (EPAs: C#5, TTP#1). 
  • Know the clinical significance of high risk lesions (e.g. dysplasia in BE, dysplasia in IBD, cancer in a colorectal polyp) and the associated risk implications (EPAs: C#5, TTP#1). 
  • Demonstrate an increasing ability to handle more of the clinical workload of the staff pathologist.  It is expected that PGY4 and PGY5 residents are able to handle the full clinical workload of the staff pathologist each day on service (EPAs: TTP#1, TTP#5, TTP#6). 


  • Consider conducting a research project or case report based on GI, liver or pancreas pathology material (EPAs: C#16, C#17, TTP#4). 
  • Review the pertinent literature relating to advances in GI, liver or pancreas pathology (e.g. Barrett’s esophagus, GIST, IBD, appendiceal mucinous neoplasms, colorectal cancer, synoptic reporting, immunohistochemical stains helpful in confirming and/or differentiating between HCC, FNH & hepatic adenomas) (EPAs: C#9, C#10, C#15, C#16, TTP#4). 

Instructional Tools 

The resident will meet with the GI subspecialty Lead and go over this document and the overall aspects of the rotation the day before the rotation starts. 

Grossing (EPAs: F1, C2, C3, TTP#2) 

  • PGY1 and PGY2 level: 
    • For junior residents a grossing week is built into their rotation block. 
    • The resident should gross at minimum the following specimen types during this grossing week:
      • At least 4 routine colectomies (colon cancers, diverticulitis) 
      • At least 4 appendectomies 
      • At least 4 cholecystectomies  
      • At least4 4 polypectomies  
  • A junior resident may also gross larger and/or complex GI specimens (as listed below) with staff approval.  This is encouraged as certain complex GI specimens are less common and the opportunity to gross these specimens may not be available during future rotations. 
  • PGY3 and PGY4 level: Although no grossing week is built into their rotation block, an expectation of grossing remains.  By their end of their senior GI pathology rotations, it is expected that the senior resident will gross larger and/or complex GI specimens: 
    • At least one Whipples or distal pancreatectomy 
    • At least 4 of the following: 
      • Esophageal and rectal carcinoma resections with neoadjuvant therapy 
      • Colectomy for dysplasia arising in the background of IBD 
      • Prophylactic gastrectomy for familial gastric cancer 
      • Extrahepatic cholangiocarcinoma  
      • Previously treated hepatocellular carcinoma 
      • Appendix with mucinous neoplasm 
  • Senior residents, including PGY5 residents, are expected to supervise and teach junior trainees in the gross room (EPA: TTP#2) 
  • Resident will complete a “grossing log” (shared filed created by the gross room director). The resident will review the slides of the case that he/she grossed and review it with the attending pathologist assigned to the case. The attending will review the gross description and will complete the EPA (which may be initiated by the staff or the resident). 


  • The resident will contact the attending pathologist that they are scheduled to sign cases with, the day before in order to arrange time of sign out and distribute cases 
  • Retrieve pertinent clinical and radiologic information from the electronic medical records system (EPA: TTD #2) 
  • Review all of the slides, recognize normal histology and areas with lesional pathology.  Be able to adequately describe the lesional areas (EPAs: C#4, C#5) 
  • Provide a diagnosis or a differential diagnosis of the identified lesion (EPAs: C#4, C#5, TTP#1) 
  • Based on the differential diagnosis, be able to provide an ancillary testing panel to work through the proposed differential diagnosis (EPAs: C#5, C#10, TTP#1) 
  • Be able to select the correct slide for ordering ancillary testing including ER, PR and Her2/neu (EPAs: C#5, C#9, C#10, TTP#1) 

Prognostic Markers                 

  • Learn how to properly interpret immunohistochemistry for GI prognostic markers including MMR and Her2/neu (EPAs: C#4, C#5, C#10, C#15) 
  • Learn indicators for MMR immunohistochemistry and FISH for Her2/neu (EPAs: C#5, C#9, C#10) 
  • Learn how to interpret MMR immunohistochemistry and FISH for Her2/neu (EPAs: C#5, C#9, C#10, C#15) 

Molecular Testing for GI cancers 

  • Learn indicators for molecular testing in GI cancers (EPAs: C#5, C#9) 
  • Learn how to interpret difficult molecular results for GI cancers and their implication for treatment (EPAs: C#5, C#9, C#15, TTP#5) 


  • All residents are expected to attend daily consensus rounds at 13:00 pm (Multihead Room) 
  • PGY1 and 2 level: Resident is expected to attend and depending on their skill level, may be asked to present at interdisciplinary rounds (on Mondays at 7:30am - colorectal rounds and Tuesdays at 7:30am - Liver/Pancreas rounds) (EPAs: C#14, C#18) 
  • PGY 3-5: Resident is expected to attend interdisciplinary rounds and present the cases (on Mondays at 7:30am - colorectal rounds and Tuesdays at 7:30am - Liver/Pancreas rounds). This implies reviewing the cases with the pathologist in charge beforehand and organizing the presentation in the appropriate format (EPAs: C#14, C#18, TTP#1, TTP#2, TTP#5, TTP#6) 


  • The resident will be given an evaluation based on the objectives and PGY level milestones. 
  • At the end of the PGY-3 or PGY-4 rotation they should give a short (30-45 min) presentation - topic of their choice 

Recommended Reading 

  • CAP protocols for all GI cancer biopsies and resections, molecular synoptics. 
  • WHO Classification of Tumours: Digestive System Tumours. 
  • GI and liver chapters in Robbins and Cotran, Pathologic Basis of Disease. 
  • Goldblum & Odze. Surgical Pathology of the GI Tract, Liver, Biliary Tract, and Pancreas
  • All chapters pertaining to GI and Liver pathology in Sternberg’s Diagnostic Surgical pathology or Rosai and Ackerman's Surgical Pathology


Updated April, 2022 

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