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John S. J. Brooks, MD

Program Director
John S. J. Brooks, MD

Note You have reached the Department of Pathology at Pennsylvania Hospital (PAH). There is a separate pathology residency training program at HUP (Hospital of the University of Pennsylvania) by the Department of Pathology and Laboratory Medicine at the Perelman School of Medicine at the University of Pennsylvania; interested candidates should visit the HUP Pathology and Lab Medicine academic website. Both hospitals are part of the University of Pennsylvania Health System (UPHS).

About the Program
Pennsylvania Hospital's Department of Pathology examines a large volume of interesting cases using state-of-the-art techniques including immunohistochemistry, and in-situ hybridization. Residents may select a combined anatomic and clinical pathology (AP/CP) program (four years) or an anatomic (AP) program only (three years). The program is has elective rotations at HUP built into the Program. A total of eight residency positions are available (two for each residency year). There are also two one-year surgical pathology fellowship positions and one one-year soft tissue/bone pathology fellowship.

Program Schedule

The First Year
Residents acquire extensive experience in both surgical and autopsy pathology and a three-month introduction to one field of clinical pathology (CP) usually blood banking. In surgical pathology, residents are responsible for gross description and dissection of cases. There is ample time for residents to review their slides prior to sign out with the attending pathologist at a teaching microscope. Residents assist in the preparation of frozen sections.

The Second Year
Residents spend the nine months in core rotations of three months each in the major disciplines of clinical pathology. These rotations may include:

  • Blood Bank: All aspects of transfusion medicine are covered with individualized practical experience and didactic instruction.
  • Chemistry: Practical experience in instrumentation, methodology and clinical pathologic correlation are emphasized.
  • Hematology: Residents gain experience in bone marrow and smear interpretation, instrumentation, evaluation of coagulation and examination of body fluids.
  • Microbiology: Residents receive extensive individualized instruction and participate in clinical-pathologic problem solving.

One of these core (CP) rotations will have been in PGY1. Residents spend three months of their PGY2 year in Anatomic Pathology.

The Third and Fourth Years
Residents gain experience in a variety of disciplines including cytopathology, subspecialties in surgical pathology as elective rotations at HUP, and molecular pathology.

Increasing responsibility is given during additional surgical and autopsy pathology rotations. Electives are available in ocular pathology at Wills Eye Hospital, pediatric pathology at Children's Hospital of Philadelphia, and the subspecialties of dermatopathology, hematopathology, gastrointestinal pathology, cytopathology and neuropathology at the Hospital of the University of Pennsylvania.

Additional experience in hematology, blood banking, microbiology and clinical chemistry are tailored to the individual interests of each resident. Research in terms of projects are encouraged in anatomic and/or clinical pathology and attendance at a national meeting is reimbursed whenever a resident presents a poster or abstract.

Our residents are well trained and pass the "boards", and go on to excellent fellowships.

Surgical Pathology Fellowship

A one-year fellowship in surgical pathology is available to residents who desire a fifth year of anatomic pathology. Fellows participate in all aspects of surgical pathology, with increased responsibility for independent decisions and diagnosis. Fellows also receive three months of electives, which may include any of the AP-related electives described below.

Bone and Soft Tissue Pathology Fellowship
A soft tissue/bone fellowship is offered to PGY4 and above residents and aimed toward the development of academically oriented surgical pathologists with a subspecialty interest in bone and soft tissue pathology. The program is under the academic direction of John S. J. Brooks, MD, Chairman of Pathology. The soft tissue/bone fellowship program provides extensive experience in microscopic evaluation of soft tissue and bone lesions using conventional microscopy, as well as immunohistochemical stains, and molecular analysis including flourescent in-situ hybridization (FISH) for a considerable number of probes useful for sarcomas.

Resident Rotations and Electives

I. Anatomic Pathology:

Surgical Pathology
Pennsylvania Hospital is a major treatment center for complex surgical problems, with particularly interesting cases in the areas of breast, gynecologic oncology, head and neck, gastrointestinal, genitourinary, pulmonary, neuropathology, and bone and soft tissue tumors. Residents gain experience in gross dissection, frozen section interpretation and microscopic diagnosis.

A core rotation in cytopathology exposes residents to all aspects of gynecologic and nongynecologic cytology including interpretation of fine needle aspiration biopsies. Residents review all abnormal gynecological material and all nongynecologic material with the attending cytopathologist at the teaching microscope. A large collection of cytology cases from all body sizes is available for study. During the core rotation, residents meet with the attending cytopathologist for individual tutorials. Additional elective rotations are available at Pennsylvania Hospital and the University of Pennsylvania for senior residents and fellows.

Autopsy Pathology
Autopsy experience is integrated into the program during all levels of a resident's training. However, the major concentration of autopsy experience is during the first year. An autopsy conference which follows all adult cases, and is attended by all residents, maximizes exposure to clinical-pathologic problem solving and gross diagnosis. Our program includes supplemental autopsies at Albert Einstein Hospital in Philadelphia.

Forensic Pathology
Residents spend one month during their residency in the Philadelphia Medical Examiner's Office to learn the essentials of forensic pathology. For interested senior residents, additional elective months are available.

II. Clinical Pathology / Laboratory Medicine:

Blood Bank
A core rotation of three months exposes residents to important aspects of transfusion medicine. Hands-on experience is received in the blood bank laboratory where residents meet regularly with the laboratory director to discuss topics in transfusion medicine. Residents are involved in clinical problem solving and patient care. A rotation at the Hospital of the University of Pennsylvania, if taken, emphasizes the fundamentals of tissue typing and apheresis; and advanced elective in blood banking at this laboratory is available to senior residents.

The emphasis in clinical chemistry is on test interpretation and utilization. Laboratory experience exposes residents to the technical aspects of the tests performed. During this three-month rotation, residents gain experience in interpreting serum immunoelectrophoresis. Residents are encouraged to participate in quality assurance initiatives and projects.

Residents spend a core rotation of three months in hematology. During this rotation residents review all unusual blood smears and lymph node biopsies with the attending, receive tutorials in hematologic interpretation, learn about the instrumentation in the hematology laboratory, and interpret body fluids and coagulation studies. Senior residents and fellows may elect to spend a month in hematopathology at the Hospital of the University of Pennsylvania.

During this three-month core rotation, residents gain practical experience in identifying micro-organisms including bacteria, fungi, viruses and parasites. Residents attend conferences given in conjunction with the hospital's Section on Infectious Diseases and are involved in clinical-pathologic studies.

III. Electives (HUP & CHOP):

A month-long elective in dermatopathology is available in the Department of Dermatology at the University of Pennsylvania.

Gastrointestinal Pathology
A month-long elective at the Hospital of the University of Pennsylvania provides extraordinary experience in interpretation of specimens from gastrointestinal tract and liver.

Molecular Pathology / Molecular Diagnostics
Residents gain experience with molecular pathology techniques during a core rotation in the molecular biology laboratory at the Hospital of University of Pennsylvania (HUP). In-situ hybridization, Southern blotting, polymerase chain reaction, cytogenetics, and cell culture are some of the techniques residents may learn during this molecular elective.

Hematopathology & Flow Cytometry
HUP has an active Hematopathology service with numerous bone marrow and lymph node specimens. Results of flow cytometry (immunophenotyping on clinical and research material) are integrated into reports. Residents may elect to spend time in this rotation.

While PAH has a high volume of neuropathology cases, the resident may elect to gain additional experience by taking a month-long elective at the Hospital of the University of Pennsylvania. This will include examination of postmortem brains as well as surgical material.

Ocular Pathology
A month-long elective in ocular pathology is offered at Wills Eye Hospital for senior residents and surgical pathology fellows.

Pediatric Pathology
Residents spend time at The Children's Hospital of Philadelphia for experience in pediatric surgical pathology biopsy and resection specimens, and also for pediatric autopsy.

Call Responsibilities
Residents cover weekend call every 10th/11th weekend with the supervision of a staff pathologist and assist with evening frozen sections. Call duties include gross description and dissection of surgical pathology cases received on a Saturday and performance of any weekend autopsies.

Conference Schedule

Everyday: There is a Daily Consensus Conference, 1 pm. for mostly Surgical Pathology cases, but also Cytopathology and occasional unusual autopsy findings.


8:30 am

Resident Talk and/or Journal Club


8:00 am

Bone and Soft Tissue Conference


Residents' Didactic Lecture

4:30 pm

Breast Conference


9:00 am

Unknown Slide Conference

4:00 pm

Gynecologic Pathology Conference


8:30 am

Cytology/Hematology Conference

12:30 pm

ENT Head & Neck Conference


8:30 am

Resident Presentation



Radiology- Pathology conference


Hematopathology conference


Individuals are eligible to begin the pathology residency at Pennsylvania Hospital upon completion of medical school and/or following one or more years spent in a clinical residency. In selected cases, transfers from other pathology programs are considered for second-, third- and fourth-year positions. All residents and fellows must have a valid Pennsylvania Training License.

How to Apply

The Residency Program and the Surgical Pathology Fellowship
For resident positions ERAS online applications accepted. Alternatively, obtain an application from the Department of Pathology and return the completed application form along with a copy of your medical school transcript, two or three letters of recommendation from individuals who know you professionally, and a letter from your dean. Graduates of foreign medical schools must provide photocopies of ECFMG and FLEX/USMLE scores. For the surgical pathology fellowship, forward your CV and three letters of reference. Send all materials to:

John S.J. Brooks, MD
Residency Program Director
Department of Pathology
Pennsylvania Hospital
800 Spruce Street
Philadelphia, PA 19107
Telephone: 215-829-3544

E-mail inquiries, address to the Residency Coordinator, Anna Marie McClain, at amcclain@pahosp.com.

The Soft Tissue/Bone Pathology Fellowship
Candidates should forward a CV together with three letters of reference as soon as possible to:

John S. J. Brooks, MD
Chair of Pathology
Pennsylvania Hospital
800 Spruce Street
Philadelphia, PA 19107

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