Clinical Pathology Program

Molecular Pathology


Rotation Directors:

Goals and Objectives:

The general goal of the Molecular Pathology rotation is to develop an understanding of when and why to order molecular tests, appreciate some of the technical and financial considerations, understand advantages and disadvantages of each of the clinically relevant technologies, and be semi-skilled in the performance and interpretation of several important nucleic acid-based assays.

The objectives of the rotation are encompassed by the six core competencies as defined by the ACGME and residents will be evaluated during their training in each of these areas. By the end of the rotation, the resident will be able to:

Patient Care that is compassionate, appropriate, and effective for the treatment of health through the following:

  • Gather essential and accurate information about patients using all relevant available modalities and incorporate into pathologic interpretations.
  • Effectively interpret molecular pathology test results.
  • Effectively consult to other clinicians in developing a diagnostic plan, when appropriate, based on specific clinical questions and relevant clinical and pathological information.
  • Effectively consult on interpretation or follow-up of unusual or unexpected molecular test results.

Medical Knowledge:

  • Use all relevant information resources to acquire and evaluate evidence-based information.
  • Develop and maintain a knowledge base in the basic and clinical sciences necessary for effective consultation in Molecular Pathology that includes testing for genetic and malignant conditions by PCR, RT-PCR, quantitative real-time PCR, FISH, Invader, Southern blot, sequencing, capillary electrophoresis, and gene arrays.
  • Understand the various levels of evidence in medicine and their translation into evidence-based practice.

Practice-based Learning and Improvement:

  • Demonstrate the ability to critically assess the scientific literature.
  • Demonstrate knowledge of evidence-based medicine and apply its principles in assay development and validation.
  • Use multiple sources, including information technology, to optimize life-long learning and support patient care decisions.
  • Develop personally effective strategies for the identification and remediation of gaps in medical knowledge needed for effective practice.

Interpersonal and Communication Skills:

  • Demonstrate the ability to write an articulate, legible, and comprehensive yet concise consultation note; provide a clear and informative report, including when appropriate a precise diagnosis, a differential diagnosis, and recommended follow-up or additional studies.
  • Demonstrate the ability to provide direct communication to the referring physician or appropriate clinical personnel when interpretation of a laboratory assay reveals an urgent, critical, or unexpected finding and document this communication in an appropriate fashion.
  • Demonstrate the ability to work with other clinicians and other health care personnel and administrators to develop clinically advantageous and cost-effective care-delivery strategies.
  • Use effective modes and mechanisms of communication.


  • Interact with others without discriminating based on religious, ethnic, sexual, or educational differences.
  • Demonstrate positive work habits, including punctuality, dependability, and professional appearance.
  • Demonstrate principles of confidentiality with all information transmitted both during and outside a patient encounter.
  • Demonstrate a commitment to excellence and ongoing professional development.
  • Demonstrate interpersonal skills in functioning as a member of a multidisciplinary health care team.

Systems-based Practice:

  • Demonstrate understanding of the role of the clinical laboratory in the health care system.
  • Demonstrate the ability to design resource-effective diagnostic plans based on knowledge of best practices in collaboration with other clinicians.
  • Demonstrate knowledge of basic health care reimbursement methods.
  • Demonstrate knowledge of the laboratory regulatory environment including issues related to home-brew assay development and validation.


  • The Molecular Pathology rotation is integrated into the Clinical Pathology (CP) Consult rotation and it is required for all residents in the Anatomic Pathology/Clinical Pathology and Clinical Pathology programs.
  • Residents are scheduled for this rotation during their senior years in the program.

Duration and Timing of the Rotation:

  • The CP Consult rotation occurs in 4 week blocks throughout the year.

Teaching Staff:

  • Clinical Pathology faculty: Michael H. Creer, MD
  • Molecular Diagnostics Laboratory Supervisor: 


During the first month of the CP Consult rotation, the resident will complete reading assignments, laboratory exercises, and discussions with the Medical Director to obtain a practical understanding of molecular biology and genetics and the molecular methods currently used in clinical laboratories. During the remaining three months of the CP Consult rotation, the resident will complete additional reading assignments on molecular testing for malignant diseases and sign out case material with the Medical Director.

1. Service Responsibilities

  • First month: There are no direct service responsibilities.
  • Later months: The resident should check the pending log in the Molecular Diagnostics database each morning and afternoon and draft appropriate interpretations for sign-out with the Medical Director. The resident should be prepared to discuss results with clinical services when necessary. The resident on the Molecular Pathology rotation may take Clinical Pathology or Anatomic Pathology call.

2. Specific Topics and Reading Assignments


MONTH ONE of CP Consult Rotation

Molecular Biology

Computer-based Molecular Biology Primer:
  • Nucleic acid structure and properties
  • Cell cycle
  • DNA replication and key enzymes
  • Gene structure and organization
  • Transcription and translation
  • Gene regulation
  • Reverse transcription
  • Endo- and exonucleases

Reading: Coleman and Tsongalis. Molecular Diagnostics for the Clinical Laboratorian (2nd Ed.). Totowa, NJ: Humana Press, 2006, Chapter 2.

DNA/RNA Extraction

Computer-based Tutorial:

  • Organic extraction virtual
  • Purity
  • Stability and storage

Laboratory I:

  • DNA extraction from whole blood
  • Pico Green to measure quantity
  • Store for future PCR lab

Molecular Techniques Overview

Computer-based Tutorial:

  • History
  • Restriction enzymes
  • Southern blotting
  • Northern and western blotting
  • DNA sequencing
  • PCR
  • FISH
  • Invader


Computer-based Tutorial:

  • Reaction conditions
  • Primer design
  • Contamination issues
  • Amplicon detection methods
  • Amplicon confirmation:  probes, nesting, RFLP, SSCP, sequencing

Reading: Coleman and Tsongalis. Molecular Diagnostics for the Clinical Laboratorian (2nd Ed.). Totowa, NJ: Humana Press, 2006, Chapters 5, 7, and 9 pages 85-92.

Assay development and validation

Computer-based "Home brew" exercise (FLT3):
  • Literature review
  • Primer and reaction condition selection
  • Validation of procedure

Laboratory II

  • Amplify FLT3 (PCR)

Laboratory III

  • Digest, separate, identify amplicon

Overview of genetic testing

Computer-based tutorial:

  • Applications
  • Risk calculations
  • Screening programs versus diagnostic w/u
  • Inheritance patterns
  • Ethics and genetic counseling

Common Genetic Disorders

Topics for discussion:

  • CF, FV Leiden, Prothrombin G20210A,Hemoglobinopathies, Hemachromatosis,Prader Willi, etc.
  • Methods of detection
  • Intellectual property issues
  • Counseling and reporting issues
  • Case studies

Laboratory IV

  • Set-up Invader assay for Factor V Leiden

Laboratory V

  • Read and interpret Invader results

Reading: Coleman and Tsongalis. Molecular Diagnostics for the Clinical Laboratorian (2nd Ed.). Totowa, NJ: Humana Press, 2006, Chapters 22 and 28.

LATER MONTHS of CP Consult Rotation

Hematology/Oncology Overview

Topics for discussion:

  • History
  • Applications
  • Clonality versus aberrant genes

Gene rearrangements

Topics for discussion:

  • Immunologic gene rearrangement
  • Detecting gene rearrangements
  • Detection by Southern blot technique
  • Detection by PCR (gel versus capillary)

Translocations and oncogenes

Topics for discussion:

  • Leukemias
  • Lymphomas
  • Sarcomas
  • Breast cancer
  • PCR/RT-PCR versus FISH
  • MRD detection

Reading: Coleman and Tsongalis. Molecular Diagnostics for the Clinical Laboratorian (2nd Ed.). Totowa, NJ: Humana Press, 2006, Chapters 32 and 33.

Quality Assurance

Reading: Coleman and Tsongalis. Molecular Diagnostics for the Clinical Laboratorian (2nd Ed.). Totowa, NJ: Humana Press, 2006, Chapters 18-21.

Residents at all levels will pursue a similar course of instruction. Although it is not a goal of the rotation that the resident becomes technically expert in laboratory procedures, the resident must gain an understanding of the technical aspects of each procedure. Adjustment may be made for those with prior molecular biology experience.

While research projects are welcome at any time, this rotation is explicitly not aimed at producing lab results, but rather at understanding what molecular pathology is and is likely to become.

 3.  Teaching Sessions

  • During all months of the Clinical Pathology Consult rotation, the resident will meet with the Medical Director on Monday and Wednesday mornings at 9:00 to discuss reading assignments, laboratory exercises, and patient interpretations.


Method(s) of Evaluation:

  • Evaluation will be performed by the Molecular Diagnostics Medical Director. Criteria used will include attendance, effort in performing bench work, and an informal assessment of knowledge gained from reading and didactic sessions with attention to integration of the knowledge with experience at the lab bench.
  • Residents will be evaluated based on direct observation by faculty
  • After each rotation, residents will be evaluated by faculty in New Innovations


Updated:  3/2012