HLA Molecular Pathology Rotation

The molecular pathology rotation will provide the resident a one month introduction to the subspecialty of molecular pathology. The course will provide an introduction to the theory and methods of molecular diagnostics as well as clinical correlation. The rotation can be completed at any point in the residency training, and the objectives will be the same. Exposure to inherited disease testing will be gained in the Molecular Genetics Laboratory with Dr. Koty. An introduction to the HLA laboratory will also be included in either the Molecular Pathology or Cytogenetic rotation, depending upon Dr. Gautreaux's schedule.

Goals and Objectives

Patient Care

Participate in interpretation and preparation of molecular reports.

Gain experience interpreting a range of molecular pathology assays including gel based and real time PCR results.

Act as a consultant to clinicians and other pathologists for the use and selection of molecular diagnostics.  Provide appropriate consultations regarding test selection and test results.

Understand the prognostic and therapeutic consequences of specific molecular test results.

Understand the rationale for specimen requirements used in molecular diagnostics.

Become familiar with basic laboratory procedures used in molecular diagnostics (see medical knowledge below).

Medical Knowledge

  • Review of basic biochemistry of nucleic acids including structure, function, replication, synthesis, and cellular expression.
  • Understand principles of PCR analysis - including real time PCR and RT-PCR.
  • Through reading and discussion with faculty, understand molecular testing methods not currently in use by the lab.
  • Read pertinent journal articles and/or book sections provided by the faculty and be prepared to summarize and discuss the reading material.
  • Prepare and present a short presentation (25-30 minutes) to the laboratory technicians and relevant faculty on a molecular pathology topic of the resident's choice.
  • Become familiar with basic laboratory procedures used in the molecular diagnostics laboratory.  Procedures observed must include:
  1. DNA/RNA extraction (both manual and automated)
  2. RT-PCR
  3. Preparation of a master mix and sample for PCR
  4. Sample set up for real time PCR and technical interpretation.
  5. Sample set up and HPV testing on the Cobas 4800
  6. Sample set up for T/B cell clonality and interpretation using Genemapper software.
  • Participate in case write-ups and research projects as interested.

Practice-Based Learning and Improvement

  • Participate in the education of other health professionals by providing consultative services regarding test requests and patient results.
  • Participate in the education of other health professionals by giving a short presentation on a molecular pathology topic of interest.
  • Manage one's time and schedule to ensure time for laboratory observation, reading, and sign out.
  • Self-assess areas of limited knowledge and focus self-study in these areas.
  • Effectively use resource materials to research new or unusual case results.
  • Appropriately use software and electronic resources to create a presentation on a molecular pathology topic of choice.
  • Select and present cases at the twice monthly CP conference.
  • Complete an evaluation of the rotation at the end of the course.

Interpersonal and Communication Skills

  • Communicate effectively with laboratory staff, clinicians, and other pathologists.
  • If more than one resident is on the rotation at a time, work effectively as a team to establish a schedule and participate in group discussions of reading assignments.
  • Provide consultative services regarding test requests and results.
  • Present a molecular pathology topic in an effective, clear, concise, and informative manner to peers.
  • Work as a team with the laboratory staff to schedule time to observe PCR procedures.


  • Act in a professional manner.  
  • Maintain patient privacy.
  • Be responsible for own schedule.
  • Be available for consults.
  • Return phone calls and pages in a timely manner.

Systems-Based Practice

  • Understand the appropriate use of molecular diagnostic services.
  • Learn about billing and reimbursement for molecular testing.
  • Review any proficiency testing results performed during the rotation.
  • Attend and participate in the weekly PCR Lab meeting.
  • Attend and participate in the monthly Anatomic Pathology quality assurance/ quality improvement meeting (“ALPO”).
  • Review CAP molecular pathology checklist questions to become familiar with the accreditation requirements.
  • Review PCR procedure manual as necessary to supplement understanding of molecular diagnostic techniques.
  • Evaluate and trouble-shoot (in conjunction with faculty) problems identified by the laboratory staff.
  • Understand the requirements for test validation.  Review data for any tests currently being validated in the lab. Participate in test development and/or validation as available.

Resident Responsibilities

  • Attend weekly PCR Lab meeting and monthly ALPO quality assurance meeting.
  • Complete assignments and meet regularly with Dr. O’Neill for molecular topic discussions.
  • Schedule time to spend in the HLA lab and meet with Dr. Gautreaux.
  • Schedule time to spend in the Molecular Genetics Lab and meet with Dr. Koty.
  • Observe laboratory procedures as detailed in the rotation syllabus (see Goals and Objectives)
  • Interpret data and prepare reports for assays performed in the PCR Lab.
  • Present cases at twice monthly CP conference.
  • Give a 25-30 minute presentation to the molecular pathology lab technologists on a molecular pathology topic of the resident’s choice.
  • Complete a course evaluation


Reading Materials

  1. Leonard, Debra G.B. (ed).  Molecular Pathology in Clinical Practice. Second Edition.  Springer International Publishing, 2016.
  2. Bartlett, John M.S, Shaaban, Abeer, and Schmitt, Fernando. (eds).  Molecular Pathology: A Practical Guide for the Surgical Pathologist and Cytopathologist. Cambridge University Press, 2015.
  3. Available Online Textbooks Through Carpenter Library
  • Leonard, Debra G.B (ed). Molecular Pathology in Clinical Practice. Springer Science and Business Media, LLC, 2007.
  • Coleman, William B and Tsongalis, Gregory J (eds).  Molecular Diagnostics: For the Clinical Laboratorian. Second Edition.  Humana Press, 2006.
  • Nussbaum, Robert L., McInnes, Roderick R., and Willard, Huntington F. Thompson & Thompson Genetics in Medicine.  Eighth Edition. Elsevier Inc, 2016.

Supplementary Materials Available

Online resources 

  1. Fundamentals of molecular pathology 
  2. Association for Molecular Pathology 
  3. Published clinical practice molecular testing guidelines
  4. Catalogue of somatic mutations in cancer
  5. Human Genome Variation Society (nomenclature for variants)
  6. Genome browser for vertebrate genomes
  7. BLAT search genome
  8. Online Mendelian Inheritance in Man


The faculty will evaluate the resident's performance at the end of the rotation with input from the laboratory technologists. Evaluation will be based on the following general points:

  • Review and interpretation of molecular results with incorporation of clinical information
  • Knowledge of molecular testing principles, basic and clinical science
  • Demonstrates skills of self-learning and professionalism
  • Reads assigned materials; able to discuss with director
  • Oral presentation skills
  • Understands general principles of billing and reimbursement
  • Demonstrates knowledge of applicable quality control and assessment

The residents will also have the opportunity to evaluate the faculty and the rotation itself.