Molecular Genetic Pathology Fellowship

Molecular Pathology Laboratory Rotation

Goals and Objectives

Medical Knowledge

Upon completion of the molecular pathology laboratory rotation(s), the fellow is expected to have in depth knowledge of:

  1. The basic structure and function of nucleic acids and proteins, and their role in cellular function.
  2. The types of genetic and epigenetic alterations that occur in various conditions including:
    1. Classical Mendelian Disorders.
    2. Disorders with repeat expansions such as Fragile X syndrome and the concept of anticipation.
    3. Imprinting disorders, including Prader Will/Angleman syndromes.
    4. Disorders associated with copy-number alterations.
    5. Individual variations in drug metabolism.
    6. Hematologic Neoplasms.
    7. Solid Tumors.
  3. Demonstrate an understanding of the relationship between the nature of these changes and the types of tests used to detect these alterations, the performance of and interpretation of these tests, and their pitfalls.
    1. Southern blot
    2. PCR and its variations: RT-PCR, Real time PCR, Real time RT-PCR, ARMS
    3. DNA sequencing and fragment length analysis on the ABI 3130
    4. High throughput sequencing approaches
    5. SNP analysis using dHPLC
    6. Array CGH
  4. Demonstrate mastery of the technical, quality control and interpretive aspects of tests performed in the Molecular Diagnostic Laboratory as well as their clinical implications. This depth of knowledge will be obtained by performing each type of testing in the laboratory according to a personalized schedule depending on prior experience.
    1. Southern Blotting and, when validated, PCR-based tests for Fragile X repeat expansions.
    2. Southern Blot tests for Prader-Willi/Angleman Syndrome.
    3. Direct DNA sequencing for BMPR2 mutations in primary pulmonary hypertension and LGI1 mutations in autosomal dominant epilepsy with auditory features, and other sequencing tests developed in the laboratory.
    4. Array-based primer extension screen for known mutations in Stargardt Disease (ABCA4) and Leber Congenital Amaurosis (multiple genes).
    5. Tests for thrombophilia susceptibility.
    6. Cystic fibrosis carrier screening.
    7. HPV tests for cervical cancer screening.
    8. B-cell and T-cell clonality testing.
    9. Tests for tumor associated translocations.
    10. JAK-2 mutation testing for myeloproliferative neoplasms.
    11. FLT3 and NPM1 mutation testing of acute leukemias.
    12. KRAS and BRAF mutation tests of colorectal cancer, for TKI resistance.
    13. Microsatellite instability testing.
    14. Other tests currently being validated in the laboratory.
  5. Demonstrate an understanding of various aspects of laboratory management. This includes:
    1. Quality assurance and troubleshooting of the above molecular diagnostic tests;
    2. Validation and evaluation of new assays developed in the laboratory (each fellow will be expected to validate at least one new assay).
    3. Evaluation of instrumentation to perform assays in the laboratory, including:
      • Automated nucleic acid extraction instrumentation.
      • Automated liquid dispensers.
      • Thermocyclers - conventional and real-time.
      • Capillary electrophoresis equipment.
      • Bead-array flow cytometer.
      • Array scanners.
      • Mass Spectrometry.
      • Other equipment used for testing.

Patient Care

Fellows shall apply the above knowledge on a continuing basis to patient care.

  1. Explain the clinical implications and limitations of the tests performed in the laboratory and, when appropriate, gather essential and accurate patient information, including data from other labs, histopathologic data, immunophenotypic data when relevant, contact clinicians as appropriate for relevant information on patient history, and integrate this information to arrive at a clinically relevant conclusion of either diagnosis, prediction, prognosis, or risk assessment.
  2. When these tests are inadequate to answer relevant clinical questions, help the treating physician identify clinically appropriate tests, laboratories performing such tests, and assist the clinician in interpreting these tests.
  3. Offer education and consultation services in MGP to health care providers.
  4. Use their knowledge of which tests have time-critical results that will drive clinical and therapeutic decisions, and contact clinicians with results of these assays.

Practice Based Learning and Improvement

Fellows shall continuously improve their ability to investigate and evaluate their diagnostic and consultative practices, appraise and assimilate scientific evidence, and improve their patient care practices. Specifically, they shall:

  1. Participate actively in the Association for Molecular Pathology, and other societies that promote MGP.
  2. Continuously update their knowledge in sciences and clinical fields related to the tests performed in the Molecular Pathology Laboratory, through literature searches and attendance at conferences.
  3. Review validation protocols of tests currently in the laboratory, and participate in new test development and/or validation.
  4. Actively educate and instruct others in matters related to MGP.
  5. Ask a definable question or questions related to tests being performed in the molecular pathology laboratory, new MGP issues that may arise or have arisen during or before the rotation, search for relevant scientific information, critically appraise the information using the principles of evidence-based medicine, evaluate the significance of this to the practice of molecular genetic pathology and present this information at departmental conferences (clinical pathology journal club, Pathology Chief of Service conference, clinical genetics conference, laboratory specific conference) and/or at
  6. national conference(s).
  7. Design, conduct, and write up a research project relevant to Molecular Genetic Pathology

Interpersonal and Communication Skills

During the rotation, fellows must demonstrate interpersonal and communication skills that result in effective information exchange with other health care providers, laboratory personnel, patients, and patients' families. Towards this end they shall:

  1. Develop effective working relationships with professional and technical staff, and outside consultants.
  2. Demonstrate effective verbal communication skills when communicating results to clinicians, at the appropriate level for the information being transmitted; convey and explain test results clearly, precisely, and concisely to physicians in direct conversations, or at conferences; communicate effectively with technical personnel when troubleshooting assays, or when managing the laboratory.
  3. Develop excellent written skills for communication of complicated results when issuing reports, for the development and implementation of new laboratory policies and procedures, and for presentation of scientific research data, as appropriate.
  4. Develop presentation skills that include selection of appropriate presentation materials and visual aids, good oral presentation and mannerisms, and the ability to answer questions effectively.

Professionalism

During the rotation, fellows must demonstrate a commitment to professional responsibilities, adherence to highest ethical standards, and respect for all. Towards this, they shall:

  1. Demonstrate respect and compassion for the patient and a dedication to patient care.
    1. Treat each sample as belonging to a patient, and not just a number.
    2. Show respect for the confidentiality of all patient information.
    3. Understand the need for and the role of appropriate informed consent prior to genetic testing.
  2. Conduct themselves with integrity and honor;
  3. If they identify any technical or clerical errors, or perceive inconsistencies that raise questions concerning the reliability of the obtained results, quickly bring this to the attention of those responsible so that reporting errors may be prevented, or corrected immediately.
  4. Demonstrate reliability in all assigned activities.
  5. Demonstrate perfect attendance at all laboratory activities.
  6. Demonstrate completeness in the workup of all cases in the molecular pathology laboratory.
  7. Educate other health care professionals in the technical functioning and clinical implications of the various functions of the molecular pathology laboratory. I am not sure what this sentence means,
  8. Actively assume responsibility and leadership roles;
    1. Progressively assume greater responsibility in the review of cases and quality control. By the second month of the rotation, the resident should be able to independently interpret laboratory results, identify problems and propose courses of action to remedy them.
    2. Progressively assume greater responsibility in the evaluation of various aspects of laboratory management.
    3. Progressively assume greater responsibility in the oversight of residents rotating in the lab. By the second month the fellow should be able to teach the residents the theoretical and technical aspects of the tests performed.
  9. Pursue continuing professional growth and educational opportunities.

Systems Based Practice

Fellows must demonstrate an awareness of and responsiveness to the larger context and system of health care and the ability to call on system resources to provide molecular genetic pathology services that are of optimal value. Towards this they shall, where appropriate:

  1. Provide guidance to clinicians and counselors to ensure that molecular testing performed in the molecular pathology is used and integrated into patient care in an appropriate and cost-efficient manner.
    1. Understand the clinical implications and cost-effectiveness of the tests performed in the molecular pathology laboratory and their implications for patient management.
    2. Provide information on alternative testing approaches that may be used, when appropriate.
  2. Demonstrate knowledge of scientific, legal, and ethical issues relating to molecular testing.
    1. Understand standards and regulations governing laboratory operations including Clinical Laboratory Improvement Amendments (CLIA), and evaluate laboratory compliance with these standards and regulations.
    2. Fellows will evaluate the compliance of the laboratory with these standards using the CAP checklists and NY State standards. They will assist the laboratory director in developing the annual laboratory Quality Improvement Program and present a review of this semi-annually at the departmental QA conference.
  3. Demonstrate an understanding of and sensitivity ethical issues related to molecular genetic testing, as well as knowledge of NY State regulations regarding informed consent for molecular genetic testing.
    1. Understand the implications not only to patients, but also their families, of results of molecular genetic tests.
    2. Understand the need for informed consent, the legal requirement for informed consents in NY State, and monitor compliance of the laboratory with this requirement.
  4. Demonstrate knowledge of the impact of laboratory management and activities on other health care professionals, organizations, and society.
  5. Understand financial and economic systems in which the molecular laboratory operates, including billing, the appropriate use of current procedural terminology codes, diagnostic codes, and health insurance and reimbursement issues.
  6. Practice cost-effective health care and resource allocation that does not compromise quality of care.
  7. Be an advocate for quality patient care and contribute to clinician education.
  8. Demonstrate the ability to assess, understand, and use the resources, personnel, and health care systems necessary to provide optimal care.
 

Administration Contact


  • Ms. Casey Schadie
  • Coordinator, Residency Training Program
  • Department of
    Pathology & Cell Biology

    Columbia University College of
    Physicians & Surgeons

    630 W. 168th Street
    New York, NY 10032
  • Tel: 212 305-5697
    e-Mail: cs2222@columbia.edu

 
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