PATU-4031 - Fundamentals of Molecular Genetics and Genomics

PATU-4031 - Fundamentals of Molecular Genetics and Genomics

Elective Title: Fundamentals of Molecular Genetics and Genomics
Course Number: PATU-4031
Elective Type: clinical Duration/Weeks: 2 Max Enrollment: 5
Prerequisites: Successful completion of Year 2
Additional Requirements: N/A
Responsible Faculty Director: Jianli Dong, MD, PhD Periods Offered: 5A-7A, 10A-12A excluding holiday period 8 Offered 100% Online
Coordinator: Tracy Wilkins Other Faculty:
Location to Report on First Day: (409) 772-4866

This elective would like to provide medical student an opportunity to have fundamental understanding of the principles and practices of genetics and genomics, to be better prepared for the age of molecular and genomic medicine.

At the conclusion of the course, students will be able to:
1. Have fundamental understanding of the principles of genetics and genomics, from basic science to clinical application.
2. Describe the organization of the human genome, the structure and function of genes. Apply knowledge of the human genome structure and function to explain how genetic and epigenetic changes influence disease onset and severity.
3. Describe the types of DNA variants in the human genome that lead to human disease. Apply knowledge of genetic/genomic variation to explain phenotypic heterogeneity.
4. Describe molecular mechanisms of disease, including dominant negative, loss of function, gain of function, haploinsufficiency, and triplosensitivity.
5. Define the terms pharmacogenetics and pharmacogenomics and explain (using Plavix and Warfarin as examples) how genetic variants can affect drug response in individual patients.
6. Compare and contrast molecular diagnostic techniques used in genetic testing including polymerase chain reaction, first, second, and third generation sequencing, fragment analysis, chromosome microarray, in situ hybridization, and MLPA. Apply knowledge of human genetics and genomics to describe the principles, uses and limitations of genetic testing technologies.
7. Identify appropriate indications for genetic testing and recognize the limitations and implications of test results.
8. Understand interpretation of various test results, and appropriate clinical follow-up.

Description of course activities
Students should be available 2-4PM Tuesday-Friday during the course period to review course material and participate in discussions.

1. Discussion of course objectives: At the beginning of the course, a 1-hour session will be used to discuss objective topics and assign learning issues. This would be a part of measuring student background and interest.
2. Didactic lectures: Four one-hour Power point lectures of laboratory genetics and genomics (germline genetics, cancer genetics, chromosome microarray/cytogenetics, genomic medicine) will be provided to students.
3. Real test based learning of genetics and genomic concepts: Tests performed in UTMB Molecular Diagnostics Laboratory (e.g., tests listed below) will be utilized for students to apply genetics and genomics principles to the use of genetics and genomics testing in medical practice to a diverse population of patients. Students will have the opportunity to describe the genetics and genomics concepts, clinical indications, and result interpretations of these tests.
4. Laboratory activity: Students will participate in clinical laboratory observation activities to compare and contrast various molecular diagnostic techniques used in the laboratory. Students will learn principles of techniques including polymerase chain reaction, DNA sequencing, fragment analysis, chromosome microarray, in situ hybridization, and next generation sequencing.

Example Laboratory Tests:
AmpliSeq solid tumor mutation panel: Examine 47 genes with diagnostic, prognostic, and predictive value for various solid tumors.
BRAF mutation: Predictive (anti-mBRAF, anti-MEK, anti-EGFR treatment), classification (MSI CRC)
CFTR NGS sequencing: Cystic fibrosis carrier screen and diagnosis
CytoScan and onco Scan chromosome microarray: Detect DNA copy number variations in blood samples
Fragile X: Diagnosis of fragile X CGG tri-nucleotide expansion
HER2/ERBB2 FISH: Companion diagnostics for anti-ERBB2 therapy
HFE mutation: Diagnosis of hereditary hemochromatosis
Huntington: Diagnosis of Huntington disease
KRAS/NRAS mutation: Predict cancer anti-EGFR/anti-MEK treatment
OncoScan chromosome microarray: Detect DNA copy number variations in degraded samples (tumor and POC)
Plavix and Warfarin pharmacogenetics (CYP2C19, CYP2C9, VKORC): Guiding Plavix and Warfarin treatment

Type of students who would benefit from the course
With the continuing growth of genetics and genomics medicine, all students who are interested in the clinical use of genetics and genomics assays will benefit from this elective.
Genomic medicine is an emerging medical discipline that involves using genomic information about an individual as part of their clinical care and the health outcomes and policy implications of that clinical use. Genomic medicine is at the frontline of translating basic research to clinical care. New genetics and genomics markers and improved methodologies are continuously introduced to clinical practice. There is a great need in research/development of genetics and genomics assays and genotype-phenotype correlations of variants in health and disease.

Weekly Schedule
  Clinical Activities (estimated schedule)  
Day of Week   AM   PM
Monday 8-12 1-5
Tuesday 8-12 1-5
Wednesday 8-12 1-5
Thursday 8-12 1-5
Friday 8-12 1-5

 Average number of patients seen per week:
 Call Schedule: N/A

Research Activities (estimated schedule)
Activity Hours per Week
Faculty Contact-Time
Self-Directed Study
Other Activity will depend on student interest and available projects.

Method of Student Evaluation
1.  Clinical Observation
  A. Where are students observed on this elective?
    Inpatient Service   Ambulatory   Surgery   Standardized patients
Patients simulators   Other
  B. Frequency - How often are students observed clinically?
    Daily by faculty and staff in Molecular Diagnostics Laboratory
  C. Format - What method(s) are used to document the student's clinical performance?
    Daily oral feedback   End of period oral feedback   Written feedback

2.  Oral Presentation
  A. Audience - To whom does the student present?
    Faculty and staff in Molecular Diagnostics
  B. Frequency / Duration of Presentation(s)?
    If interested, once during the rotation
  C. Format - What guidelines are set for the student's presentation?
    PowerPoint presentation
  D. Assessment - Who assesses the student's presentation performance?
    Self-assessment   Peer assessment   Faculty assessment
  E. Method of content selection
    Current cases  Student-selected topic   Assigned topic

3.  Written Assignment (H&P's, notes, papers, abstracts, etc.)
  A. Frequency of written assignment(s)?
  B. Format - What guidelines are set for the student's written work?
    Describe 1-2 tests observed during the elective, including genetics principles, clinical indications, methods, result interpretation.
  C. Length of written assignment(s)?
    Abstract   Annotated bibliography   1 - 2 page paper   3+ page paper
  D. Are recent references required?   No    If yes, how are they selected?
  E. Method of content selection - e.g. student-selected, relate to cases, etc.?
  F. Audience - Who assesses the student's written performance?
    Peer Assessment     Faculty Assessment     Other

4.  Examination
    Oral   Written multiple choice   Written essay / short answer   OSCE

5.  Extra Course Activities
  What expectations do you have for the student to demonstrate participation in the elective (e.g. small group activities, seminars, thoughtful questions, providing resources, journal club, resident lecture attendance)?
    Student will participate in Molecular Conferences. Student is encouraged to discuss new advance in genetics and genomics medicine.

6.  Additional Costs
  Please list any additional costs and/or purchases (books, materials, movies to watch, etc.) that are required for this course. Include an estimated total cost. If there are no additional costs, please enter "None".

7.  Other Modes of Evaluation
  Please explain below.

8.  If this course is an Acting Internship, please complete the following:
  A. Objectives for the AI should relate directly to the Entrustable Professional Activities (EPAs). Each AI should describe how the four key Year-4 EPAs that our school has identified as being Year-4 skills are assessed. The Year-4 objectives are:
1. Entering and discussing orders/prescriptions.
2. Give or receive patient handover to transition care responsibility.
3. Recognizing a patient requiring urgent or emergent care and initiating management.
4. Obtaining informed consent for tests and procedures.
Specify how the student will be given formative feedback on their clinical skills.

Year-4 students should demonstrate mastery of EPAs they developed in the clerkship year, including recommending and interpreting common diagnostic and screening tests, and performing general procedures of a physician. They should be able to demonstrate masterfully and independently skills they mastered in Years 2-3, including efficiently performing comprehensive admission-notes and succinct daily progress notes and perform accurate, concise, and hypothesis-driven clinical presentations, form clinical questions and retrieve evidence to advance patient care. They should be able to demonstrate basic understanding of and beginning mastery of collaborate as a member of the interprofessional team and identify system failures and contribute to a culture of safety improvement.

List advanced clinical skills that a student will be assured an opportunity to practice.

How specifically will this AI build on developing skills from the clerkship year to prepare students for internship?

What opportunities will typically be available to all students who take this AI (procedures, required presentations, etc.)? What opportunities may be available based on patient load/presentation or student initiative (ie. Writing a case report)?

An AI should have expectation of a minimum of 32 hours per week of clinical responsibilities. Duty hours should be capped at ACGME limits for an intern, thus up to 24 hours followed by 4 hours of activities related to patient safety, education, and handoff. Students cannot work more than 80 hours per week averaged over 4 weeks. They can only have 1 day off in a 7-day work week with 8 hours off between shifts.

Clinical responsibilities will vary depending on specialty, but how is the student functioning with work commensurate to a PGY1 with an appropriate level of training?

How is the student demonstrating drawing clinical conclusions and/or developing a management plan and documentation as an intern would do?

How and by whom will midpoint feedback be provided to the student? How will you remediate deficiencies identified at midpoint?

Acting Internship students often seek letters of recommendation following their experience. How many different Faculty will work directly with the student and have knowledge of the student's abilities to detail in a written evaluation? Describe the degree of supervision and interaction with faculty vs. residents or other providers and how feedback will be obtained if more direct work is with residents or other providers.