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: 1A-5A, 7A, 8AB, 10A-12A excluding holiday period 8 Offered 100% Online
Coordinator: Tracy Wilkins Other Faculty:
Location to Report on First Day:
jidong@utmb.edu (409) 772-4866

Goals
This elective aims to provide medical students with a fundamental understanding of the principles and practices of genetics and genomics, preparing them for the era of molecular and genomic medicine.

Objectives
At the conclusion of the course, students will be able to:
1. Demonstrate a fundamental understanding of the principles of genetics and genomics, from basic science to clinical application.
2. Describe the organization of the human genome and the structure and function of genes, and apply this knowledge to explain how genetic and epigenetic changes influence disease onset and severity.
3. Explain the types of DNA variants in the human genome that contribute to human disease, and apply knowledge of genetic and genomic variation to account for phenotypic heterogeneity.
4. Describe molecular mechanisms of disease, including dominant negative effects, loss of function, gain of function, haploinsufficiency, and triplosensitivity.
5. Define the terms pharmacogenetics and pharmacogenomics, and illustrate (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 (PCR), first-, second-, and third-generation sequencing, fragment analysis, chromosome microarray, in situ hybridization, and MLPA; apply this knowledge to describe the principles, applications, and limitations of these technologies.
7. Identify appropriate clinical indications for genetic testing and recognize the limitations and implications of test results.
8. Interpret various types of genetic test results and determine appropriate clinical follow-up based on those findings.

Description of course activities
Students are expected to be available from 2:00–4:00 PM during the course period to review course materials and participate in scheduled meeting discussions.
1. Pre-Test Assessments
At the start of the elective, students will receive pre-test quizzes from Dr. Dong via email. This closed-book assessment is designed to evaluate each student’s baseline understanding of key genetics and genomics concepts.
2. Didactic Lectures
Students will receive four PowerPoint-based lectures covering key topics in laboratory genetics and genomics, including:
• Germline genetics
• Cancer genetics
• Genomic medicine
• Chromosome microarray and cytogenetics
3. Meetings
There will be three one-hour discussion sessions conducted via Microsoft Teams, covering topics from the quizzes and lectures, including Germline Genetics, Cancer Genetics, Genomic Medicine, and Cytogenetics.
4. Case Descriptions
Students will receive a list of selected in-house cases with corresponding UH numbers. Each student will choose one or more cases and write a 1–2 page summary for each, following the provided template. The summary should include the test indications, testing methods, and clinical follow-up of test results, based on information available in Epic.
5. Required Reading
Please read Chapters 2 and 5 from Thompson & Thompson: Genetics in Medicine (8th Edition). These chapters provide essential foundational knowledge for the course.


Example Laboratory Tests:
TSO500 solid tumor mutation panel: Comprehensive genome profiling 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 germline and tumor 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 continued growth of genetics and genomic medicine, this elective will benefit all students interested in the clinical application of genetic and genomic assays.
Genomic medicine is an emerging discipline that integrates an individual’s genomic information into their clinical care, with implications for health outcomes, research, and healthcare policy. It represents the forefront of translating basic genetic research into clinical practice. As new genetic and genomic markers and advanced methodologies are continually introduced into clinical settings, there is an increasing need for research and development of novel assays, as well as for the study of genotype–phenotype correlations underlying health and disease.

    Weekly Schedule
          Estimated Course Activities (Start-Time/Finish-Time):
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
Saturday
Sunday

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

Research / Other Course Activities
(estimated schedule)
Activity Hours per Week
Faculty Contact-Time
Self-Directed Study
Data-Collection/Analysis
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?
   
  C. Format - What method(s) are used to document the student's clinical performance?
    Daily oral feedback   End of period oral feedback   Written feedback
Other

2.  Oral Presentation
  A. Audience - To whom does the student present?
   
  B. Frequency / Duration of Presentation(s)?
   
  C. Format - What guidelines are set for the student's 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)?
    One
  B. Format - What guidelines are set for the student's written work?
    Describe one or more interesting cases including the underlying genetic principles, clinical indications, testing methods, and 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
  Format
    Oral   Written multiple choice   Written essay / short answer   OSCE
Other

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)?
    Students will participate in scheduled meetings, enhance their quiz performance, and submit a comprehensive case description.

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".
    None

7.  Other Modes of Evaluation
  Please explain below.
    None

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.
   
 
B.
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.
   
 
C.
How specifically will this AI build on developing skills from the clerkship year to prepare students for internship?
   
 
D.
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)?
   
 
E.
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?
   
 
F.
How is the student demonstrating drawing clinical conclusions and/or developing a management plan and documentation as an intern would do?
   
 
G.
How and by whom will midpoint feedback be provided to the student? How will you remediate deficiencies identified at midpoint?
   
 
H.
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.