Pharmacogenomics: Introductory Cases

In an effort to expand pharmacogenomics knowledge/education, we are providing introductory cases for use by instructors. We will continue to add more cases over time. Please note that the PGx information should be used in conjunction with other data as a component of overall clinical decision-making. While these cases are strictly PGx-related, we do not want to convey that this is the only information to be considered. These are basic PGx cases intended to introduce students to PGx and evidence-based guidelines from the Clinical Pharmacogenetics Implementation Consortium (CPIC).

Resources

Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines. CPIC Guidelines

Pharmacogenomics Knowledge Base (PharmGKB) guideline annotations. PharmGKB Annotations

Obtaining Instructor Keys

Case instructor keys: As an instructor, email dfkisor@manchester.edu to request the instructor keys for each case-PGx testing report combination. In order to maintain instructor access to the keys, the email must be received from a .edu site, and the instructor must provide a link to their listing as a faculty member of their institution. As an example:

Faculty name: David F. Kisor

Faculty email: dfkisor@manchester.edu

Link to faculty listing: https://www.manchester.edu/academics/colleges/college-of-pharmacy-natural-health-sciences/academic-programs/pharmacy/about-pharmacy/faculty-and-staff-profiles/kisor-david

Suggested Directions for Pharmacogenomics Cases

  1. Choose a case by selecting a “Student Recommendation Form”. This form contains a case and fields requesting information that the student provides based on their assigned “PGx testing report”.
  2. Assign a “PGx testing report” to each student. Currently there are 65 reports available. Click on the following if you want to choose a specific "PGx testing report" relative to a given gene and genotype or phenotype: PGx Testing Report By Gene. Note that for the oncology case, there are three specific PGx testing reports: Onc Results Report 00001, 00002, and 00003.
  3. Have the students complete the “Student Recommendation Form” relative to their assigned “PGx testing report”. Have the student provide the following information:
    • The PGx testing report number in the "Based on report number:" field
    • The relevant gene or genes in the "Relevant gene(s):" field
    • The diplotype for each gene in the "Patient diplotype:" field
    • The metabolism/function/carrier phenotype(s) in the "Patient phenotype:" field
    • Their recommendation based on the case in the "Recommendation:" field
    • Any additional notes in the "Notes:" field
    • Citation(s) that support their recommendation in the "Recommended based on:" field
    • The source (URL) of the citation in the "Found at:" field
  4. Have the student turn-in the completed “Student Recommendation Form” for grading. The point value or other grading associated with each case are up to the instructor.
  5. Use the received instructor keys that are emailed, after supplying the above information (Directions), to grade the “Student Recommendation Form.”
Note: 3/2/20 Note that related to CYP2D6, the definitions of activity scores (AS) has been updated from a consensus study. Please see Standardizing CYP2D6 Genotype to Phenotype Translation. As an example, CYP2D6 *1/*4 is designated as an "extensive metabolizer" in the 2014 CYP2D6-Codeine CPIC guideline update, whereas PharmGKB notes that CYP2D6 *1/*4 relates to the intermediate metabolizer phenotype. The activity score for CYP2D6 *1/*4 is calculated as *1 (1) + *4 (0) = 1. The original CPIC AS range for the extensive/normal metabolizer was 1-2. The new AS consensus for normal metabolizer phenotype is defined as 1.25 ≤ x ≤ 2.25. The *1/*4 value of 1 falls below this range and is now designated as an intermediate metabolizer phenotype, being in the range of 0 < x < 1.25. Please note that the CPIC recommendations for Codeine based on CYP2D6 phenotype are the same for the EM/NM and IM individuals. Our results reports will soon be updated to include the new AS definitions.

Note
: 2/6/20 Soon, we will be updating the PGx testing reports to add a broader panel of results, i.e., more genes. The new genes added to the report include CYP4F2, CFTR, DPYD, TPMT, NUDT15, UGT1A1, and G6PD (G6PD results will be presented to be used with female or male patient cases).

Note: 12/11/19 You can access all of the PGx Testing Reports as a single document (PDF) by clicking on "All Reports_U".

Note: 9/18/19 The testing results reports were updated to include other testing results, specifically HLA-A*31:01. No other changes were made to the results reports. The "_U" denotes the update.

The following students have contributed to the content on the "Pharmacogenomics: Introductory Cases" page and are acknowledged here: Joseph Brown, Ellen Line, Tumi Vo, Mark Botros, Eric Beard

PGx testing reports