Lecture #7 Flashcards
FDA approved PGx drug labels
drug labels: stat very clearly what exactly the drug is used for: one gene-multiple drugs; one drug-multiple genes; one gene-multiple alleles
LUMAKRAS inhibitor of RAS GTPase family indicated for the tx of adult pts with KRAS G12C mutation; targets the KRAS G12C allele, only use this drug with that allele
Who performs PGx tests
CLIA certified labs
clinical laboratory improvement amendments of 1988 are US federal regulatory standards that apply to all clinical lab testing performed on humans in the US, except clinical trials and basic research
CLIA lab can use FDA-approved platform/technology to perform PGx test
Prescription of a PGx test
collect enough information: work closely with the therapeutic team, discuss with the patient, understand the FDA labeling/CPIC guidelines, know the principle of technologies
make informed decisions: strength of the PGx information vs other factors, cost vs benefit, selection of technologies
Understand the clinical implication of a PGx test
the strength between a PGx marker and a clinical consequence varies: nature of PGx studies for discovering the marker: how convincing - sample size, design, replication; evidence in applying the PGx in clinical practice: how effective - genotyping the patients first, and test the outcome; overall impact of the genotype on the phenotype: how important - 20-90% in all drugs
Know the limitations of PGx
PK/PD issues are complex
not all FDA apporved PGx testing is a mandatory test for all related drugs
cost may not bring enough benefit (value is hard to determine)
PK/PD issues are complex
many genetic and non-genetic factors involved
don’t rely on PGx along especially when there is a sign of dangerous ADR
don’t forget non-genetic factors: age, gender, BMI, diet, supplement intake
Not all FDA approved PGx testing is a mandatory test for all related drugs
influence of PGx markers on inter-patient variability in drug response is variable: most somatic PGx markers are necessary, evidence for many germline markers is weak, balance CPIC guidelines and other guidelines
Cost many not bring enough benefit (value is hard to determine)
many tests are not covered by insurance, severe toxicity for many drugs is very rare, few patients may benefit from the test, should consider when PGx info is already available: warfarin
consideration for the technologies
know the strength and limitations of different methods for a PGx test: a targeted test focusing on the major alleles could be cheaper and quicker, but many miss other rare/uncommon important alleles: without testing rare alleles, a haplotype can be assigned to the reference allele: CYP2C9*1 vs 17
balance the cost and info you need: CYP2C95-11 may be more important for african descendants
Other important factors to be considered
family history
race and ethnicity
vulnerable populations
consent/assent
Family history
Family history often indicates an involvement of genetic factors:
* Patient him/herself: previous ADR
* Genetically related relatives
Race and ethnicity
Allele frequency/mutation rate can be very different between populations
* CYP2C9
Vulnerable populations
Children: drug metabolism can be different from adults; Patients with diminished competence and/or decision-making capacity due to medical conditions: schizophrenia, bipolar disorders, some dementias, etc; PGx prescription might be preferred given potentially incomplete information from the patient
Consent/assent
patient/patient’s guardian
Samples for PGx testing
- DNA is the target!
- Any nucleated cells/tissue contains germline DNA
- Principles: Easy to collect; Avoid contamination; Less invasive; Availability of standard procedure (e.g.,commercial kits)
Peripheral blood: white blood cells
White blood cells: DNA
* 2-6ml as a standard amount
* Prefer EDTA-anticoagulant tube (purple top)
* Use sterile technique to prevent bacterial contamination
* Room temperature same day/overnight delivery (1-2 day)
Peripheral blood advantages
- Good and stable yield of DNA
- Less contamination with other DNA sources
- Standard handling procedure
- The most commonly used medical sample
Peripheral blood limitations
- Invasive
- Requires more professional collection and handling
- Pay attention to special patients: Patients treated with chemotherapy, radiotherapy: fewer cells, DNA sequence may be altered; Bone marrow transplantation patients: different DNA
Can we get DNA from RBCs?
no, RBCs do not have a nucleus, therefore no DNA
Cheek swab/brush
- Buccal epithelial cells
- Easy to collect
- Noninvasive
- Room temperature handling
- Less DNA yield than blood: 1-5 μg, but still enough for many types of assays
- DNA yield is variable from patient to patient
- Possible contaminated: food, bacteria etc.: Non-patient DNA, Inhibitors for downstream reaction, Rinse your mouth!
- Some studies showed a lower DNA quality
Tissue
Tumor: fresh biopsy -
High yield of DNA, Snap frozen in liquid N2, -80 ̊C for long term storage-ALWAYS, Dry ice for transportation
Formalin Fixed and Paraffin Embedded (FFPE): DNA is usually degraded, however, many detections are still doable
Tissue samples for testing
foundationone CDx: first FDA approved broad companion diagnostic with Medicare coverage for qualifying pts across all solid tumors including: NSCLC, colorectal, breast, ovarian, melanoma
DNA handling
- DNA is very stable, especially pure and dried (RNA is less stable)
- Factors that affect DNA quality: pH (neutral), avoid oxidants, UV; Repeated freezing and thawing; Bacteria contamination; 4 ̊C for short term storage (1-2 m); -80 ̊C for long term storage
(years); Aliquot into small volume if possible
