Lecture 6: PGx Testing Flashcards
FDA-approved PGx Drug labels
-one gene-multiple drugs
-one drug-multiple genes
-one gene-multiple alleles
-mutations listed in indications/dosing
Who performs PGx tests
-CLIA certified using FDA-approved technology
-find a specific test with the GTR (genetic testing registry)
Prescription of PGx test
-collect enough info (work w team, patient, understand FDA labeling and CPIC guidelines, know principle of tech)
-make informed decision (strength of PGx info vs other factors, cost v benefit, selection of technologies
Clinical implication of PGx test
-strength between PGx marker and clinical consequence varies
-how convincing are PGx studies for discovering the marker (sample size, design, replication))
-how effective is applying PGx in clinical practice (genotype then test outcome)
-overall impact of the genotype on phenotype (20-90% in all drugs
-PGx is still young
PGx levels
-genetic testing required
-recommended
-actional PGx (drug label mentioned, you determine)
-informative PGx
Limitations of PGx
-PK/PD issues are complex
-many genetic and non-genetic factors involved
-dont rely on PGx alone (ex ADR)
-dont forget non-genetic factors (age, BMI, etc)
-not all FDA-approvedPGx testing is mandatory for all drugs
-cost v benefit
Influence of PGx markers on inter-patient variability in drug response is variable (not all PGx testing is mandatory)
-most somatic PGx markers are necessary
-evidence for germline markers is weak
-balance CPIC guidelines and other guidelines
Cost v benefit of PGx testing
-many tests not covered by insurance
-severe toxicity is rare
-few pt may benefit
-consider when PGx information is already available (warfarin)
Consideration for the tech
-know strength and limitations of different methods for PGx test (targeted testing)
-balance cost and info you need (CYP2C9*5-11 may be more important for African)
Targeted test
-focus on major alleles
-cheaper and quicker
-could miss other uncommon/rare alleles
-without testing rare alleles, haplotype can be assigned to the reference allele CYP2C9*1 vs *17
Other factors to consider
-fam hx
-race/ethnicity
-vulnerable populations
-consent/assent (guardians)
Fam history
-often indicates genetic factors
race and ethnicity
-allele freq/mutation rate can be very dif between populations
-CYP2C9
Vulnerable populations
-children (metabolism dif)
-pt w limited competence (schizophrenia, BPD, dementia)
-PGx might be preferred given potentially incomplete info from pt
Samples for PGx testing
-DNA is target
-any nucleated cell/tissue contains germline DNA
-easy to collect, avoid contamination, less invasive, availability of standard procedure (kits)
Peripheral blood
-white blood cells
-2-6mL
-prefer EDTA-anticoagulant tube (purple)
-use sterile technique
-room temp same day/overnight delivery
advantages of blood sample
-good yield of DNA
-less contamination
-standard handling procedure
-most commonly used med sample
limitations of blood sample
-invasive
-more professional collection/handling
-pay attention to special pt (chemo, radiotherapy = fewer cells and DNA seq might be altered, bone marrow transplantation pt have dif DNA)
Cheek Swab/brush
-buccal epithelial cells
-easy, noninvasive, room temp
-less DNA yield than blood (1-5ug)
-yield varies between pt
-possible contamination (food, bacteria, rinse your mouth)
-lower DNA quality
Tissue sample
-fresh biopsy
-formalin fixed and paraffin embedded (FFPE)
fresh tumor biopsy sample
-high yeild
-snap frozen in liquid N2
- -80degrees C long term
-dry ice for transportation
Formalin fixed and paraffin embedded (FFPE) sample
-DNA usually degraded
-many detections still doable
-FoundationONE
-
DNA handling
-DNA very stable, esp pure and dried
-RNA les table
Factors that affect DNA quality
-pH, avoid oxidants, UV
-repeated freezing/thawing
-bacteria contamination
-4C for short term storage (1-2months)
- -80C for long term storage (years)
-aliquot into small volume if possible
