Lecture 7 - Testing Technology Pt1 Flashcards
What are the different drug labels?
- One gene-multiple drugs
- One drug-multiple genes
- One gene-multiple alleles
Who performs pgx tests?
CLIA certified labs
What is the Clinical Laboratory Improvement Amendments of 1988?
US federal regulatory standards that apply to all clinical laboratory testing performed on humans in US, except clinical trials and basic research
What are CLIA labs allowed to use?
FDA approved platform/technology to perform the pgx test
Where can someone find a CLIA lab for a specific test?
GTR: genetic testing registry
What are the specifics of collecting enough info of a prescription of a pgx test?
- Work closely with therapeutic team
- Discuss w the pt
- Understand FDA labeling/CPIC guidelines
- Know principle of tech
What are the specifics of making an informed decision in prescription of a pgx test?
- Strength of pgx info v other factors
- Cost v benefit
- Selection of tech
Why is it important to know the strength and limitations of different methods for pgx test?
A targeted test focusing on major alleles could be cheaper and quicker, but may miss other rare important alleles
What are important factors to be considered?
- Family hx
- Race and ethnicity
- Vulnerable populations
- Consent/assent
What is the samples for pgx testing?
- DNA
- Any nucleated cells/tissue contains germline DNA
What are the principles for collecting a DNA sample for pgx testing?
- Easy to collect
- Avoid contamination
- Less invasive
- Availability of standard procedure
What is peripheral blood?
White blood cells: DNA
What is the standard collecting amount of peripheral blood?
2-6 ml
What is the preferred tube to collect peripheral blood?
EDTA-anticoagulant tube (purple top)
What technique must be used to collect peripheral blood and why?
Use sterile technique to prevent bacterial contamination
What temp and delivery method should be used to deliver peripheral blood sample?
Room temp and same day/overnight delivery (1-2 day)
What are the advantages of using peripheral blood?
- Good and stable yield of DNA
- Less contamination vs other DNA sources
- Standard handling procedure
- Most commonly used medical sample
What are the limitations of using peripheral blood?
- Invasive
- Requires more professional collection and handling
- Pay attention to special patients (ex. bone marrow transplantation patients will have different DNA)
What is collected from a cheek swab/brush?
Buccaneers epithelial cells
What are advantages of the cheek swab/brush?
- Easy to collect
- Noninvasive
- Room temp handling
What are disadvantages of cheek swab/brush?
- Less DNA yield than blood: 1-5 microgram but enough for many types of assays
- DNA yield is variable by patient
- Possibly contaminated
What is collected from tissue collection?
Tumor:
Fresh biopsy:
- High yield of DNA
- Snap frozen in liquid N2 (-80C for long term storage and dry ice for transportation)
Formalin Fixed and paraffin embedded (FFPE):
- DNA is usually degraded
- However, many detections are still doable
What is the first FDA approved tissue sample test?
FoundationOneCDx
How stable is DNA and when?
DNA is very stable, especially pure and dried (RNA is less table)
What are the factors that affect DNA quality?
- pH (neutral), avoid oxidants, UV
- Repeated freezing and thawing
- Bacterial contamination
- 4C for short term storage (1-2 minutes)
- -80C for long term storage (years)
- Aliquot into small volume if possible
