Lecture 7 - Testing Technology Pt1

Question 1

What are the different drug labels?

Answer 1

• One gene-multiple drugs
• One drug-multiple genes
• One gene-multiple alleles

Question 2

Who performs pgx tests?

Answer 2

CLIA certified labs

Question 3

What is the Clinical Laboratory Improvement Amendments of 1988?

Answer 3

US federal regulatory standards that apply to all clinical laboratory testing performed on humans in US, except clinical trials and basic research

Question 4

What are CLIA labs allowed to use?

Answer 4

FDA approved platform/technology to perform the pgx test

Question 5

Where can someone find a CLIA lab for a specific test?

Answer 5

GTR: genetic testing registry

Question 6

What are the specifics of collecting enough info of a prescription of a pgx test?

Answer 6

• Work closely with therapeutic team
• Discuss w the pt
• Understand FDA labeling/CPIC guidelines
• Know principle of tech

Question 7

What are the specifics of making an informed decision in prescription of a pgx test?

Answer 7

• Strength of pgx info v other factors
• Cost v benefit
• Selection of tech

Question 8

Why is it important to know the strength and limitations of different methods for pgx test?

Answer 8

A targeted test focusing on major alleles could be cheaper and quicker, but may miss other rare important alleles

Question 9

What are important factors to be considered?

Answer 9

• Family hx
• Race and ethnicity
• Vulnerable populations
• Consent/assent

Question 10

What is the samples for pgx testing?

Answer 10

• DNA
• Any nucleated cells/tissue contains germline DNA

Question 11

What are the principles for collecting a DNA sample for pgx testing?

Answer 11

• Easy to collect
• Avoid contamination
• Less invasive
• Availability of standard procedure

Question 12

What is peripheral blood?

Answer 12

White blood cells: DNA

Question 13

What is the standard collecting amount of peripheral blood?

Answer 13

2-6 ml

Question 14

What is the preferred tube to collect peripheral blood?

Answer 14

EDTA-anticoagulant tube (purple top)

Question 15

What technique must be used to collect peripheral blood and why?

Answer 15

Use sterile technique to prevent bacterial contamination

Question 16

What temp and delivery method should be used to deliver peripheral blood sample?

Answer 16

Room temp and same day/overnight delivery (1-2 day)

Question 17

What are the advantages of using peripheral blood?

Answer 17

• Good and stable yield of DNA
• Less contamination vs other DNA sources
• Standard handling procedure
• Most commonly used medical sample

Question 18

What are the limitations of using peripheral blood?

Answer 18

• Invasive
• Requires more professional collection and handling
• Pay attention to special patients (ex. bone marrow transplantation patients will have different DNA)

Question 19

What is collected from a cheek swab/brush?

Answer 19

Buccaneers epithelial cells

Question 20

What are advantages of the cheek swab/brush?

Answer 20

• Easy to collect
• Noninvasive
• Room temp handling

Question 21

What are disadvantages of cheek swab/brush?

Answer 21

• Less DNA yield than blood: 1-5 microgram but enough for many types of assays
• DNA yield is variable by patient
• Possibly contaminated

Question 22

What is collected from tissue collection?

Answer 22

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

Question 23

What is the first FDA approved tissue sample test?

Answer 23

FoundationOneCDx

Question 24

How stable is DNA and when?

Answer 24

DNA is very stable, especially pure and dried (RNA is less table)

Question 25

What are the factors that affect DNA quality?

Answer 25

• 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