Quiz 2 (Lectures 5-8)

Question 1

which labs perform PGx testing?

Answer 1

CLIA certified labs (clinical laboratory improvement amednments)

Question 2

where can we find a CLIA lab for a specific test?

Answer 2

GTR (genetic testing registry)

Question 3

what are the 4 PGx levels?

Answer 3

-genetic testing required
-genetic testing recommended
-actionable PGx (drug label mentions, you determine)
-informative PGx (suggestive)

Question 4

CYP2C9*5-11 may be important for which population?

Answer 4

African descendants

Question 5

important factors to consider for PGx testing (4 of them)

Answer 5

-family history
-race and ethnicity
-vulnerable populations (ex. children, pts with medical conditions)
-consent/assent (parent/guardian)

Question 6

target for PGx testing

Answer 6

DNA

Question 7

any _______ cells/tissue contains germline DNA

Answer 7

nucleated

Question 8

sample for PGx testing need to meet what 4 principles?

Answer 8

-easy to collect
-avoid contamination
-less invasive
-availability of standard procedure (e.g. commercial kits)

Question 9

how many mL of WBC do we need to sequence?

Answer 9

2-6 mL

Question 10

to obtain WBCs from sample for testing, which agent is preferred?

Answer 10

EDTA

Question 11

do we use RBCs as a sample for PGx testing?

Answer 11

no, they do not have nucleus, so there is no DNA to be tested

Question 12

which patients do we have to pay special attention to when getting sample of their WBCs for PGx testing?

Answer 12

-pts treated with chemo or radiotherapy (fewer cells, DNA sequence may be altered)
-bone marrow transplant pts (different DNA)

Question 13

what is the yield for a cheek swab for PGx testing?

Answer 13

1-5 ug (less DNA yield than blood, but still enough for many types of assays)

Question 14

why should we rinse our mouth before a cheek swab for PGx testing?

Answer 14

we could have contamination in our mouth from food, bacteria, etc.

Question 15

what is the long term storage temperature for a tumor tissue sample for PGx testing?

Answer 15

-80 C (and always use dry ice for transportation)

Question 16

two processes for tumor tissue sample collection

Answer 16

-fresh biopsy
-formalin fixed and paraffin embedded (FFPE)

Question 17

what is Foundation One CDx?

Answer 17

first FDA-approved broad companion diagnostic that is clinically and analytically validated for all solid tumors.

Question 18

which is more stable, DNA or RNA?

Answer 18

DNA

Question 19

what temperature should be used for short-term storage of DNA?

Answer 19

4 C

Question 20

what buffers are needed for PCR?

Answer 20

pH and Mg2+

Question 21

which enzyme is used for PCR?

Answer 21

Taq DNA polymerase

Question 22

PCR amplifies DNA from ____ DNA molecules of _________ chromosomes

Answer 22

both; homologous

Question 23

which PGx testing detects only known alleles and SNPs?

a. DNA chip
b. sequencing

Answer 23

a. DNA chip

Question 24

which PGx testing detects both known and unknown alleles?

a. DNA chip
b. sequencing

Answer 24

b. sequencing

Question 25

is DNA chip high or low throughput?

Answer 25

high (up to 5 million SNPs can by genotyped simultaneously)

Question 26

which of the following is described below?

-low throughput
-targeted sequencing (one specific DNA fragment)

a. Sanger sequencing
b. next gen sequencing

Answer 26

a. Sanger sequencing

Question 26

which of the following is described below?

-high-throughput
-parallel sequencing
-massive sequencing (multiple DNA fragments simultaneously)

a. Sanger sequencing
b. next gen sequencing

Answer 26

b. next gen sequencing

Question 27

Sanger sequencing incorporates what kind of nucleotides?

Answer 27

chain-terminating dideoxynucleotides (ddNTPs)

Question 28

true or false: Sanger sequencing can detect both known and unknown alleles

Answer 28

true

Question 29

which is more expensive per base pair, Sanger sequencing or DNA chip?

Answer 29

Sanger sequencing

Question 30

true or false: next gen sequencing has a higher total cost and higher cost per SNP than DNA

Answer 30

false (has higher total cost but very low cost per SNP)

Question 31

true or false: next gen sequencing can detect all known or unknown alleles

Answer 31

true

Question 32

which of the following is not high-throughput?

a. DNA chip
b. Sanger sequencing
c. next gen sequencing

Answer 32

b. Sanger sequencing

Question 33

what is sequencing coverage?

Answer 33

the avg number of reads that align to, or “cover”, known reference bases

Question 34

what is the normal depth of coverage for detecting human genome mutations?

Answer 34

10x to 30x

Question 35

true or false: next gen sequencing is slow but has a low error rate

Answer 35

false (fast but high error rate)

Question 36

what are the two reasons why NGS requires sequencing every base in a sample several times?

Answer 36

-need multiple observations per base to come to a “reliable base call”
-reads are not distributed evenly over entire genome, bc the reads will sample the genome in a random and independent manner

Question 37

which of the two is acquired?

a. germline
b. somatic

Answer 37

b. somatic

Question 38

which can be passed to a child?

a. germline
b. somatic

Answer 38

a. germline

Question 39

true or false: the germline does not exist in the somatic genome

Answer 39

false

Question 40

true or false: somatic does not exist in the germline genome

Answer 40

true

Question 41

which of the following is not usually used for somatic mutation detection?

a. Sanger sequencing
b. NGS
c. DNA chips
d. karyotyping
e. immunohitobiochemistry (IHC)

Answer 41

c. DNA chips