Quiz 2 (Lectures 5-8) Flashcards
which labs perform PGx testing?
CLIA certified labs (clinical laboratory improvement amednments)
where can we find a CLIA lab for a specific test?
GTR (genetic testing registry)
what are the 4 PGx levels?
-genetic testing required
-genetic testing recommended
-actionable PGx (drug label mentions, you determine)
-informative PGx (suggestive)
CYP2C9*5-11 may be important for which population?
African descendants
important factors to consider for PGx testing (4 of them)
-family history
-race and ethnicity
-vulnerable populations (ex. children, pts with medical conditions)
-consent/assent (parent/guardian)
target for PGx testing
DNA
any _______ cells/tissue contains germline DNA
nucleated
sample for PGx testing need to meet what 4 principles?
-easy to collect
-avoid contamination
-less invasive
-availability of standard procedure (e.g. commercial kits)
how many mL of WBC do we need to sequence?
2-6 mL
to obtain WBCs from sample for testing, which agent is preferred?
EDTA
do we use RBCs as a sample for PGx testing?
no, they do not have nucleus, so there is no DNA to be tested
which patients do we have to pay special attention to when getting sample of their WBCs for PGx testing?
-pts treated with chemo or radiotherapy (fewer cells, DNA sequence may be altered)
-bone marrow transplant pts (different DNA)
what is the yield for a cheek swab for PGx testing?
1-5 ug (less DNA yield than blood, but still enough for many types of assays)
why should we rinse our mouth before a cheek swab for PGx testing?
we could have contamination in our mouth from food, bacteria, etc.
what is the long term storage temperature for a tumor tissue sample for PGx testing?
-80 C (and always use dry ice for transportation)
two processes for tumor tissue sample collection
-fresh biopsy
-formalin fixed and paraffin embedded (FFPE)
what is Foundation One CDx?
first FDA-approved broad companion diagnostic that is clinically and analytically validated for all solid tumors.
which is more stable, DNA or RNA?
DNA
what temperature should be used for short-term storage of DNA?
4 C
what buffers are needed for PCR?
pH and Mg2+
which enzyme is used for PCR?
Taq DNA polymerase
PCR amplifies DNA from ____ DNA molecules of _________ chromosomes
both; homologous
which PGx testing detects only known alleles and SNPs?
a. DNA chip
b. sequencing
a. DNA chip
which PGx testing detects both known and unknown alleles?
a. DNA chip
b. sequencing
b. sequencing
is DNA chip high or low throughput?
high (up to 5 million SNPs can by genotyped simultaneously)
which of the following is described below?
-low throughput
-targeted sequencing (one specific DNA fragment)
a. Sanger sequencing
b. next gen sequencing
a. Sanger sequencing
which of the following is described below?
-high-throughput
-parallel sequencing
-massive sequencing (multiple DNA fragments simultaneously)
a. Sanger sequencing
b. next gen sequencing
b. next gen sequencing
Sanger sequencing incorporates what kind of nucleotides?
chain-terminating dideoxynucleotides (ddNTPs)
true or false: Sanger sequencing can detect both known and unknown alleles
true
which is more expensive per base pair, Sanger sequencing or DNA chip?
Sanger sequencing
true or false: next gen sequencing has a higher total cost and higher cost per SNP than DNA
false (has higher total cost but very low cost per SNP)
true or false: next gen sequencing can detect all known or unknown alleles
true
which of the following is not high-throughput?
a. DNA chip
b. Sanger sequencing
c. next gen sequencing
b. Sanger sequencing
what is sequencing coverage?
the avg number of reads that align to, or “cover”, known reference bases
what is the normal depth of coverage for detecting human genome mutations?
10x to 30x
true or false: next gen sequencing is slow but has a low error rate
false (fast but high error rate)
what are the two reasons why NGS requires sequencing every base in a sample several times?
-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
which of the two is acquired?
a. germline
b. somatic
b. somatic
which can be passed to a child?
a. germline
b. somatic
a. germline
true or false: the germline does not exist in the somatic genome
false
true or false: somatic does not exist in the germline genome
true
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)
c. DNA chips
