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PHRM 847 > Midterm > Flashcards

Midterm Flashcards

1
Q

Number of Codons

A

64

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2
Q

Stop Codons

A

UAA
UAG
UGA

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3
Q

Start Codon

A

ATG (AUG)

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4
Q

Number of Amino Acids

A

20

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5
Q

Non-synonymous SNP

A

changing amino acid in the protein

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6
Q

Non-synonymous SNP: Missense SNP

A

AA substitution that could lead to either gain- or loss-of-function for the protein depending on what AA it changes to

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7
Q

Non-synonymous SNP: Nonsense SNP

A

AA changes to stop codon (normally lead to loss-of-function)

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8
Q

Synonymous SNP (silent)

A

does not change AA, usually does not change gene/protein

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9
Q

Reading Nomenclature: MDR1 G2677T

A

Gene: MDR1

G2677T: a G to T polymorphism at the nucleotide position of 2677 of the mRNA sequence relative to the first coding nucleotide

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10
Q

Reading Nomenclature: CYP4F2 V433M

A

Protein: CYP4F2

V433M: AA Val at the position 433 is changed to a MET

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11
Q

Reading Nomenclature: 1297G>A

A

the first nucleotide of the coding DNA sequence A of ATG as +1

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12
Q

Reading Nomenclature: c.1297G>A

A

count from the first nucleotide of coding DNA sequence (ATG)

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13
Q

Reading Nomenclature: p.Val433Met

A

p = protein position

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14
Q

Calculating number of T allele

A

2Q+R

Q=# of persons with T/T
R=# of persons with TC

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15
Q

Calculating number of C allele

A

2S+R

S=# of persons with C/C
R=# of persons with TC

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16
Q

Calculating T allele%

A

(2Q+R)/2N

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17
Q

Calculating C allele%

A

(2S+R)/2N

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18
Q

Finding allele%

A

homozygote% +1/2heterozygote%

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19
Q

Rare Allele

A

a rare allele in one population can be a common allele in another populations

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20
Q

Linkage Disequilibrium

A

non-random association of alleles at different loci on the same chromosome

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21
Q

When there are infinite recombination

A

no LD (R2=0)

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22
Q

When there is no recombination

A

complete/perfect LD (R2=1)

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23
Q

When recombination occurs in a portion of chromosomes

A

incomplete LD (R2<1)

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24
Q

Interpretation of P value: P>0.1

A

no presumption against the null hypothesis

no significant association

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25
Interpretation of P value: 0.05
low presumption against null hypothesis marginal association
26
Interpretation of P value: P<0.05
strong presumption against null hypothesis significant association
27
Interpretation of P value: <0.01
very strong presumption agonist against null hypothesis (very significant association)
28
Does p value measure the strength of an association relationship?
No
29
Correction for P values for gene sequencing
5x10^-8 due to a large number of tests for many SNPs vs the single phenotype, there will be much high probability to have many SNPs associated with the phenotype just by chance (false positive), so called multiple-testing
30
If the 95% CI is greater than 1, there is a ____________ effect
significant risk
31
If the 95% CI contains 1, there is _______________
no statistical significance
32
If the 95% CI less than 1, there is a ______________ effect
significant protective
33
What is the 95% CI
statistical probability for odds ratio
34
Polymerase Chain Reaction (PCR)
amplifies a specific region from a genome for making billions of copies (~2^35) detectable amplication: 50-1000 bp
35
Substrates of PCR
DNA template dNTPs (dATP, dGTP, dCTP, dTTP) primers: 2 short sequencing specific to the region of interest buffer: pH, Mg2+ Enzyme: Taq DNA polymerase
36
Products of PCR
DNA molecules (fragments start and end with primers)
37
DNA Chip
detecting known SNPs or targeted SNPs high throughput: up to 5M SNPs can be genotyped simultaneously low per SNP cost genome-wide based studies s mid throughput use for PGx testing
38
Sanger Sequencing
detect both known and unknown alleles (SNPs, indel, small CNV) low throughput (96 samples per overnight for one DNA fragment ~700 bp) higher cost per base pair high per SNP cost widely used in PGx testing
39
Next Generation Sequencing
Sequencing by the synthesis in parallel high throughput sequence 100s and 1000s of DNA at one time known and unknown alleles whole genome/whole exome higher total cost very low cost per SNP detect almost all kinds of polymorphisms
40
People with PSCK9 _______ mutations are ___________
nonsense, extremely healthy
41
PSCK9 impact on LDL
PCSK9 is a pro-protein convertase which is involved int he degradation of LDL receptors in the liver when PCSK9 binds to LDL receptors, it blocks LDL-R recycling, leading to a reduction of LDL-R on the surface of hepatocytes increases LDL blood levels
42
PCSK9 Inhibitors
human monoclonal antibody against PCSK9 that blocks the PCSK9/LDL-R interaction leads to increased LDL-R recycling and serum concentration
43
Evolocumab and Alirocumab
Repatha and Praluent mAB
44
patients with hypercholesterolemia carry ________-of-function PCSK9 varients
gain
45
ICER
incremental cost-effectiveness ratio
46
QALY
quality adjusted life-year
47
ICER Equation
(Cost2-Cost1) ------------------- (QALY2-QALY1)
48
RNA Interference via Antisense Oligonucleotides (ASO) use
reduce mRNA level, thus less protein will be made (for gain-of-function mutation)
49
mRNA medicine
introduce exogenous mRNA into the body so cells can make proteins based on the introduced mRNA (COVID-19 vaccine)
50
Monoclonal Antibody and Antibody Drug Conjugate (ADC)
specifically binds to target to block function of that target or to help recognize specific group of cells that express the target protein (for gain-of-function)
51
Gene Therapy
for loss-of-function
52
CRISPR-mediated gene editing and mutation repair
blood disorder sickle cell disease and beta thalassemia correct a point mutation (find and replace)
53
Stem Cell (iPSCs) Therapy
still being developed generate any cell types in the body to replace damaged tissue
54
What goes into mRNA medicine?
virus spike protein coded from mRNA sequence lipid coating
55
Gene therapy with adeno-associated virus (AAV)
Zolgensma biologic drug consisting of AAV9 capsids that contain a SMN1 transgene along with synthetic promoters
56
How AAV gene therapy works
1. Transgene is packaged into AAV vectors 2. one-time IV infusion; AAVs carrying transgene target the liver 3. AAV vectors deliver transgene to the nucleus of liver cells to enable production of therapeutic protein
57
PD-1 Blockers
Pembrolizumab (Keytruda) Nivolumab (Opdivo) Cemiplimab (Libtayo)
58
PD-L1 Blockers
Atezolizumab (Tecentriq) Avelumab (Bavencio) Durvalumab (Imfinzi)
59
PARP Inhbitors
used to treat cancer cells with BRCA1 mutations
60
PARP inhibitor MOA
PARP and BRCA-mediated pathways can repair DNA By blocking PARP, both repair pathways are disrupted
61
Synthetic Lethality
situation in which mutations in two genes together result in cell death, but a mutation in either gene alone does not In BRCA-mutated cells DNA repair can still occur via the PARP pathway, but the accuracy is low need PARP inhibitor to induce synthetic lethality in cancer cells with BRCA1 mutation
62
Drugs that target BRCA 1
olaparib niraparib talazoparib rucaparib
63
Drugs that target KRAS
binimetinib trametinib cobimetinib
64
What specific KRAS mutation are inhibitors targeting
KRAC G12C
65
CDK4 and CDK6 Inhibitor
palbociclib ribociclib abemaciclib
66
What does CDKN2A encode for?
tumor suppressors p14ARF and p16INK4a
67
What does CDKN2B encode for?
tumor suppressor p15INK4B
68
Why cancer cells might be sensitive to CDK4/6 inhibition
CDKN2A and CDKN2B are involved in CDK4/6 and MDM2 pathways CDKN2A loss may release the inhibition of the CDK4/6 pathway and MDM2 pathway works on cell cycle progression
69

PHRM 847 (2 decks)

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