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Genomics > Midterm > Flashcards

Midterm Flashcards

1
Q

how many stop codons are there

A

3

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2
Q

what are the stop codons

A

UAA
UAG
UGA

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3
Q

what are the two types of SNPs

A

non-synonymous SNP
synonymous SNP

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4
Q

what is a non-synonymous SNP

A

changing amino acid in the protein

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5
Q

what are the two non-synonymous SNPs

A

missense SNP
nonsense SNP

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6
Q

what is a missense SNP

A

amino acid substitution that could lead to either gain or loss of function

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7
Q

what is a nonsense SNP

A

amino acid changes to a stop codon and normally leads to loss of function

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8
Q

what is a synonymous SNP

A

does not change amino acids and does not change gene/protein function

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9
Q

what is MDR for

A

nucleotide coding

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10
Q

what is CYP for

A

protein sequence

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11
Q

what does c. CYP refer to

A

means to count from the first nucleotide of coding DNA sequence

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12
Q

what does p. CYP refer to

A

means to know protein sequence

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13
Q

what does MAF mean

A

minor allele frequency

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14
Q

what is RAF

A

rare allele frequency

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15
Q

how do rare alleles transfer amongst populations

A

rare alleles are mostly rare in one population and then common allele in another population

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16
Q

what is LD

A

linkage disequilibrium

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17
Q

what is linkage disequilibrium

A

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

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18
Q

R2 = 0 meaning

A

infinite recombination
no LD

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19
Q

R2 = 1

A

no recombination
complete/perfect LD

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20
Q

R2 >= 0.8

A

recombination partial chromosome
incomplete LD

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21
Q

P > 0.1

A

no presumption against null
no significant association

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22
Q

0.05 < P < 0.1

A

low presumption against null
marginal association

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23
Q

P < 0.05

A

strong presumption against null
significant association

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24
Q

P < 0.01

A

very strong presumption against
very significant association

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24
Q

how do P values measure strength of association

A

they do not measure the strength of an association relationship

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24
Q

how are p values affected

A

by sample size
by allele frequency

25
Q

why do p values need corrections

A

large number of tests for many SNPs vs a single phenotype so there is a much higher probability of a false positive

25
Q

what is the bonferroni correction

A

P = 0.05/N (total SNPs tested)

26
Q

what is the correction P value for GWAS

A

5x10^8

27
Q

CI of significant risk

A

greater than 1

28
Q

CI with no statistical significance

A

containing 1

29
Q

CI with significant protective effect

A

less than 1

30
Q

what are polymerase chain reactions used for

A

technique for DNA amplification
amplify specific region from the genome for making billions of copies detectable
enzymatic reaction

31
Q

what are the substrates for polymerase chain reactions

A

DNA template
dNTPs
primers: 2 short sequences specific to region of interest
buffer: pH, Mg2+
enzyme: Taq DNA polymerase

32
Q

what is a DNA chip used for

A

identify known and unknow alleles
high throughput

33
Q

when to use DNA chip

A

low/medium cost overall
large scale used for research

34
Q

what is sanger sequencing

A

detects both known and unknown alleles
SNPs, indel, small CNV
low throughput

35
Q

when to use sanger sequencing

A

higher cost
used for Pgx testing

36
Q

what is next generation sequencing

A

simultaneously sequence DNA of multiple individuals with customizable capacities
detect all known or unknow alleles and all kinds of polymorphisms

37
Q

when to use next generation sequencing

A

high throughput
higher cost
whole genomes/exomes

38
Q

how does PCSK9 work

A

PSCK9 secreted and binds to LDL-r then routes them for lysosomal degradation rather than recycling
inhibitors prevent this from happening

39
Q

how does loss of PCSK9 make people healthier

A

it means there are more LDL receptors that are working and being recycled, therefore, more LDL is being taken up out of the blood stream

40
Q

what do RNA interference drugs do

A

reduce mRNA levels

41
Q

what are RNA interference drugs

A

antisense oligonucleotides, ASO

42
Q

what does mRNA medicine do

A

introduce exogenous mRNA into the body, so cells can make proteins based on the introduced mRNA

43
Q

what is an example of mRNA medicine

A

covid vaccine

44
Q

what do monoclonal antibody and antibody-drug conjugate do

A

y shape protein that specifically binds to its target to block the function of that target protein: or to help recognize a specific group of cells that express the target protein

45
Q

what are monoclonal antibody drugs

A

PD1
PD-L1

46
Q

what do gene therapies do

A

virus as a vehicle to deliver genes

47
Q

what is a gene therapy example

A

Luxturna vaccine

48
Q

what are stem cells for

A

generate any cell type in the body to replace damaged tissue

48
Q

what is CRISPR for

A

gene editing and mutation repair

49
Q

how do AAV vaccines work

A

transgene packaged into AAV vectors
delivered one time via IV infusion: AAVs carry transgene to target liver
transgene is delivered to nucleus of liver cells to enable production of therapeutic protein

50
Q

what is the AAV drug name

A

zelgensma

51
Q

what does zelgensma contain

A

AAV9 capsids that contain a SMN1 transgene along with synthetic promoters

52
Q

what are PD-1 blocker drugs

A

pembrolizumab, nivolumab, cemiplimab

53
Q

what are PD-L1 blocker drugs

A

atezolizumab, avelumab, durvalumab

54
Q

what is synthetic lethality

A

when DNA has breakage and cell dies

55
Q

why do we induce synthetic lethality

A

to cause cell death in cancer cells and tumors

56
Q

what are BRCA1 drugs

A

olaparib, niraparib, talazoparib, rucaparib

57
Q

what are KRAS drugs

A

binimetinib, trametinib, cobimetinib

58
Q

what is AMG510

A

small molecule that specifically and irreversibly inhibits KRAS G12C by locking it in an inactive GDP-bound state to slow cell growth and proliferation

59
Q

what is KRAS

A

gene that plays large role in pathways with cell growth and division. mutations in this gene are frequently found in colorectal, lung, and pancreatic cancer

Genomics (1 decks)

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