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Pharmacogenomics > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

precision medicine

A

tailoring disease prevention and treatment taking into account differences in indv genes, environments, and lifestyles

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2
Q

precision therapeutics

A

customizing medications to pts categorized by molecular + cellular biomarkers to improve treatment outcomes

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3
Q

pharmacogenetics

A

study of individual gene-drug interactions, usually involving 1 or 2 genes that have a dominant effect on a drug response (simple relationships)

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4
Q

Pharmacogenomics

A

study of genomic effects on drug response, often using high throughput data (sequencing, SNP chip, expression, etc) - COMPLEX interactions

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5
Q

What determines drug response

A

genetics
disease
environment
lifestyle
concomitant medications

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6
Q

Effects of genetic variation on medication therapy

A

varied drug absorption
varied metabolism rates
varied elimination rates
variations in receptors leading to variation in drug effect

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7
Q

Genome

A

organism’s entire genetic material found in cells, including genes and regulatory elements

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8
Q

Chromosome

A

Cellular structure containing genes (composed of DNA + proteins)

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9
Q

Gene

A

segment of DNA that contains info for making protein or RNA molecule

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10
Q

Nucleotide

A

building block of DNA/RNA including 1 base, 1 phosphate, and 1 sugar molecule

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11
Q

Allele

A

one of 2+ alternate forms of a gene containing specific inheritance characteristics

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12
Q

Genotype

A

genetic constitution

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13
Q

Phenotype

A

outward characteristic

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14
Q

Single Nucleotide Polymorphisms

A

Common genetic single nucleotide variants resulting from a single base pair change

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15
Q

Synonymous SNP

A

no change in amino acids, can alter mRNA stability

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16
Q

Non-synonymous SNP

A

nucleotide that alters amino acid sequence of protein

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17
Q

Missense SNP

A

change in 1 DNA base pair that results in substitution of one amino acid for another in the resulting protein

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18
Q

Nonsense SNP

A

results in insertion of stop codon

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19
Q

SNP nomenclature

A

C for coding DNA sequence (c. 67A>T)
P for protein sequence (p. tryp24cys)

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20
Q

normal/extensive metabolizer phenotype

A

normal function/decreased function alleles -> fully functional enzyme

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21
Q

intermediate metabolizer phenotype

A

combo of normal function and decreased function/no function alleles -> slightly decreased enzyme activity

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22
Q

poor metabolizer phenotype

A

combo of decreased function and no function alleles -> significantly decreased or absent enzyme activity

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23
Q

rapid metabolizer phenotype

A

combo of normal function and increased function alleles -> increased enzyme activity

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24
Q

ultra-rapid metabolizer phenotype

A

combo of increased function alleles or >2 normal function alleles -> very increased enzyme activity

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25
Q

CPIC

A

Clinical Pharmacogenetics Implementation Consortium that posts gene/drug clinical guidelines

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26
Q

CPIC level A/B

A

have evidence for prescribing action

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27
Q

CPIC levels C/D

A

Do not have adequate evidence for prescribing action

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28
Q

CPIC recommendation levels

A

Strong, moderate, optional, none

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29
Q

Which drugs does CPIC provide guidelines for

A
  1. drugs with a PharmGKB clinical annotation level of evidence 1a,1b,2a,2b
  2. drug with PharmGKB level/FDA drug label recommendations of actionable PGX genetic testing
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30
Q

PharmGKB

A

pharmacogenomics knowledge base - more scientific than clincial

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31
Q

What population is used to determine pgx recommendations in package inserts

A

a “ballpark estimate” of the population

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32
Q

Benefits of PGX guided decision making

A

decrease adverse reactions
optimize med response
improve clinical outcomes
decrease length of treatment
decrease total healthcare costs

33
Q

Gene chips

A

use panels of polymorphisms to calculate relative risk/benefit ratio of therapeutic course for individual patient

34
Q

diplotype

A

includes one paternal and one maternal allele

35
Q

Genes that affect warfarin metabolism

A

CYP 2C9
VKORC1

36
Q

Cardiovascular drugs w/ PGX recommendations

A

clopidogrel
warfarin
simvastatin

37
Q

Hypersensitivity reaction PGX testing recommendations

A

abacavir
allopurinol
carbamazepine

38
Q

Neuro drugs with PGX recommendations

A

phenytoin
opioids
SSRIs
TCAs

39
Q

Oncology drugs with PGX recommendations

A

TPMT
DPYD

40
Q

Sanger sequencing benefits

A

confirmation of variants
detects rare/novel SNPs
high accuracy

41
Q

Sanger sequencing limitations

A

low throughput
not targeted

42
Q

Next Generation Sequencing

A

category of several different sequencing methods. Standard in clinical diagnostics and research

43
Q

Examples of next generation sequencing

A

pyrosequencing
ion semiconductor sequencing
dye sequencing

44
Q

Next Gen Sequencing benefits

A

high throughput
detects rare/novel SNPs
able to be targeted

45
Q

Limitations of Next Gen Sequencing

A

high cost
more sophisticated
need informatics

46
Q

Long Read Sequencing

A

reads 10,000-2,000,000 base pairs

47
Q

Long Read Sequencing Limitations

A

lower accuracy
need improvement in sample preparation/DNA isolation protocols to produce ultralong HMW DNA
Analysis, mapping, and variant calling tools are less mature
scalability is an issue due to duration and # of samples needed

48
Q

Genotyping

A

process of determining which genetic variants an individual possesses
QPCR and micro-array

49
Q

Allelic discrimination strategies

A

primer extension
hybridization
ligation
enzymatic cleavage

50
Q

Allelic detection methods

A

Mass spectrometry
fluorescence
chemiluminescence

51
Q

qPCR

A

Quantitative PCR
a type of genotyping

52
Q

qPCR benefits

A

low cost
high throughput

53
Q

qPCR limitations

A

small number of SNPS/genes
small number of samples
works with known variants only

54
Q

Microarray/Chip

A

type of genotyping in which specific probes are fixed to a solid surface and can detect SNPs, CNV, gene expression, and methylation

55
Q

Microarray benefits

A

low cost
high throughput
recognizes many SNPs/genes

56
Q

Microarray limitations

A

known variants only
small number of samples

57
Q

FDA approved tests

A

include companion diagnostics and some direct to consumer tests

58
Q

What does premarket review of FDA approved tests establish

A

analytical validity
clinical validity
complexity level

59
Q

Companion diagnostics

A

medical device that provides information essential for the safe and effective use of a corresponding drug or biological product

60
Q

Direct to consumer tests

A

marketed directly to consumers without involvement of healthcare professional

61
Q

Direct to consumer test FDA review

A

tests only reviewed if for “moderate to high risk medical purposes”

62
Q

Which direct to consumer tests has received FDA marketing authorization

A

23 and Me

63
Q

Lab Developed Tests

A

in vitro diagnostic tests manufactured and used within a single lab
recent framework for oversight from the FDA

64
Q

CLIA

A

Clinical Laboratory Improvement Amendments - goal to ensure quality lab testing and is regulated by CMS. CLIA certification is required for clinical PGX labs

65
Q

CLIA certification levles

A

CLIA-Waived
Moderate Complexity
High Complexity
CLIA Accreditation (optional)

66
Q

PGX Lab accredidation bodies

A

J. Co
College of American Pathologists

67
Q

PGX professional organizations

A

College of American Pathologists
Association for Molecular Pathology

68
Q

Phase 1 Metabolism

A

oxidation, reduction, hydrolysis
CYP450s

69
Q

Phase 2 Metabolism

A

Conjugationreactions
UGTs, TPMT, NAT

70
Q

Clopidogrel CYP

A

CYP 2C19

71
Q

Clopidogrel MOA

A

pro-drug
binds to P2Y12 receptor to irreversible inhibit platelet aggregation

72
Q

Clopidogrel ultra-rapid metabolizer

A

17/17 OR 1/17

73
Q

Clopidogrel intermediate metabolizer

A

1/2

74
Q

Clopidogrel poor metabolizer

A

2/2

75
Q

Increased clopidogrel metabolism

A

increased active drug -> lower platelet aggregation

76
Q

NAT2 gene

A

codes for N-acetyl transferase protein -> affects isoniazid acetylation

77
Q

SLCO1B1 gene

A

codes for OATP1B1 uptake transporter - affects statin metabolism

78
Q

521T>C polymorphism

A

reduces uptake of statin into hepatocytes, increasing serum level

Pharmacogenomics (1 decks)

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