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Pharmacogenomics > Exam 1 > Flashcards

Exam 1 Flashcards

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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
CPIC
Clinical Pharmacogenetics Implementation Consortium that posts gene/drug clinical guidelines
26
CPIC level A/B
have evidence for prescribing action
27
CPIC levels C/D
Do not have adequate evidence for prescribing action
28
CPIC recommendation levels
Strong, moderate, optional, none
29
Which drugs does CPIC provide guidelines for
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
30
PharmGKB
pharmacogenomics knowledge base - more scientific than clincial
31
What population is used to determine pgx recommendations in package inserts
a "ballpark estimate" of the population
32
Benefits of PGX guided decision making
decrease adverse reactions optimize med response improve clinical outcomes decrease length of treatment decrease total healthcare costs
33
Gene chips
use panels of polymorphisms to calculate relative risk/benefit ratio of therapeutic course for individual patient
34
diplotype
includes one paternal and one maternal allele
35
Genes that affect warfarin metabolism
CYP 2C9 VKORC1
36
Cardiovascular drugs w/ PGX recommendations
clopidogrel warfarin simvastatin
37
Hypersensitivity reaction PGX testing recommendations
abacavir allopurinol carbamazepine
38
Neuro drugs with PGX recommendations
phenytoin opioids SSRIs TCAs
39
Oncology drugs with PGX recommendations
TPMT DPYD
40
Sanger sequencing benefits
confirmation of variants detects rare/novel SNPs high accuracy
41
Sanger sequencing limitations
low throughput not targeted
42
Next Generation Sequencing
category of several different sequencing methods. Standard in clinical diagnostics and research
43
Examples of next generation sequencing
pyrosequencing ion semiconductor sequencing dye sequencing
44
Next Gen Sequencing benefits
high throughput detects rare/novel SNPs able to be targeted
45
Limitations of Next Gen Sequencing
high cost more sophisticated need informatics
46
Long Read Sequencing
reads 10,000-2,000,000 base pairs
47
Long Read Sequencing Limitations
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
Genotyping
process of determining which genetic variants an individual possesses QPCR and micro-array
49
Allelic discrimination strategies
primer extension hybridization ligation enzymatic cleavage
50
Allelic detection methods
Mass spectrometry fluorescence chemiluminescence
51
qPCR
Quantitative PCR a type of genotyping
52
qPCR benefits
low cost high throughput
53
qPCR limitations
small number of SNPS/genes small number of samples works with known variants only
54
Microarray/Chip
type of genotyping in which specific probes are fixed to a solid surface and can detect SNPs, CNV, gene expression, and methylation
55
Microarray benefits
low cost high throughput recognizes many SNPs/genes
56
Microarray limitations
known variants only small number of samples
57
FDA approved tests
include companion diagnostics and some direct to consumer tests
58
What does premarket review of FDA approved tests establish
analytical validity clinical validity complexity level
59
Companion diagnostics
medical device that provides information essential for the safe and effective use of a corresponding drug or biological product
60
Direct to consumer tests
marketed directly to consumers without involvement of healthcare professional
61
Direct to consumer test FDA review
tests only reviewed if for "moderate to high risk medical purposes"
62
Which direct to consumer tests has received FDA marketing authorization
23 and Me
63
Lab Developed Tests
in vitro diagnostic tests manufactured and used within a single lab recent framework for oversight from the FDA
64
CLIA
Clinical Laboratory Improvement Amendments - goal to ensure quality lab testing and is regulated by CMS. CLIA certification is required for clinical PGX labs
65
CLIA certification levles
CLIA-Waived Moderate Complexity High Complexity CLIA Accreditation (optional)
66
PGX Lab accredidation bodies
J. Co College of American Pathologists
67
PGX professional organizations
College of American Pathologists Association for Molecular Pathology
68
Phase 1 Metabolism
oxidation, reduction, hydrolysis CYP450s
69
Phase 2 Metabolism
Conjugationreactions UGTs, TPMT, NAT
70
Clopidogrel CYP
CYP 2C19
71
Clopidogrel MOA
pro-drug binds to P2Y12 receptor to irreversible inhibit platelet aggregation
72
Clopidogrel ultra-rapid metabolizer
*17/*17 OR *1/*17
73
Clopidogrel intermediate metabolizer
*1/*2
74
Clopidogrel poor metabolizer
*2/*2
75
Increased clopidogrel metabolism
increased active drug -> lower platelet aggregation
76
NAT2 gene
codes for N-acetyl transferase protein -> affects isoniazid acetylation
77
SLCO1B1 gene
codes for OATP1B1 uptake transporter - affects statin metabolism
78
521T>C polymorphism
reduces uptake of statin into hepatocytes, increasing serum level

Pharmacogenomics (1 decks)

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