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Drug Foundations II > Pharmacogenomics > Flashcards

Pharmacogenomics Flashcards

1
Q

Project ENCODE

A

ENCyclopedia Of DNA Elements

- collaboration of research groups funded by National Human Genome Research Institute (NHGRI)

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2
Q

Project ENCODE

A

ENCyclopedia Of DNA Elements

- collaboration of research groups funded by National Human Genome Research Institute (NHGRI)

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3
Q

Goal of ENCODE? How do they if a gene is active?

A
  • build a comprehensive parts list of functional elements in the human genome
  • including elements that act at the protein and RNA levels, and regulatory elements
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4
Q

How many genes in a human?

A

20,000

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5
Q

How many chromosomes?

A

23

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6
Q

How many base pairs?

A

3 x 10^9 bp

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7
Q

Relationship between chimpanzee and human?

A

96% homology; 120 x 10^6 bp difference

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8
Q

Genome?

A

all the genetic material (DNA) of an organism

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9
Q

Genetics?

A

the study of single genes and its effects

ex: cystic fibrosis, Hunting’s disease

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10
Q

Genomics?

A

study of all the genes in the genome, including their interactions with environmental factors
ex: heart disease, asthma

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11
Q

Pharmacogenetics?

A 
study of genetic influences on an individual's response to drugs
-specific gene, or group of genes to predict responses to a specific drug or class of drugs
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12
Q

Pharmacogenomics? (large scale study)

A

study of all genes collectively that influence drug responses
- genome-wide analysis

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13
Q

Genome-wide analysis?

A

identify genes in the search for novel drugs targets; key determinants of drug reactions

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14
Q

How many bp in the human genome?

A

3 billion

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15
Q

Pharmaceutical relevance of human genome?

A
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16
Q

What makes pharmacogenomics easy today?

A
  • The human genome sequenced
  • ADVANCES in genome seq tech
  • AUTOMATIZATION significantly reduced cost in seq
  • COMPUTER TECHNOLOGY; handling data
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17
Q

drug spec. trial and error?

A
  • man drugs for certain illnesses
  • not enough info about patient (so get info
  • Drugs specified by trial and error (does it work, if not tweak it)
  • side effects even unknown ones, serious ones
  • FDA approval vis DRUG TRIALS
  • drugs abandoned b/c of benefited population not convinced
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18
Q

What can help avoid drug spec. trial and error?

A

Genome based characterization

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19
Q

Cost of drug development?

A

$500 to $700 million

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20
Q

Drug development timeframe?

A

12 years

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21
Q

Time until patent expires?

A

7 years

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22
Q

What is efficacy?

A

% patients cured at given dose

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23
Q

What is toxicity?

A

% patients exhibiting side effects at a given dose

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24
Q

Therapeutic index?

A

Dose range at which drug shows highest efficacy and low toxicity

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25
Q

List 9 of the top 10 causes of death in the U.S. that have genetic component?

A 
1 Heart disease
2 Cancer
3 Cerebrovascular disease
4 Chronic lower respiratory disease
5 (Accidents/unintentional injuries)
6 Diabetes
7 Pneumonia/influenze
8 Alzheimer's disease
9 Kidney disease
10 Septicemia
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26
Q

What are factors the influence drug response?

A
  • gender
  • age
  • body mass
  • diet
  • presence of other drugs
  • disease
  • exposure to certain
  • chemicals or toxins
  • genetic factors
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27
Q

What can you do to prevent gene-environment interactions?

A
  • screening and medical recommendations
  • exposure interventions or prevention to environmental factors
  • target messages and interventions aimed at changing behaviors
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28
Q

Current impact of pharmacogenomics in Healthcare practice?

A
  • pharmaceutical industry
  • public and private companies
  • personalized medicine
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29
Q

Future trends of pharmacogenomics in Heatlhcare practice?

A

Point-of-care genetic testing

  • personal genomics
  • population sequencing
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30
Q

Personalized medicine?

A
  • use of individual’s genetic profile
  • genetic variation of enzymes that break down or activate drugs (side effects/efficacy)
  • prediction of chemotherapy response
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31
Q

Interaction between DNA and Environment: drug

A

Epigenetic modifications which alter gene expression

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32
Q

Interaction between Environment (drug) and phenotype: drug response?

A

Drug exposure of sufficient quantity/duration to alter phenotype

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33
Q

Interaction between DNA and Phenotype: drug response?

A

Functional gene variants: coding SNP promoter variants

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34
Q

Using genetic info to enhance the therapeutic index helps by?

A
  • identifying Non-responders
  • not treating those most affected by toxicity
  • adjust dose to maximize efficacy while avoiding toxicity; individualized
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35
Q

Clinical implications: Efficacy

A
  • maximize beneficial and therapeutic repsonse
  • measure of clinical effectiveness
  • % of recipients who show a therapeutic response
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36
Q

Clinical Implications: Toxicity

A
  • unwanted or harmful health effects
  • % of patients who show adverse side effects at a given dose
  • extreme dose responders
  • non responders, drug ineffective
  • adverse responders, drug causes major harmful side-effects
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37
Q

Optimal dose range?

A

Efficacy is greatest and toxicity is lowest

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38
Q

How do you handle non-responders?

A

increase dose or alternative medication

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39
Q

How do handle adverse responders?

A

Greatly decrease dose or an alternative form of medication

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40
Q

Describe point-of-care?

A

Responders treated with drug

Nonresponders enrolled genomically guided clinical trials

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41
Q

How many genes cause exhibit an inherited phenotype?

A

1200 genes

cystic fibrosis, huntington’s disease

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42
Q

What disease are predisposed by certain genes?

A

cancer, retinoblastoma, breast cancer, polyposis colorectal cancer

How well did you know this?
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43
Q

Transcriptome? (Connecting the Genome to gene function)

A
  • all of the expressed RNA molecules in a cell at a given time
  • information about how highly various genes are expressed
  • different and specific for every cell
  • changes in transcriptional activity contributes to a disease
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44
Q

Proteome? (discovering the structure and function of proteins)

A
  • shape-shifting (proteins are continually being synthesized, modified, degraded)
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45
Q

Epigenome? (new tool in studying complex diseases)

A
  • the study of changes in the regulation of gene activity and expression that are not dependent on gene
How well did you know this?
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46
Q

How is system biology useful?

A
  • screen can bridge the vast amount of molecular characteristics of the disease with
How well did you know this?
1
Not at all
2
3
4
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47
Q

Goal of ENCODE? How do they if a gene is active?

A
  • build a comprehensive parts list of functional elements in the human genome
  • including elements that act at the protein and RNA levels, and regulatory elements
48
Q

How many genes in a human?

A

20,000

49
Q

How many chromosomes?

A

23

50
Q

How many base pairs?

A

3 x 10^9 bp

51
Q

Relationship between chimpanzee and human?

A

96% homology; 120 x 10^6 bp difference

52
Q

Genome?

A

all the genetic material (DNA) of an organism

53
Q

Genetics?

A

the study of single genes and its effects

ex: cystic fibrosis, Hunting’s disease

54
Q

Genomics?

A

study of all the genes in the genome, including their interactions with environmental factors
ex: heart disease, asthma

55
Q

Pharmacogenetics?

A 
study of genetic influences on an individual's response to drugs
-specific gene, or group of genes to predict responses to a specific drug or class of drugs
56
Q

Pharmacogenomics? (large scale study)

A

study of all genes collectively that influence drug responses
- genome-wide analysis

57
Q

Genome-wide analysis?

A

identify genes in the search for novel drugs targets; key determinants of drug reactions

58
Q

How many bp in the human genome?

A

3 billion

59
Q

Pharmaceutical relevance of human genome?

A
60
Q

What makes pharmacogenomics easy today?

A
  • The human genome sequenced
  • ADVANCES in genome seq tech
  • AUTOMATIZATION significantly reduced cost in seq
  • COMPUTER TECHNOLOGY; handling data
61
Q

drug spec. trial and error?

A
  • man drugs for certain illnesses
  • not enough info about patient (so get info
  • Drugs specified by trial and error (does it work, if not tweak it)
  • side effects even unknown ones, serious ones
  • FDA approval vis DRUG TRIALS
  • drugs abandoned b/c of benefited population not convinced
62
Q

What can help avoid drug spec. trial and error?

A

Genome based characterization

63
Q

Cost of drug development?

A

$500 to $700 million

64
Q

Drug development timeframe?

A

12 years

65
Q

Time until patent expires?

A

7 years

66
Q

What is efficacy?

A

% patients cured at given dose

67
Q

What is toxicity?

A

% patients exhibiting side effects at a given dose

68
Q

Therapeutic index?

A

Dose range at which drug shows highest efficacy and low toxicity

69
Q

List 9 of the top 10 causes of death in the U.S. that have genetic component?

A 
1 Heart disease
2 Cancer
3 Cerebrovascular disease
4 Chronic lower respiratory disease
5 (Accidents/unintentional injuries)
6 Diabetes
7 Pneumonia/influenze
8 Alzheimer's disease
9 Kidney disease
10 Septicemia
70
Q

What are factors the influence drug response?

A
  • gender
  • age
  • body mass
  • diet
  • presence of other drugs
  • disease
  • exposure to certain
  • chemicals or toxins
  • genetic factors
71
Q

What can you do to prevent gene-environment interactions?

A
  • screening and medical recommendations
  • exposure interventions or prevention to environmental factors
  • target messages and interventions aimed at changing behaviors
72
Q

Current impact of pharmacogenomics in Healthcare practice?

A
  • pharmaceutical industry
  • public and private companies
  • personalized medicine
73
Q

Future trends of pharmacogenomics in Heatlhcare practice?

A

Point-of-care genetic testing

  • personal genomics
  • population sequencing
74
Q

Personalized medicine?

A
  • use of individual’s genetic profile
  • genetic variation of enzymes that break down or activate drugs (side effects/efficacy)
  • prediction of chemotherapy response
75
Q

Interaction between DNA and Environment: drug

A

Epigenetic modifications which alter gene expression

76
Q

Interaction between Environment (drug) and phenotype: drug response?

A

Drug exposure of sufficient quantity/duration to alter phenotype

77
Q

Interaction between DNA and Phenotype: drug response?

A

Functional gene variants: coding SNP promoter variants

78
Q

Using genetic info to enhance the therapeutic index helps by?

A
  • identifying Non-responders
  • not treating those most affected by toxicity
  • adjust dose to maximize efficacy while avoiding toxicity; individualized
79
Q

Clinical implications: Efficacy

A
  • maximize beneficial and therapeutic repsonse
  • measure of clinical effectiveness
  • % of recipients who show a therapeutic response
80
Q

Clinical Implications: Toxicity

A
  • unwanted or harmful health effects
  • % of patients who show adverse side effects at a given dose
  • extreme dose responders
  • non responders, drug ineffective
  • adverse responders, drug causes major harmful side-effects
81
Q

Optimal dose range?

A

Efficacy is greatest and toxicity is lowest

82
Q

How do you handle non-responders?

A

increase dose or alternative medication

83
Q

How do handle adverse responders?

A

Greatly decrease dose or an alternative form of medication

84
Q

Describe point-of-care?

A

Responders treated with drug

Nonresponders enrolled genomically guided clinical trials

85
Q

How many genes cause exhibit an inherited phenotype?

A

1200 genes

cystic fibrosis, huntington’s disease

86
Q

What disease are predisposed by certain genes?

A

cancer, retinoblastoma, breast cancer, polyposis colorectal cancer

87
Q

Transcriptome? (Connecting the Genome to gene function)

A
  • all of the expressed RNA molecules in a cell at a given time
  • information about how highly various genes are expressed
  • different and specific for every cell
  • changes in transcriptional activity contributes to a disease
88
Q

Proteome? (discovering the structure and function of proteins)

A
  • shape-shifting (proteins are continually being synthesized, modified, degraded)
89
Q

Epigenome? (new tool in studying complex diseases)

A
  • the study of changes in the regulation of gene activity and expression that are not dependent on gene
90
Q

How is system biology useful?

A
  • (personalized medicine) screen can bridge the vast amount of molecular characteristics of the disease with pharmacogenomics
  • integrate patient specific data sets with drug-response profiles
91
Q

What can one RNA do?

A

It has the potential to make several proteins because of splicing

92
Q

What are the five stages following drug administration?

A
  • absorption
  • distribution
  • target interaction (binding to cellular receptors or ion channels)
  • metabolic processing
    excretion
93
Q

How much will genetic factors account for?

A

20% - 95% variation of drug response between individuals

94
Q

What properties influence pharmacokinetics properties of drugs?

A
  • drug metabolizing enzymes

- drug transporters

95
Q

What properties influence pharmacogenomics properties of drugs?

A
  • drug targets (enzymes, receptors, ion channels)
96
Q

What is SNP?

A

single nucleotide polymorphisms

97
Q

What are sets of closely linked SNPs called?

A

haplotypes

98
Q

What is a Haplotype?

A
  • group of SNPs
  • group of alleles that are rarely separated by recombination
  • group of genes that was inherited together from single parent
99
Q

What is the size of human haplotypes?

A

60, 000 bp

100
Q

How many SNPs travel as a group in human haplotypes?

A

60 SNPs

101
Q

Missense

A
  • change in amino acid sequence
  • about half in the coding sequence
  • alter protein function
  • cause of most monogenetic diseases
102
Q

Nonsense

A
  • change in amino acid sequence
  • stop codon
  • same sequence as missense
103
Q

How many SNPs does the human genome have?

A

3 million, randomly

104
Q

Which two deoxynucleotides are involved in two of three SNPs?

A

Cytosine to thymine

105
Q

What region of the genome do SNPs occur?

A

coding and noncoding

106
Q

What has no effect on cell function, but could predispose people to disease or influence a their drug response?

A

SNPs

107
Q

What are three benefits of SNPs?

A

Research
Pharmaceutical products
medical diagnostics

108
Q

True or false. Are SNPs evolutionarily stable?

A

True

109
Q

What is SNP cosortium (TSC)?

A

A partnership of scientists and funding agencies to determine the freqency of certain SNPs in three major world populations

110
Q

Which countries are the scientists and funding agencies from for TSC?

A

Canada, China, Japan, Nigeria, United Kingdom, and the U.S.

111
Q

What does the future hold with pharmacogenetics?

A

testing prior to drug use (chemotherapeutics)
- selecting the optimal drug; impact on both cost and prognosis
- increasing understanding multiple genetic influences on drug action
- new technologies, reduce costs
personalized medicine

112
Q

What’s one thing that pharmacogenetics can only enhance, but never replace?

A

proper clinical management

113
Q

What are several DNA-binding transcription factors?

A
  • ATP-dependent chromatin remodeling complexes
  • Histone chaperone complexes
  • Histone modifying enzyme complexes
  • Mediator complexes
114
Q

What are the processes in epigenetics?

A

Activation and repression

115
Q

Activated genes are?

A

Acetylated or methylated

116
Q

Repressed genes are?

A

methylated

117
Q

What is the difference between euchromatin and heterochromatin?

A

Euchromatin is lightly packed while heterochromatin is tightly packed

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