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final Flashcards

1
Q

The individual above has 3 copies of the CYP2D6 gene, assuming that all 3 copies code for normal function enzymes, the CYP2D6 phenotype assignment would be an –

A

UM

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2
Q

– is one of the rare pharmacogenes where people can inherit more than
two copies of the gene

A

CYP2D6
(COPY NUMBER VARIATION)

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3
Q

Some individuals may carry just one copy of the CYP2D6 gene,
Commonly reported as –* allele, which means the allele is —

A

*5 allele
deleted

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4
Q

The function of CYP2D6 / 2D7 hybrids depends on the — variants present in the hybrid gene and is for the most part still under investigation

A

-CYP2D6
-this is called the Hybridization of the CYP2D6 gene with the CYP2D7 pseudogene, where parts of the CYP2D6 gene are often deleted.
-CYP2D6 / 2D7 hybrids can also be on the same chromosome strand with a normal copy of the CYP2D6 gene.
-It is important to know whether the genetic testing laboratories can identify CYP2D6 hybrids

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5
Q

1/2 duplication
means

A

Means the patient has a *2 variant and more than 2 copies of the CYP2D6 gene, but it is not known how many extra copies the patient has

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6
Q

1xN/2

A

Means the patient has more than 2 copies of the CYP2D6 gene, and that the *1 allele is duplicated, but it is unknown how many duplicated copies exist

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7
Q

(1/2)xN

A

Means the patient has three or more copies of the CYP2D6 gene but it is unknown which allele is duplicated and how many copies the patient actually has

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8
Q

what are the values of the activity score system used to assign CYP2D6 phenotypes (from UM to PM)

A

-UM >2.25
-NM 1.25<x<2.25
-IM 0 <x<1.25
-PM 0

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8
Q

what are the values of the activity value system used to assign CYP2D6 enzyme functional status

A

-Increased function: >1
-Normal function: 1
-Decreased function: 0.25 and 0.5
-No function: 0

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9
Q

The CYP2C19*17 allele is characterized by — CYP2C19 enzyme function

A

increased
-Unlike CYP2D6, the CYP2C19 RM and UM phenotypes are assigned in the presence of increased function alleles instead of having multiple copies of a gene.

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10
Q

Polymorphism in the promoter region of the CYP2C19 gene increases —

A

transcription

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11
Q

what are genotype definitions of UM compared to RM for CYP2C19

A

-UM: increased act compared to RM and have 2 increased fucn alleles.
-RM: inc act compared to NM but less than UM: has combinations of normal func and increased func alleles.

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12
Q

— allele frequencies are dependent on race and ethnicity
-which are the most common variants

A

-CYP2C19
- *2 and *3 alleles (principal nonfunctional alleles
)

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13
Q

CYP2C19 are present in the following races:
-*2 allele:
–% of Asians
–% of Caucasians and African Americans

-*3 allele:
–% of Asians
–% of Caucasians and African Americans

-PM phenotype
–% of Asians
–% of Caucasians and African Americans

A

-*2 allele:
30% of Asians
15% of Caucasians and African Americans

-*3 allele:
8% of Asians
less than 1% of Caucasians and African Americans

-PM phenotype
25% of Asians
~5% of Caucasians and African Americans

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14
Q

The CYP2C19 —— allele shares the same promoter region SNP as the increased function CYP2C19*17 allele (-806C>T)

A

no function *4B

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15
Q

It is important to test for — in addition to – to make an accurate CYP2C19 allele assignment

A

-1A>G (in *4B)
- -806C>T

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16
Q

the activity score system is used to assign CYP2C9 phenotypes

A

-NM: 2
-IM: 1 or 1.5
-PM: 0 or 0.5

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17
Q

Each CYP2C9 allele is assigned an activity value that will contribute to the final activity score number

A

-normal function 1
-decreased function 0.5
-no function 0

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18
Q

— enzymes are located both in the gut and the liver
-Patients who express the CYP3A5 gene are CYP3A5 – and – metabolizers.
-Patients who do not express the CYP3A5 gene are CYP3A5 – metabolizers

A

CYP3A5
-normal and intermediate
-poor

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19
Q

-It is common for individuals of – descent to express CYP3A5
enzymes.
-It is common for individuals of – descent NOT to have any
CYP3A5 enzymes (PM)

A

-African
-European

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20
Q

— phenotype is the low-risk phenotype: no dosage adjustments are required for patients with this phenotype.

— are the high-risk phenotypes
Dosing modifications may be necessary for certain medications for patients with these phenotypes

A

-CYP3A5 PM
-CYP3A5 IM and NM phenotypes

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21
Q

– polymorphisms have been associated with reduced glucuronidation in patients who have inherited decreased or no function variants

A

UGT1A1

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22
Q

— genotyping is used o diagnose Gilbert and Crigler-Najjar syndromes

A

UGT1A1

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22
Q

-– Gilbert syndrome
Decreased — activity (~30% of normal)
Patients who have – function variants (-,-,-)
– Crigler-Najjar syndrome (types 1 and 2)
Type 1: — of UGT1A1 activity
Type 2: — enzyme activity

A

– Gilbert syndrome
Decreased hepatic UGT1A1 activity (~30% of normal)
Patients who have two decreased function variants (*6, *28, *37)
– Crigler-Najjar syndrome (types 1 and 2)
Type 1: almost complete absence of UGT1A1 activity
Type 2: severely decreased but detectable UGT1A1 enzyme activity

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23
Q

UGT1A1 expression is regulated by the number of — repeats in the promoter region of the gene

A

thymine-adenine (TA)

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24
Q

UGT1A1
– Normal function alleles carry – TA repeats
– The decreased function variants are characterized by – TA repeats
– The increased function variant *– is characterized by – TA repeats (this condition is typically benign)

A

-6 (28)
-7
-36 - 5

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25
Q

UGT *6 allele is more common in – decent
28 is less common in –
-36 and 37 are more common in africants
-60 allele is – function more common in —

A

-asians
-asians
-africans
-normal function: african americans

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26
Q

DPYD activity score

A

-NM: 2
-IM: 1 or 1.5
PM: 0 or 0.5

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27
Q

DPYD activity value

A

-N fucntion: 1
-dec func: 0.5
-no func: 0

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28
Q

Each DPYD allele is assigned an activity — that will contribute to the final activity — number

A

value that will contribute to –score.

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29
Q

— starting doses of warfarin are recommended in individuals carrying a decreased function allele (CYP4F2*3)

A

higher

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30
Q

CYP4F2 is not involved in the metabolism of —, and it plays a role in —- which explains why patients need altered doses of –

A

-warfarin
-vitamin K oxidation
-warfarin

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31
Q

the —- gene belongs to solute carrier organic anion transporter
family

A

SLCO1B1 member 1B1

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32
Q

which is the membrane-bound transporter expressed in the
liver to remove many substrates from blood
- these substrates include

A

SLCO1B1 or OATP1B1
- Substrates include
many endogenous and
xenobiotic compounds including HMG-CoA reductase inhibitors (statins), bilirubin, and methotrexate

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33
Q

rs4149056 is
-encoded by: — gene
-on chromosome
— kilobases
— exons
-confers — function for several substrates
- associated with —

A

-encoded by: SLCO1B1 gene
-on chromosome 12
- 109 kilobases
- 15 exons
-confers REDUCED function for several substrates
- associated with simvastatin-induced myopathy

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34
Q

associated with simvastatin-induced myopathy

A

rs4149056 encoded by SLCO4149056 *5 and *15: NO FUNCTION ALLELES
due to low elimination of statin leading to muscle weakness

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35
Q

— is merging and renaming
alleles

A

PharmVar

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35
Q

— is merging and renaming
alleles

A

PharmVar

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36
Q

-SLCO1B11 (or 1A) allele: common in —-
-SLCO1B11B allele: common in —
-SLCO1B15 & SLCO1B115 alleles: — function alleles containing the rs4149056 variant associated with simvastatin-induced myopathy
-SLCO1B12 & 3: — function alleles
-SLCO1B114 & *35: — function alleles

A

SLCO1B11 (or 1A) allele: common in Caucasians
SLCO1B11B allele: common in Africans
SLCO1B15 & SLCO1B115 alleles: no function alleles containing the rs4149056 variant associated with simvastatin-induced myopathy
SLCO1B12 & 3: no function alleles
SLCO1B114 & *35: increased function alleles

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37
Q

what are genotypes for the following SLCO1B1 phenotypes:
-IF:
-NF:
-DF:
-PF:

A

-IF: 1 or more inc func alleles
-NF: 2 norm func alleles
-DF: 1 norm func and 1 no func alleles
-PF: 2 no func alleles

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38
Q

—— occur commonly for drug target proteins,
including receptors, enzymes, and ion channels

A

Genetic polymorphisms

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39
Q

—- gene: major metabolizing enzyme for S warfarin and vitamin K oxidoreductase (VKOR).

A

CYP2C9

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40
Q

Warfarin inhibits —, thus
preventing the formation of
reduced vitamin K1,
which is a necessary cofactor for
— and activation of
clotting factors II, VII, IX, X, (F2, F7, F9 and F11) and
proteins C and S.

A

-VKOR
γ-carboxylation

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41
Q

A common SNP in the VKORC1 regulatory region, —–,
significantly contributes to the interpatient variability in warfarin
response, as it modulates VKORC1 gene expression

A

c.1639G>A

genotypes:
-AA high sens 3mg/d
-AG int sens 5mg/d
-GG low sens 6-7mg/d

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42
Q

Warfarin dose requirements vary by ancestry, with higher dose
requirements among individuals of — ancestry and
lower
requirements among patients of — ancestry compared with
patients of European (AG) ancestry.
-this variability is explained by

A

-African GG
-asian AA

-VKORC1
genotype frequency

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43
Q

There are two common nonsynonymous SNPs in the — at codons 49
(p.Ser49Gly) and 389 (p.Arg389Gly).

A

ADRB1
- these SNPs also appear to modulate blood pressure and clinical responses to ß1receptor blockade

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44
Q

The —– and —– SNPs are in strong linkage disequilibrium

A

Ser49Gly and Arg389Gly

45
Q

The Ser49Arg389 haplotype is associated with an increased risk for death among patients with —-
-this risk can be abolished with — ttt

A

coronary heart disease
-atenolol

46
Q

— patients who were— for the Ser49Arg389
haplotype were found to have greater blood pressure reductions with
metoprolol, compared with carriers of the Gly49 and/or Gly389
alleles

A

-Hypertensive
-homozygous

47
Q

Among patients with heart failure, the Arg/Arg389 genotype was
associated with greater improvements in left ventricular ejection
fraction with carvedilol and metoprolol treatment

A

—Arg/Arg389 ADRB1

48
Q

Although a common polymorphism, —, results in lower protein expression, its contribution to individual differences in
opioid response is unclear (OPRM1)

A

A118G

49
Q

The evidence associated with the OPRM1 gene is ranked as CPIC
level –, meaning that no prescribing action is recommended
based on genotype results.

A

level C

50
Q

HLA genes are highly polymorphic with — alone having over 1500
identified alleles

A

HLA-B

51
Q

diplotype definition: presence of 1 or 2 —- alleles mean positive HLA phenotype and absence of the — allele mean negative HLA phenotype

A

HLA-B*57:01

52
Q

-HLA-B57:01 test has a positive predictive value of –% for
immunologically confirmed hypersensitivity: Some HLA-B57:01 positive patients can be safely treated with —-
-HLA-B*57:01 genotype test has a high negative predictive value (>
–%)

A

-~50% - abacavir
->99%

53
Q

Some clinical laboratories in Asia are offering more comprehensive
HLA testing for certain drug-induced — diseases:

A

-skin
- Carbamazepine: HLA-B15:08, HLA-B15:11, HLA-B*15:21

54
Q

which HLA is the most common serotype in Southeast Asia

A

HLA-B*15:02

55
Q

The RYR1 gene contains instructions for the body’s cells to produce a
protein called the ryanodine receptor (RyR1) which is important for
— function

A

muscle

56
Q

The — gene provides instructions for making the main piece
(subunit) of a structure called a calcium channel in the skeletal
muscles.

A

CACNA1S

57
Q

Variations in the RYR1 and CACNA1S genes are associated with the
development of —– in patients exposed to which drugs

A

-malignant hyperthermia
-Succinylcholine: Depolarizing muscle relaxants and
-Fluorinated inhaled anesthetics: halothane, isoflurane, desflurane,
enflurane, sevoflurane

58
Q

Mutations of the RYR1 AND CACNA1S
genes are —; patients are susceptible to developing malignant hyperthermia when one variant allele is
inherited

A

autosomal dominant

59
Q

implications for family members of patients who develop
malignant hyperthermia

A
  • Pharmacogenomic testing for RYR1 and CACNA1S can help
    determine susceptibility
    -Education of a high-risk result implications on family members
    could be done in conjunction with genetic counselors
60
Q

-mt-RNR1 is a gene in the mitochondrial DNA that codes for the —-

A

-12S
ribosomal RNA (rRNA)

61
Q

Certain genetic variations in the mt-RNR1 gene lead to changes in the
shape of the ribosome, which can make the human ribosome look more
like bacterial ribosomes, ———- interferes with bacterial protein synthesis by binding to
30S ribosomal subunit, resulting in a defective bacterial cell membrane

A

Aminoglycosides
- Certain variations in the mt-RNR1 gene cause the human ribosome to look
more like bacterial ribosomes
* Aminoglycosides lose their specificity for bacterial ribosomes, bind to
human ribosomes

62
Q

presence of high risk variant (m.1555A>G) leads to

A

aminoglycoside-induced hearing loss (Mt-RNR1 variations)
-Confirmatory mt-RNR1 genotyping of each family member is not required

63
Q

Genetic material is extracted from the nucleus when the cell at
— (during sell division)

A

prometaphase
because at this stage, the genetic material is condensed and appears as road shape structure called chromosomes

64
Q

2q34 refers to:

A

Chromosome 2, long arm, region3 and band 4

65
Q

banding technique uses — stain where each chromosome shows distinct alternate light and dark bans, and Each arm is divided into numbered regions (e.g. 1. 2, 3. …) from centromere outward
* In each region the bands are numerically ordered

A

Gimsa

66
Q

what type of chromosomal abnormality leads to 3n(69) triploidy

A

Euploidy numerical cytogenic or chromosomal abnormality

67
Q

what type of chromosomal abnormality leads to trisomy 21

A

Aneuploidy numerical cytogenic or chromosomal abnormality

68
Q

what type of chromosomal abnormality leads to monosomy

A

Aneuploidy numerical cytogenic or chromosomal abnormality

69
Q

—– is a rare condition where ovum is fertilized with 2 sperms, it is a type of — chromosomal abnormality

A

-triploid
-Euploidy numerical cytogenic or chromosomal abnormality

70
Q

what are types of structural chromosomal abnormalities

A

-A-reciprocal translocation
-B-robertsonian translocation

71
Q

in B-robertsonian translocation, breaks occur close to the centromeres of —- chromosomes (numbers—)

A

-acrocentric chromosomes
(13, 14, 15, 21, 22)

72
Q

-what are the cytogenic disorders involving autosomes

–what are the cytogenic disorders involving sex chromosomes

A

-down synd (trisomy 21)
-edwad synd (trisomy 18)
-patau synd (trisomy 13)

-sex chrom: kilnefelter synd (47, XXY)

73
Q

Marfan syndrome is what type of chromosomal abnormality

A

-monogenic (single-gene) disease
-autosomal dominant
-FBN1 mutation on gene encoding for fibrillin (connective tissue) leading to skelatal, eyes and CVS system abnormality.
clinical features: floppy mitral valve, tall stature and long fingers, aortic aneurysm & aortic dissection.

74
Q

sickle cell anemia is what type of chromosomal abnormality

A

-monogenic (single-gene) disease
-autosomal recessive
-HBB gene mutation encoding for hemoglobin
-LETHAL AS HOMOZYGOUS and
heterozygous generally unaffected

75
Q

Rett syndrome is what type of chromosomal abnormality

A

-monogenic (single-gene) disease
-X-linked dominant
-MECP2 gene mutation leading to brain damage
-normal girl up tp 18 months where mental retardation appears such as regressive language and movement, microcephaly and seizures

76
Q

Hemophilia A

A

-monogenic (single-gene) disease
-X-linked recessive
-F8 gene mutation leading to coagulation defect (factor Vlll) - leading to bleeding

77
Q

DM, CHG, and HTN are what type of genetic abnormalities

A

Polygenic (Multiple-gene )Diseases

78
Q

Multifactorial (Complex)Diseases are influenceed by both — and —

A

envoronment (AIDS, influenza, and measles) AND genetics (sickle cell and hemophilia A)

79
Q

Mutagenicity is related to — changes in DNA composition or chromosome structure

A

heritable

80
Q

—- is a general term for any type of DNA damage, chromosomal
alteration which may not always lead to a heritable mutation..

A

Genotoxicity

81
Q

Not all exposures cause a mutagenic event as there are — repair DNA systems present

A

biological

82
Q

—- are also referred to as
expression profiles

A

Transcriptomics

83
Q

—-—the study of how an
individual’s genetic makeup affects gene
expression, protein expression and activity,
and metabolism in response to exposures to
potentially toxic compounds.
* —–—the study of how the
genome as a whole responds to exposures to
potentially toxic compounds.
* —–—the evaluation of mRNA
expression levels in cells or tissues.
—– are also referred to as
expression profiles. —- may be
used in toxicological studies to evaluate the
effects of an exposure on mRNA expression

A

TOXICOGENETICS
TOXICOGENOMICS
TRANSCRIPTOMICS

84
Q

—- may be used in
toxicological studies to evaluate the effects of an exposure on gene
and mRNA expression.

MRNA AND GENE

A

Proteomics: the study of the relative levels of protein expression and activity in animals, cells, or tissues.

85
Q

— may be used in toxicological studies to evaluate the effects of an exposure on protein
expression and activity

A

Metabolomics
the study of the relative production of metabolites
in animals, cells, or tissues

86
Q

—- is cellular division which
occurs in non-reproductive
(somatic cells)

A

Mitosis

87
Q

—- is
cell division which occurs in the reproductive (germ) cells

A

meiosis

88
Q

Toxicogenomic data from —— studies may be complemented by proteomics and metabolomics studies to evaluate the effects of an exposure

A

DNA microarray

89
Q

——– methods may replace microarrays genotyping methods for high-throughput genotyping.

A

next-generation DNA sequencing

90
Q

statement

A

In the pharmaceutical industry, toxicogenomics is already able to predict
the toxicities of many compounds, especially those that are hepatotoxins
or nephrotoxins

91
Q

Genes that influence drug toxicity have been generally grouped into
one of three categories:

A
  • those that code for drug-metabolizing enzymes
  • those that code for transporters
  • those that code for human leukocyte antigens (HLAs)
92
Q

lower activity variants of the metabolizing enzymes CYP2C9 of warfarin
CYP2C9-, and CYP2C9–, are at higher risk for over-anticoagulation
or bleeding

A

CYP2C92, and CYP2C93

93
Q

VKORC1 has several polymorphic alleles, and the —— variant
has been found to be significantly associated with dose variability and
to contribute to the risk of patients experiencing over-anticoagulation
or bleeding events

A

c.1639G>A

94
Q

During Korean War, the G6PD deficiency was found to be responsible for
the severe hemolytic anemia suffered by some soldiers with the use of
——

A

Primaquine

95
Q

medications that can cause hemolytic anemia in the presence of
G6PD deficiency include

A

-Primaquine
-antimicrobial Dapsone used to treat leprosy
and
-Rasburicase used to treat hyperuricemia in cancer patients

96
Q

6-MP is metabolized to cytotoxic metabolites that cause significant adverse
effects.
* 6-MP is inactivated in part by thiol methylation catalyzed by the polymorphic
thiopurine —— enzyme.
* Low-activity variants of the — enzyme have been identified.

A

thiopurine S-methyltransferase (TPMT)

97
Q

Patients who are genetic ——– for the low-activity variant of TPMT have
intermediate levels of TPMT activity,
while those who are ———- for the
low-activity allele have low or no TPMT activity.

A

-heterozygotes
-homozygotes

98
Q
  • Decreased TPMT activity puts patients at risk for developing significant
    ——– with azathioprine and 6-MP administration, because high
    levels of 6-MP are then available for metabolism to the cytotoxic
    metabolites that accumulate.
A

myelotoxicity

99
Q
  • A low-activity variant of UGT1A1, UGT1A1*28, has been identified and is
    associated with an increased risk of cancer patients developing severe
    ——- during ——- treatment due to increasing levels of SN-38.
A

-neutropenia
-irinotecan

100
Q
  • Very serious dermatological reactions that include Stevens-Johnson Syndrome
    (SJS) and toxic epidermal necrolysis (TEN) can occur in some patients taking ———-
A

carbamazepine

101
Q

An association has been found between the risk of developing SJS and TEN and
the presence of a genetic variant of HLA-B, HLA-B*15:02
* This association appears to be most prevalent in patients of ——- ancestry.

A

Asian

102
Q

HLA-B*57:01, has been found to be
associated with a severe hypersensitivity reaction to ——–.

A

abacavir
-not SJS or TEN like carbamazepine, but a clinical syndrome involving
multiple organs.

103
Q

statement

A
  • CPIC guidelines are designed to help clinicians understand HOW
    available genetic test results should be used to optimize drug therapy
  • – Not WHETHER tests should be ordered
104
Q

Key assumption:
* – Clinical high-throughput and ——- will become
more widespread
* – Clinicians will be faced with having patients’ genotypes available
even if they did not order test with drug in mind

A

preemptive genotyping

105
Q

which resources create gene/drug pairs guidelines that provide guidance on how to use eisting pharmacogenomic test results to optimize medication therapy

A

CPIC and DPWG

106
Q

centralized database of genetic testing labs worldwide and their offering created via voluntary submissions

A

genetic testing registry (GTR)

107
Q

searchable database of curated phg literature and information including clinical guidelines and drug labeling from around the world
also includes imp pharmacogene summary and phg pathway diagrams

A

PharmGKB

107
Q

online repository for pharmacogene nomeclature key info about imp phgenes

A

phrmacoene variation consortium (pharmVAR)

108
Q

pharmGKB Strength of evidence

A

-level 1A: cpic pgx guidelines
-level 1B: preponderance evid shows association

-level 2A: qualifies for 2b where the variant is within a Very Important
Pharmacogenes
-level 2B: moderate evidence of an association
– Level 3: single significant not yet replicated study or multiple studies but lacking
clear evidence of an association
* – Level 4: case report, non-significant study or in vitro, molecular or functional assay
evidence only

109
Q

Within the context of pharmacogenomics, testing involves
searching for genetic variations linked to medication — or —
rather than to disease susceptibility.

A

efficacy or toxicity

109
Q

Currently there is no international standard for ———–.

A

genetic testing

110
Q

In many instances, ———– testing will carry little risk for ethical, legal,
and social concerns.

A

pharmacogenomics

111
Q

An individual may experience ——— from family, friends, and
coworkers on knowledge that a specific disease will not respond to
therapy or if one is identified as a “poor metabolizer” of a specific medication.

A

Stigmatization is defined as “a social process that begins with
distinguishing and labelling some feature of a person such as
occupation, disease, or skin color.”

112
Q

Recent examples of potential “blockbuster” drugs that have been recalled
from the market for adverse drug events or toxicity include –

A

cerivastatin,
cisapride, alosetron, and troglitazone
- The ability to recover R&D expenses from these market failures by reintroducing
these agents for a targeted patient group would provide SHORT-term revenues for the
industry

genomics (2 decks)

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