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5302 Final > PGx Lecture 10 > Flashcards

PGx Lecture 10 Flashcards

1
Q

Four distinct genetic tests

A

paternity/maternity
DNA forensics
Disease predisposition
Pharmacogenomics

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2
Q

Steps in PGx testing

A
  1. DNA sample collection
  2. DNA isolation
  3. DNA target sequence amplification via polymerase chain reaction (PCR)
  4. Genotyping
  5. Data Interpretation
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3
Q

Types of DNA samples

A

Human Genomic DNA

Nonhuman DNA

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4
Q

examples of Human DNA

A 
holds complete set of genetic data 
obtained from any cell
blood lymphocytes (non-nucleated) (peripheral whole blood) = gold standard
buccal cells
saliva sample
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5
Q

examples of nonhuman DNA

A

tumor, bacteria, virus

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6
Q

why is blood the gold standard for DNA samples

A

pure, high quality, large quantity, easy to amplify target sequence. DNA obtained from WBC

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7
Q

To determine a person’s TPMT genotype, which of the following DNA sample needs to be used?

A

human genomic DNA

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8
Q

Purposes for Nonhuman DNA collection

A

somatic mutations in tumors

infectious disease - to sequence viral DNA (HIV)

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9
Q

To determine the genotype of codon 389 in beta1-adrenergic receptor gene (ADRB1), which of the following DNA samples needs to be used

A

human

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10
Q

Most pharmacogenomic markers require what type of DNA

A

human

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11
Q

Only tumor biomarkers related to what type of mutation use tumor DNA

A

somatic mutations

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12
Q

Gene-specific analysis

A

to identify specific SNPs of interest - eg, to determine a person’s genotype for CYP2C19 or a panel of drug metabolizing enzyme genes

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13
Q

PGx test categories

A

Gene-specific analysis

genome-wide analysis

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14
Q

Types of PGx tests

A

cytogenetic
DNA-based genotyping
matabolic assay

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15
Q

cytogenetic

A

FISH
Flourescent in situ hybridization
A technique used to identify the presence of specific chromosomes or chromosomal regions through hybridization (attachment) of flourescently-labeled DNA probes to denatured chromosomal DNA

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16
Q

Steps in FISH/cytogenetic test

A
  1. preparation of probe. A probe is a florescent-labeled segment of DNA complementary to a chromosomal region of interest
  2. Hybridization. Denatured chromosomes fixed on a microscope slide are exposed to the florescent-labeled probe. Hybridization (attachment) occurs between the probe and complementary (matching) chromosomal DNA
  3. slide examined under a fluorescent microscope. Fluorescent signals indicate the presence of complementary chromosomal DNA’ absence signals absence of complementary chromosomal DNA
17
Q

FISH Green signal

A

normal control
two green signals
two pink signals

18
Q

FISH Pink signal

A

chromosomal region of interest
Patient with deletion:
two green signals
one pink signal

19
Q

What does FISH detect

A

deletions

duplications

20
Q

Common DNA-based genotyping methods

A
  • restriction fragment length polymorphisms (RFLP) analysis
  • TaqMan SNP
  • mass spectrometry
  • Microarray (gene clip)
  • DNA sequencing
    often a combo of methods is used
21
Q

Why is whole-genome so expensive

A

lots of redundancy

can only sequence once b/c of cost and time –> mistakes easy to make

22
Q

Metabolic test

A

measure MR to identify extensive and poor metabolizers

23
Q

do metabolic tests identify genotype or phenotype

A

phenotype

24
Q

problems with metabolic tests

A

phenotype not always stable, metabolic capacity affected by various factors

25
Q

Enzyme assay

A

metabolic test

measurement of enzyme activity with a particular substrate (ex TPMT)

26
Q

Two examples of FDA-approved genotyping tests

A
  1. Roche AmpliChip CYP450 test
    - to identify a pts CYP2D6 and CYP2C19 genotype
  2. Invader UGT1A1 Molecular Assay
    - genotyping of alleles in the UGT1A1 gene
    - specifically *1 and *28
27
Q

First approved test

A 
Roche AmpliChip CYP450 test
extracted from whole blood sample
DNA microarray using Affymetrix gene chip technology
assay of 27 alleles of 2D6
get genotype results
28
Q

Invader UGT1A1 molecular assay

A

for the detection and genotyping of the *1 (TA6) and *28 (TA7) alleles in the UGT1A1 gene in genomic DNA obtained from whole blood

29
Q

What does UGT1A1 determine

A

genotype. homozygous –> reduce dose of irinotecan therapy

30
Q

PGx testing in key therapeutic areas

A 
infectious diseases
oncology
cardiovascular disease
psychiatry
neurology
organ transplantation
31
Q

Tamoxifen test

A

Tamoxifen -> CYP2D6

32
Q

Trastuzumab test

A

HER2IHC

HER2/CEP17, FISH

33
Q

Mercaptopurine test

A

PredictRx, TPMT

34
Q

Irinotecan test

A

Invader

UGT1A1

35
Q

Warfarin test

A

CYP2C9 and VKORC1

36
Q

Abacavir test

A

HLA-B*5701

5302 Final (3 decks)

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