Application of

Real Time
PCR
Dr. Amira A. T. AL-Hosary
Lecturer of Infectious Diseases
Faculty of Veterinary Medicine
Assiut University
 Advantages of qRT-PCR
1. Rapid cycling times (1 hour).
2. High sample throughput (~200 samples/day).
3. Low contamination risk (sealed reactions).
4. Very sensitive (3pg or 1 genome eq of DNA).
5. Broad dynamic range (10 - 1010 copies).
6. Allows for quantitation of results.
7. Software driven operation.
 Disadvantage
• Current technology has limited capacity for
multiplexing.
Simultaneous detection of 2 targets is the limit.

• Development of protocols needs high level of

technical skill and/or support.

• High capital equipment costs ($ 50,000 -

160,000).
 Application
The exponential amplification via reverse
transcription polymerase chain reaction provides for
a highly sensitive technique in which a very low copy
number of RNA molecules can be detected.

There are different applications for quantitative

polymerase chain reaction (RT-PCR).
 Application
It is commonly used for:
1. Diagnostic uses.
2. Food safety and Industry include the
quantification of microbial load in foods.
3. Gene expersion.
4. Basic research.
5. Agriculture.
6. GMOs (Genetically modified organisms).
7. Drug industry.
8. In forensic Medicine.
1. Diagnostic uses
qRT-PCR usually applied for rapid detection as
well as quantification of nucleic acids of different
pathogens.

A. Diagnosis of infectious diseases especially

newly emerging diseases, such as new strains
of flu.
B. Diagnosis of Virus
• Viruses can be present in humans due to direct
infection or co-infections which
makes diagnosis difficult using classical
techniques and can result in an
incorrect prognosis and treatment.
• The use of qPCR allows both the
quantification and genotyping
(characterization of the strain).
• Detect anti-viral drug resistance ≠ Detect anti-
viral drug efficacy.
C. Cancer Detection

Diagnosis, prognosis and monitor response to

therapy.

Circulating tumor cells produce unique mRNA

transcripts depending on the type of cancer, this
serve as the best biomarkers for a particular cancer
cell type and then analyze its expression levels with
RT-PCR.
 2. Microbiological uses and food
industry (Microbial load testing):
Microbial risk assessment:

• Food safety, food spoilage and fermentation.

• Water quality for public health protection.

For commensal organisms determine a
“normal” microbial load.
• Detect active infection by increasing load
3. Uses in research
(Gene expression)
•Upstream region of a
gene, which regulates
when/where the gene is to
be transcribed.
• Essentially the promoter
region acts as the “on
switch” for the gene.
 Gene expression
• Reverse transcription (RT) followed by polymerase chain
reaction (PCR) represents a powerful tool for the
detection and quantification of mRNA.

• It is the most sensitive method for the detection and

quantification of gene expression levels, in particular for
low abundant transcripts in tissues with low RNA
concentrations, from limited tissue sample.
 Gene expression studies by
quantification of messenger RNA:
Presence of mRNA is:
• Starting point for determining expression.
Synthesize cDNA Using RT
mRNA

Reverse Transcriptase

cDNA
Amplify cDNA Using Primers

FW

RV

Polymerase Chain Reaction

 4. Uses in research
Gene transcription/Expression.
A. Determining how the gene expression and gene
changes over time, such as in:
1The response of tissue and cell cultures to
an administration of a pharmacological agent,
2Progression of cell differentiation,

3Response to changes in environmental

conditions.
Uses in research
B. It is also used for the determination of zygosity
(Zygosity is the degree of similarity of the alleles
for a trait in an organism) of transgenic animals
used in research.

C. Gene Insertion

RT-PCR can also be very useful in the insertion of

eukaryotic genes into prokaryotes.
4. Agriculture
A. Detection of phytopathogens

The agricultural industry is constantly striving to

produce plant propagules or seedlings that are free of
pathogens in order to prevent economic losses and
safeguard health.
• Discrimination between the DNA of the
pathogen and the plant is based on the
amplification of specific sequences
in ribosomal RNA gene’s coding area, which
are characteristic for each taxon.
 Genetically modified organisms (GMO)
• A genetically modified organism (GMO) is a
living organism, e.g. a plant, whose genetic
composition has been altered by means of gene
technology.
• The genetic modification usually involves
insertion of a piece of DNA (the insert), a
synthetic combination of several smaller pieces
of DNA, into the genome of the organism to be
modified.
• These smaller pieces of DNA are usually taken
from other naturally occurring organisms.
 Genetically modified organisms (GMO) :

• A typical insert (gene construct) in a GMO is

composed of three elements:
1) The promoter element functions as an on/off
switch for reading of the inserted/altered
gene.
2) The gene that has been inserted.
3) The terminator element functions as a stop
signal for reading of the inserted/altered
gene.
5. Detection of genetically modified organisms
(GMOs):

qPCR using reverse transcription (RT-qPCR) can be

used to detect GMOs given its sensitivity and
dynamic range in detecting DNA.
5. Detection of genetically modified
organisms (GMOs):
• Specific primers are used that amplify
the promoter, terminator or even intermediate
sequences used during the process of engineering
the vector.

• This is often carried out by relative quantification

using a control gene from the treated species that
is only present as a single copy
 6-pharmatheutical uses:
Detection of Anti-inflammatory effects of
peptides
• The epithelium lining the airways is the first tissue
to encounter pathogens and their products; it is
therefore, critical to the innate immune system and
is the front line of the host defense.
• Some peptides which are classified in an
antimicrobial group , can have an effect on
immune system, for example Intercellular
adhesion molecule-1(ICAM-1) is expressed at a
low level in a subpopulation of haematopoietic
cells, vascular endothelium, fibroblasts and
epithelial cells.
 6-pharmatheutical uses:
Detection of Anti-inflammatory effects of
peptides

• However, its expression is dramatically

increased at sites of inflammation.
• Increase in Expression of 1(ICAM-1) will be
lowered due to the effect of antimicrobial
peptide & this can be detected by Real time
PCR using SYBR Green.
 7. Real time PCR in forensic medicine
• The main task in The Forensic Medicine is to investigate
deaths from unnatural causes.
• Forensic science has embraced the use of DNA molecular
biology tools for diagnostic purposes.
• The process of routine forensic human identification
involves sensitive PCR and can be performed
successfully on most evidence materials found at a crime
scene.
• This real-time technology monitors the accumulation of
PCR product with each cycle and allows assessment of
each sample individually during the exponential growth
phase. quantification assay has proven to be highly
sensitive, specific, rapid, cost-effective and flexible assay
for analysis of forensic casework samples.
 7. Real time PCR in forensic medicine

DNA tests performed by a U.S. laboratory have proved that

bone fragments exhumed in the Ural Mountains in 2007
belong to two children of Russia's last czar.
 Amira AL-Hosary
(00201004477501)
[email protected]