PCR
Defined
Diagnoses of
Specific Diseases
Future Role of PCR in Clinical
Diagnostics
Questions to Ask Your PCR
LAB
A. PCR Defined
A1.
What is
PCR? PCR--Polymerase Chain Reaction is a DNA-based
method that amplifies a precisely defined segment of target DNA.
Target DNA is specified by design of two primers. The DNA undergoes
logarithmic amplification resulting in a single copy being
multiplied into billions.
A2. How is PCR
detected? Electrophoresis on an agarose gel stained with
Ethidium Bromide and observed under UV
light.
B. Diagnoses of Specific
Diseases
B1. What are the current PCR
methods? There are three (3) PCR
Methods:
1) Single PCR
Method:
-
Used for Toxoplasma, Ehrlichia, Bartonella,
FeLV, Mycobacterium, Feline Herpes, Equine
Herpes.
-
Difficulty interpreting results because PCR
indicates organisms present but not causing disease. For example,
Toxoplasma PCR on cats with uveitis: 19% PCR Positive compared
with cats without uveitis 9%
positive
2) Nested PCR
Method:
-
Used to detect target organisms at low
concentrations
-
Utilizes a second round of
amplification
-
Main disadvantage is turnover time--requires two
runs
3) Reverse Transcription PCR (RT-PCR)
Method
B2. What specific diseases can be diagnosed with PCR
testing? FeLV (Feline Leukemia
Virus)
-
Single PCR method.
-
Synbiotics
research: 62 feline blood samples from Antech Labs were analyzed
by ELISA, IFA and Synbiotics FeLV PCR. PCR had good correlation
with strong positive IFA and strong positive ELISA. However, weak
positive IFA conflicted with PCR.
-
45 samples strong
positive ELISA/42 PCR Positive/93% correlation. 5 samples weak
positive ELISA/2 PCR Positive/40%
correlation
-
PCR is helpful in resolving conflicts between
antibody based
tests.
FIV (Feline
Immunodeficiency Virus)
-
Double PCR Method.
-
Single PCR results
with 12 antibody positive cats: 7 FIV PCR
positive.
-
Double PCR on the
same 12 cats: 12 PCR positive.
-
Note: Some cats
fail to produce antibodies after infection, i.e., False Negative
ELISA & Western Blots. False positive ELISA in kittens less
than 6 months.
-
PCR is more sensitive for FIV detection--patent
restrictions prohibit its commercial
application.
FIP (Feline
Infectious Peritonitis)
-
RT-PCR (Reverse
Transcription Polymerase Chain Reaction).
-
RNA must be
converted to DNA in two-step procedure.
-
Test detects small amounts of virus in
effusions, plasma, and feces. Symbiotics
-
Study: 40 cases
from Antech Laboratories analyzed by the Synbiotics PCR Assay. All
40 cases presented with effusive e fluid. Results: 18 cases PCR
Negative: 14-not FIP, 3 FIP, 1 Uncertain. 22 Cases Positive FIP
PCR: 20-FIP positive, 1-Negative, and 1-Uncertain. All confirmed
FIP Positive cats Died (Necropsy, cytology, histology, clinical
outcome). All FIP Negative Cats are
alive.
-
Accuracy: 87% for sensitivity and 93% for
specificity.
-
Considerations: Cats with dry FIP or a
localized lesion may not have virus in the blood that may result
in false negative results. FIP-PCR is specific and works well on
effusions but lacks sensitivity when performed on whole blood. RNA
is very fragile and may degrade if the sample is stored
incorrectly or is too old. Keep it cold but not frozen in an EDTA
(lavender top)
tube.
Haemobartonella felis
(FIA)
-
Single PCR. PCR more sensitive than cytology, e.g., cat
with profound FIA-induced anemia was cytology positive
and PCR
positive.
-
Treated with antibiotics.
-
After
treatment, cat became cytology negative and PCR positive for
several weeks. (Symbiotics Data). 20 suspect FIA cats were PCR
positive 10 known negative FIA cats PCR negative (Synbiotics
data)
B3. Are there other single step PCR Tests
are available?
-
Bartonella henselae (Cat
Scratch)
-
Canine parvovirus
-
Chlamydia psittaci
-
Cryptosporidium
-
Ehrlichia canis
-
Ehrlichia risticci (Potomac
Fever)
-
Ehrlichia ewingii
-
Equine herpes
-
Feline herpes
-
Giardia
-
Mycobacterum spp (M. avium, M. bovix, M.
tuberculosis)
-
Tick multiplex (Ehrlichia canis, Rocky
Mountain Spotted Fever, Lymes)
-
Yersinia
pestis
B4. Are there other RT-PCR Tests
available?
Canine Distemper
(very sensitive as a research issue is whether Distemper PCR tests
will detect vaccine virus in recently vaccinated
dogs)
C. Future Role of PCR in
Clinical Diagnostics
C1. What is the biggest
challenge to PCR? It is contamination, which can generate billions
of copies of PCR product and thus produces false positive
results.
C2. What
is the remedy to contamination?
- Separate rooms for
DNA/RNA extractions and PCR preparation.
- PCR preps in a
sterile environment (e.g. laminar flow or "PCR"
Hood")
- Decontaminate with
special chemicals such as RNA-ASE Away, DNA-ASE
Away
- Ozone
decontamination (Alpine
ozonators)
D. Questions to Ask Your PCR
Lab
D1. Does your PCR lab
quantitative the DNA? Samples vary in the amount of DNA that is
successfully extracted. In some samples recovery may be too high or
too low. Too much DNA or too little has an effect on results. Was an
adequate amount of DNA recovered from the extraction? Quantification
allows the technician to make proper adjustments from the sample for
optimum sensitivity.
D2. Does your Laboratory
archive and photodocument results? In cases where there may be a legal action or
complaint filed against a practitioner, photos of the
electrophoresis gels are acceptable as definitive
proof.
D3. Does your laboratory
prepare their reactions in a sterile environment, such as a laminar
flow hood or a special PCR Hood that is equipped with UV
light? This is
extremely important to avoid
contamination.
D4. Is your PCR
laboratory equipped with an autoclave and a microwave?
This may seem to be a
rather silly question, but in order to prevent contamination
laboratory equipment and consumables need sterilization often and
routinely. There are PCR laboratories in business that do not have
these essentials.
D5. What is your PCR Lab's policy with regard to when
results are released? A reputable laboratory may choose to release
results with appropriate positive and negative controls included
with the test sample. Our laboratory chooses to hold results and
rerun the tests if there is a discrepancy in the
controls.
D6. Does your PCR lab
run positive and negative controls? Positive control to confirm that the PCR is
working properly. Negative controls to confirm positives are
true positive results.
For a consultation contact DyNAgenics
Veterinary Diagnostics
today! |