User Guide

SPECIALfinder DETECTION ASSAY
CASHEW
Cat. N. PAV08A
User Guide
1 - Introduction
Food allergies are an adverse immune response to a food protein that are the most common
allergic compound. Food allergies are an important concern for human health; in fact, the presence of
specific proteins in any food matrix can cause an allergic reaction IgE mediated. Allergic reactions may
have a broad spectrum, which varies on the basis of the individual sensitivity thus generating in some
cases severe anaphylactic reactions. Indeed, food correct labeling is of great importance to inform
consumers about presence of any allergic substance other than achieve a high level of health
protection. Unfortunately, although known allergens can be included in the product (and in the
product label) by the food producer, potentially hazardous allergenic residues/contaminants can be
present as result of common industrial practices. Cross-contamination between raw materials,
production lines or equipment, is a common cause of unwanted allergen transfer between products
intended for different scopes.
For all these reasons, developing a detection method for allergic substances ensures customers
protection in accordance with food labeling regulations. The SPECIALfinder Cashew Detection Assay
provide the user with a simple and reliable procedure for the detection of DNA related to species
potentially allergenic, in food and feed matrices as well as swabs. Such a detection is an Indirect Proof
of the potential presence of the Cashew proteins into the matrix, being proteins the real allergens.
This assay utilizes the polymerase chain reaction (PCR) to amplify a genetic target typical of the
allergenic species. PCR technique can typically detect up to 1-10 copies of the target sequence but
the real detection/quantification limit depends on industrial processing degree, sample matrix, DNA
extraction and, lastly, on the DNA content of the sample. Genome size of the complex samples under
investigation can deeply impact the Limit Of Detection (LOD) also, in addition it does exist a
theoretical LOD you cannot go below, given an advised maximum load between 2 and 4 ng DNA/µl
reaction mix.
Generon in-house validation: the LOD has been calculated as copy number by means of ddPCR
(Droplet Digital PCR), a novel technique capable to count physically the copy number of a selected
amplifiable target. With SPECIALfinder Cashew an average count of 5-10 copies was obtained. DNA
was extracted using Generon ION Force DNA Extractor FAST (Cat. N. EXD001).
The LOD for this assay was experimentally determined between 1 and 0.5 ppm and depends on
sample matrix, processing grade, DNA preparation and DNA content.
User guide - SPECIALfinder Cashew Detection Assay - Rev 1 26/11/2014
2
2 - SPECIALfinder Cashew Detection Assay
When used along with GENERase PLUS Mastermix (Cat. N. ENG002) this Real-Time PCR assay detects
a specific DNA sequence in the DNA of Cashew in less than 1.5 hours. The amplification of the target
sequence is measured by the use of a specific fluorescence-labeled probe (FAM).
2.1 - Assay Content
Box 50 reactions
N. vials
Volume (μl)
250
Box 100 reactions
N. vials
Volume (μl)
SPECIALfinder OLIGO Mix * (OLIGOS and Probe pre-blended mix)
1
2
250
Positive Control
1
85
2
85
Negative Control
1
200
1
200
* reagents are supplied with a 5% of extra volume.
We suggest to use SPECIALfinder Cashew Detection Assay along with the following Polymerase
Enzyme Ready-to-use mastermix: GENERase PLUS Mastermix (Cat. N. ENG002). When using this
GENERase PLUS an additional detection channel (HEX) becomes available to detect the Internal
Amplification Control (IAC) to excluding false negative results due to a PCR inhibition.
2.2 - Storage & Expiry information
Expiry date: see date on the packaging, product validity refers to the product kept intact in its original
packaging. Protect reagents from light exposure as far as OLIGO Mix reagents are photosensitive.
Store frozen.
User guide - SPECIALfinder Cashew Detection Assay - Rev 1 26/11/2014
3
3 – Materials and equipments needed
3.1 – Extraction(1)
Material/Equipment
Source
Extraction Kit
Generon ION Force DNA Extractor FAST (Cat. N. EXD001)
Chemicals: n-esane
Lab Suppliers
Tubes, 50 ml and 15 ml
Generon or other Lab Suppliers
DNAse/RNAse Free Water
Generon or other Lab Suppliers
Vortexer
Generon or other Lab Suppliers
Benchtop Centrifuge for 50 ml Tubes
Generon or other Lab Suppliers
Thermal Water Bath or Block
Generon or other Lab Suppliers
Pipette sets
Generon or other Lab Suppliers
Pipette tips (Barrier)
Generon or other Lab Suppliers
Tube rack for 1.5 ml tubes
Generon or other Lab Suppliers
2.0 and 1.5 ml micro-tubes
Generon or other Lab Suppliers
Micro centrifuge for 1.5-2.0 ml micro-tubes
Generon or other Lab Suppliers
DNA Extraction VACUUM BOX + Vacuum pump or Venturi meter
Generon or other Lab Suppliers
Each step of sample preparation (grinding, transferring, weighing, etc.) must be done according to
GLP so that chance of cross-contamination between samples is minimized. It is recommended to use
disposable equipment when possible.
If the food samples are not in a powdered or granular form, they should be processed (grinded or
blended) before DNA extraction. The majority of DNA extraction methods supports from 20 to 50 mg
of starting material. Generon ION Force DNA Extractor FAST (Cat. N. EXD001) allows processing up to
20 grams of starting material in order to maximize sample’s lot representation.
Once the sample has been pulverized/homogenized, it can be weighed and the appropriate amount
extracted according to DNA extraction method selected. Refer to manufacturer user manual for
extraction procedure details.
3.3 – Detection via Real-Time PCR
Material/Equipment
Real-Time PCR System
(2)
Source
Generon or other Lab Suppliers
Specialfinder Cashew Detection Assay
Generon (Cat. N. PAV08A)
GENERase PLUS Mastermix
Generon (Cat. N. ENG002)
Optical Adhesive Seal and Optical reaction plate or
Optical Caps and Strips
Generon or other Lab Suppliers
Micropipette sets
Generon or other Lab Suppliers
(1) Equipment necessary only when ION Force DNA Extractor FAST (Cat. N. EXD001) is used.
(2) The assay can be used with Biorad CFX and MiniOpticon, Stratagene MxSeries, ABI 7300-7500-7900-StepONE-StepONE Plus,
Light Cycler 480, Eppendorf realplex, Rotor-Gene Q etc. The assay is not compatible with Roche Light Cycler I and II.
User guide - SPECIALfinder Cashew Detection Assay - Rev 1 26/11/2014
4
4 – Real-Time PCR detection
4.1 – Reaction setup
I.
Allow the reagents to thaw (GENERase PLUS Mastermix, SPECIALfinder OLIGO MIX, Positive
Control and Negative Control). Vortex tubes when thawed and spin to collect contents at the
bottom of the vial.
II.
Mix 250 µl of SPECIALfinder OLIGO Mix with 500 µl of GENERase PLUS Mastermix to prepare
SPECIALfinder Working Mastermix (WMX).
III.
Vortex briefly and spin down in order to homogenize the mix.
IV.
Transfer 15 µl of WMX into each well.
V.
Add 5 µl of Negative Control into wells acting as negative control.
VI.
Add 5 µl of each sample into wells testing the unknown samples.
VII.
Add 5 µl of Positive Control into wells acting as positive control.
VIII.
Close wells and ensure no bubbles are present at the bottom of the wells.
IX.
Spin briefly optical PCR tubes or plates.
4.2 – Instrument setup
With GENERase PLUS Mastermix set the following parameters on your thermocycler:
I.
Total Reaction volume: 20 µl
II.
Fluorophores/Quenchers: Target Cashew (FAM/BHQ1-NFQ); Internal Amplification Control
(HEX/BHQ1-NFQ). Depending on your thermocycler, you can replace HEX detector in the plate
setting with VIC or JOE in case your own Real Time Platform does not possess the HEX reading
channel.
III.
Thermal profile:
Step
T (°C)
Duration
Loops
UNG
50
2 min
1
Taq Activation
95
10 min
1
DNA Denaturation
95
15 sec
Annealing/Extension + Plate Reading
60
60 sec
45
User guide - SPECIALfinder Cashew Detection Assay - Rev 1 26/11/2014
5
5 – Data Interpretation
Results evaluation must be done according to the analysis software recommended by the Real-Time
PCR instrument manufacturer. After performing PCR, each individual sample is analyzed through the
instrument software to produce a Cq value (quantification cycle) for each reporter dye. These values
are used to determine the presence (Qualitative Test) of allergen into the sample. See below an
example of the graphics obtained for a positive (Fig. A) and a negative (Fig. B) control, respectively for
the allergen target amplification (blue line) and for the IAC amplification (green line).
HEX
FAM
HEX
A
B
After setting the baseline, the analysis outcome should be evaluated following the indications below.
If the following conditions are met:
TEST
Cashew (FAM )
Internal Amplification Control (HEX)
Positive Control
+
+
Negative Control
-
+
TEST
Cashew (FAM )
Internal Amplification Control (HEX)
Positive Sample
+
+/-
Negative Sample
-
+
Invalid Sample (inhibited)
-
-
Then the possible results for any sample are:
In case of inhibition DNA isolation and purification for the sample need to be improved or you may
need to dilute your sample before performing a new test. Refer to the Troubleshooting paragraph
(section 8) for further suggestions.
6 – Inclusivity Panel
Species tested for inclusivity
Cashew(Anacardium
occidentalis)
User guide - SPECIALfinder Cashew Detection Assay - Rev 1 26/11/2014
6
7 – Exclusivity Panel
The following DNA extracts showed no amplification curve in a 20 μl total reaction volume:
Meat
Beef (Bos taurus)
Goat (Capra hircus)
Rabbit (Oryctolagus cuniculus)
Buffalo (Bubalus bubalis)
Horse (Equus caballus)
Sheep (Ovis aries)
Donkey (Equus asinus)
Poultry (Gallus gallus domesticus)
Swine (Sus scrofa domesticus)
Duck (Anas spp.)
Quail (Coturnix coturnix)
Turkey (Meleagris gallopavo)
Wild boar (Sus scrofa)
Crustaceans and Molluscs
Clam (Venus gallina)
Cuttlefish (Sepia officinalis)
Norway lobster (Nephrops
norvegicus)
Prawn (Penaeus vannamei)
Hake (Merluccius
merluccius)
Salmon (Oncorhynchus kisutch)
Mussel (Mytilus edulis)
Squid (Loligo edulis)
Sea bream (Sparus aurata)
Tuna (Thunnus albacares)
Vegetables Allergens
Sesame (Sesamum indicum)
Almond (Prunus dulcis)
Hazelnut (Corylus avellana)
Oat (Avena sativa)
Barley (Hordeum vulgare)
Kamut (Triticum turgidum)
Peanut (Arachis hypogaea)
Soft Wheat (Triticum aestivum)
Brasilian Walnut
(Bertholletia excelsa)
Lupine (Lupinus albus)
Pecan Nut (Carya illinoinensis)
Soybean (Glycine max)
Celery(Apium graveolens)
Macadamia Nut (Macadamia
integrifolia)
Pistachio (Pistacia vera)
Spelt (Triticum monococcum)
Durum Wheat (Triticum
durum)
Mustard (Brassica nigra)
Rye (Secale cereale)
Walnut (Juglans regia)
Durum Wheat (Triticum durum)
Ananas (Ananas comossus)
Cocoa (Theobroma cacao)
Mandarine (Citrus reticulata)
Plum (Prunus domestica)
Apple (Malus domestica)
Coconut (Cocos nucifera)
Mushroom (Agaricus campestris)
Pomelo (Citrus maxima)
Apricot (Prunus armeniaca)
Corn (Zea mays)
Olive (Olea europaea)
Potato (Solanum tuberosum)
Banana (Musa acuminata)
Cucumber (Cucumis sativus)
Onion (Allium cepa)
Radish (Raphanus sativus)
Basil (Ocimum basilicum)
Eggplant (Solanum melongena)
Orange (Citrus aurantium)
Rapessed (Brassica napus)
Fennel (Foeniculum vulgare)
Parsley (Petroselinum crispum)
Rice (Oryza sativa)
Garlic (Allium sativum)
Peach (Prunus persica)
Strawberry (Fragaria x ananassa)
Carrot (Daucus carota)
Grapefruit (Citrus × paradisi)
Pear (Pyrus communis)
Sunflower (Helianthus annuus)
Chard (Beta vulgaris var. cicla)
Grapes (Vitis vinifera)
Peas (Pisum sativum)
Tomato (Solanum lycopersicon)
Cherry (Prunus avium)
Green Beans (Phaseolus vulgaris)
Pepper (Capsicum annuum)
Zucchini (Cucurbita pepo)
Chestnut (Castanea vulgaris)
Lemon (Citrus limonia)
Pine Nuts (Pinus pinea)
Broccoli (Brassica oleracea var.
italica)
Buckwheat (Fagopyrum
esculentum)
User guide - SPECIALfinder Cashew Detection Assay - Rev 1 26/11/2014
7
8 – Troubleshooting
I.
II.
Concomitant no target or IAC amplification, or amplification plots grossly abnormal. Possible
causes and corrective actions:
•
An excess of DNA in the target might inhibit the reaction and IAC may be affected due to
an excess of DNA and/or PCR inhibitors. Test samples diluted 1:10 and 1:100. Please, use
DNase/RNase Free Water to prepare dilutions.
•
Inadequate sealing of optical caps/film caused sample evaporation. Redo the analysis
using proper tools and proper optical caps/film to secure perfect sealing.
•
Did not use the proper consumables. Redo the analysis and use only optical grade 96-well
plates and optical adhesive seal or optical 8-well strips and caps.
•
Samples were not properly prepared. Remake the sample DNA preps. Ensure that the
DNA extraction method is properly performed.
Positive Control reactions failed to amplify, but other reactions appear correct (e.g. the IAC is
amplified):
•
Positive Control DNA was not added to the reaction wells. If other reactions look normal,
there may be no need to repeat the run.
III. Negative Control reactions are positive:
•
Contamination of the Negative Control vial or the SPECIALfinder PCR mix with
SPECIALfinder-positive DNA. Use more care to prevent contamination while handling
assay reagents and setting up assays.
In case support is needed contact Generon at: support@generon.it
9 – Disclaimers
The product is intended for research use only. Generon makes no warranty of any kind, either
expressed or implied, except that the materials from which its products are made of standard quality.
If any materials are defective, Generon will provide a replacement product. Generon shall not be
liable for any damages, including special or consequential damage, or expense arising directly or
indirectly from the use of this product. Please do not interchange components between assays of
different lot numbers. This assay is designed to be used by laboratory personnel following the
common molecular biology precautions.
User guide - SPECIALfinder Cashew Detection Assay - Rev 1 26/11/2014
8
Quick Reference Guide
Product Line:
Part Number:
Type:
Storage:
Execution time:
Expiry date:
Page 1
SPECIALfinder
PAV08A
Qualitative
Frozen
about 120 minutes
see date on the packaging, product validity refers to the product kept intact in its
original packaging and constantly under suitable temperature conditions as
mentioned above.
Assay Box Content
Box 50 reactions
N. vials
Volume (μl)
Box 100 reactions
N. vials
Volume (μl)
SPECIALfinder OLIGO Mix (OLIGOS and Probe pre-blended mix)
1
250
2
250
Positive Control
1
85
2
85
Negative Control
1
200
1
200
All reagents are supplied with a 5% of extra volume.
Not Provided Article: GENERase PLUS Mastermix (Cat. N. ENG002) or equivalent.
Reaction Set-Up
Protect reagents from light exposure as far as OLIGO Mix reagents are photosensitive.
Before setting the analysis, we strongly advise to leave the reagents to warm up at room temperature. Vortex briefly
OLIGO mix, afterwards spin to collect contents at the bottom of the vials. Spin GENERase PLUS Mastermix before opening
it.
Prepare SPECIALfinder WORKING Mastermix by adding 250 μl of SPECIALfinder OLIGO Mix into each tube prefilled with
500 μl of GENERase PLUS Mastermix (Cat. N. ENG002) in order to obtain a single volume of 750 μl of SPECIALfinder
WORKING Mastermix. Vortex briefly SPECIALfinder WORKING Mastermix with the aim of homogenizing the mix and
excluding MgCl2 gradient that could impair the results. Spin to collect contents at the bottom of the vial (Note: label
GENERase PLUS vials with target name after OLIGO Mix addition). Vortex briefly Positive Control and samples before
proceeding further, spin to collect contents at the bottom of the vial.
Transfer SPECIALfinder WORKING Mastermix and samples into the plate as follows:
Reagents per well
Unknown Sample
Positive Control
Negative Control
SPECIALfinder WORKING Mastermix
Final Volume
Volume
5 μl
15 μl
20 μl
Detector Setup
Target
Cashew
IAC (Internal Amplification Control)
Reporter Dye
FAM
HEX (*)
Quencher Dye
BHQ1-NFQ
BHQ1-NFQ
(*)According to your thermocycler you can replace HEX detector in the plate setting with VIC or JOE in case your own Real
Time Platform does not possess the HEX reading channel.
User guide - SPECIALfinder Cashew Detection Assay - Rev 1 26/11/2014
9
Quick Reference Guide
Page 2
Thermal cycling
Step
UNG
Taq Activation
DNA Denaturation
Annealing/Extension + Plate Reading
T (°C)
50
95
95
60
Duration
2 min
10 min
15 sec
60 sec
Loops
1
1
45
The thermal profile presented above was optimized for GENERase PLUS Mastermix (Cat. N. ENG002).
Results analysis
If the following conditions are met:
TEST
Cashew (FAM)
Internal Amplification Control (HEX)
Positive Control
+
+
Negative Control
-
+
TEST
Cashew (FAM )
Internal Amplification Control (HEX)
Positive Sample
+
+/-
Negative Sample
-
+
Invalid Sample (Inhibited)
-
-
Then the possible results for any sample are:
In case of inhibition DNA isolation and purification for the sample need to be improved or you may need to dilute your
sample before performing a new test. Refer to the Troubleshooting paragraph, section 8 in the User Guide, for further
suggestions.
Warning and Precaution
Please, do not interchange components of assays with different lot numbers. This assay is designed to be used by
laboratory personnel following the common molecular biology precautions (GLP).
Disclaimer
Generon s.r.l. guarantees the buyer exclusively concerning the quality of reagents and of the components used to produce the Assay. Generon S.r.l. is
not responsible and cannot anyway be considered responsible or jointly responsible for possible damages resulting from the utilization of the product
by the user. The user consciously and under his own responsibilities decides for the utilization purposes of the product and uses it the way he considers
most suitable in order to reach his goals and/or objectives.
Generon S.r.l. is not responsible for the data resulting from the use of the products, for the utilization that the user independently decides to make of
them or for the damages possibly resulting from the disclosure or transmission of the data themselves to third parties under any form or circumstance.
This clause is automatically accepted by the user when purchasing the products. The patent for performing PCR is held by Hoffmann/La Roche.
Authorization to use PCR can be obtained on licence from Hoffmann-LaRoche. The product, equipment and information included in the assay consists of
assembled and reagents. The licence and licence and authorisation for PCR use are not included in the assay. The user is responsible for setting prefixed
goals, choosing whether or not to perform the PCR reaction and to apply for register his own licence. The use assay is designed for the services supply,
quality control or any other application that is not exclusively an internal company’s research and requires a specific licence for PCR use. This PCR use
licence to supply a service on food analysis field has to be requested directly from Applied Biosystems”. This assay requires the use of Taq Polymerase
enzyme.
The product was internally tested by our quality control. Any responsibility is waivered if the warranty of quality control does not refer to the specific
product. The user is personally responsible for data that he will obtained and/or he will supply to third parties using this assay. Once the sealed package
is open the user accepts all the conditions without fail; if the package is still sealed the product can be returned and the user can be refunded.
User guide - SPECIALfinder Cashew Detection Assay - Rev 1 26/11/2014
10
Download PDF