ISO/TS 20224-9:2022
(Main)Molecular biomarker analysis — Detection of animal-derived materials in foodstuffs and feedstuffs by real-time PCR — Part 9: Goose DNA detection method
Molecular biomarker analysis — Detection of animal-derived materials in foodstuffs and feedstuffs by real-time PCR — Part 9: Goose DNA detection method
This document specifies a real-time polymerase chain reaction (real-time PCR) method for the qualitative detection of goose-specific DNA derived from food and feed. It requires the extraction of an adequate amount of PCR amplifiable DNA from the relevant matrix and can be applied to the detection of goose material derived from domestic breeds of swan goose (Anser cygnoides domesticus) and domestic goose (Anser anser domesticus). Cross detection of Anser brachyrhynchus, Anser indicus, Branta canadensis, Cygnus atratus, Cygnus buccinator, Cygnus cygnus, Cygnus olor, Nettapus auritus, Oxyura jamaicensis and Stictonetta naevosa of Anseriformes is expected. The method can be applied to distinguish domestic breeds of swan goose (Anser cygnoides domesticus) and domestic goose (Anser anser domesticus) from domestic chicken, duck and turkey which are the most common adulterants of foie gras.[1] It is also able to differentiate the domestic goose from other high-end domestic poultry meats (quail, pigeon, pheasant). The target sequence is a partial fragment of the Anser cygnoides isolate SCWG-2014 breed Sichuan white goose unplaced genomic scaffold, GooseV1.0 scaffold320 (i.e. GenBank accession number NW_025927981.1)[2], which is present as a single copy per haploid genome. The provided PCR assay for this target has an absolute limit of detection of five copies per reaction, with ≥ 95 % confidence at this concentration (LOD95 %).
Analyse de biomarqueurs moléculaires — Détection de matériaux d'origine animale dans les denrées alimentaires et les aliments pour animaux par PCR en temps réel — Partie 9: Méthode de détection de l'ADN d'oie
General Information
Buy Standard
Standards Content (Sample)
TECHNICAL ISO/TS
SPECIFICATION 20224-9
First edition
2022-10
Molecular biomarker analysis —
Detection of animal-derived materials
in foodstuffs and feedstuffs by real-
time PCR —
Part 9:
Goose DNA detection method
Analyse de biomarqueurs moléculaires — Détection de matériaux
d'origine animale dans les denrées alimentaires et les aliments pour
animaux par PCR en temps réel —
Partie 9: Méthode de détection de l'ADN d'oie
Reference number
ISO/TS 20224-9:2022(E)
© ISO 2022
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ISO/TS 20224-9:2022(E)
COPYRIGHT PROTECTED DOCUMENT
© ISO 2022
All rights reserved. Unless otherwise specified, or required in the context of its implementation, no part of this publication may
be reproduced or utilized otherwise in any form or by any means, electronic or mechanical, including photocopying, or posting on
the internet or an intranet, without prior written permission. Permission can be requested from either ISO at the address below
or ISO’s member body in the country of the requester.
ISO copyright office
CP 401 • Ch. de Blandonnet 8
CH-1214 Vernier, Geneva
Phone: +41 22 749 01 11
Email: copyright@iso.org
Website: www.iso.org
Published in Switzerland
ii
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ISO/TS 20224-9:2022(E)
Contents Page
Foreword .iv
Introduction .v
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 1
4 Scientific basis . 2
5 Reagents and materials . 2
5.1 General . 2
5.2 PCR reagents . 2
6 Apparatus . 3
7 Procedure .3
7.1 Preparation of the test portion/sample . 3
7.2 Preparation of DNA extracts . 3
7.3 PCR setup. 3
7.3.1 Reaction mixes . 3
7.3.2 PCR controls . 4
7.3.3 Real-time PCR thermocycler plate set-up. 4
7.4 Temperature-time programme. 4
8 Accept/reject criteria . 5
8.1 General . 5
8.2 Identification . 5
9 Validation status and performance criteria . 5
9.1 General . 5
9.2 Robustness . 5
9.3 Reproducibility . 6
9.4 Sensitivity . 6
9.5 Specificity . 9
10 Test report .11
Annex A (informative) BlastN +2.12.0 results for query of GenBank RefSeq Genome (refseq_
genomes) and Whole-genome Shotgun Contigs (wgs) .12
Bibliography .19
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ISO/TS 20224-9:2022(E)
Foreword
ISO (the International Organization for Standardization) is a worldwide federation of national standards
bodies (ISO member bodies). The work of preparing International Standards is normally carried out
through ISO technical committees. Each member body interested in a subject for which a technical
committee has been established has the right to be represented on that committee. International
organizations, governmental and non-governmental, in liaison with ISO, also take part in the work.
ISO collaborates closely with the International Electrotechnical Commission (IEC) on all matters of
electrotechnical standardization.
The procedures used to develop this document and those intended for its further maintenance are
described in the ISO/IEC Directives, Part 1. In particular, the different approval criteria needed for the
different types of ISO documents should be noted. This document was drafted in accordance with the
editorial rules of the ISO/IEC Directives, Part 2 (see www.iso.org/directives).
Attention is drawn to the possibility that some of the elements of this document may be the subject of
patent rights. ISO shall not be held responsible for identifying any or all such patent rights. Details of
any patent rights identified during the development of the document will be in the Introduction and/or
on the ISO list of patent declarations received (see www.iso.org/patents).
Any trade name used in this document is information given for the convenience of users and does not
constitute an endorsement.
For an explanation of the voluntary nature of standards, the meaning of ISO specific terms and
expressions related to conformity assessment, as well as information about ISO’s adherence to
the World Trade Organization (WTO) principles in the Technical Barriers to Trade (TBT), see
www.iso.org/iso/foreword.html.
This document was prepared by Technical Committee ISO/TC 34, Food products, Subcommittee SC 16,
Horizontal methods for molecular biomarker analysis.
A list of all parts in the ISO 20224 series can be found on the ISO website.
Any feedback or questions on this document should be directed to the user’s national standards body. A
complete listing of these bodies can be found at www.iso.org/members.html.
iv
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ISO/TS 20224-9:2022(E)
Introduction
Fraudulent adulteration of meat in food and feed threatens both public safety and commerce.
Adulteration can affect those adhering to ethnological dietary rules, economic development and social
stability. This document provides a real-time polymerase chain reaction (real-time PCR) analytical
method for the identification of meat animal species from nucleic acid present in the ingredients of food
and feed.
Animal-derived biological materials in food and feed are detected and identified in the laboratory with
the following successive (or simultaneous) steps: preparation of the test portion/sample, nucleic acid
extraction and purification, PCR amplification and interpretation of results. This document provides
guidance for PCR amplification to detect domestic commercial breeds of swan goose (Anser cygnoides
domesticus) and domestic goose (Anser anser domesticus) and interpretation of results. Cross detection
of Anser brachyrhynchus, Anser indicus, Branta canadensis, Cygnus atratus, Cygnus buccinator, Cygnus
cygnus, Cygnus olor, Nettapus auritus, Oxyura jamaicensis and Stictonetta naevosa of Anseriformes
is expected. The method can be applied to distinguish domestic goose from domestic chicken, duck
[1]
and turkey which are most common adulterants of foie gras. The method is also able to differentiate
domestic goose from other high-end domestic poultry meats (quail, pigeon, pheasant).
The ISO 20224 series consists of technical specifications that describe specific applications. New
species DNA detection methods established in the future will be added as independent parts.
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TECHNICAL SPECIFICATION ISO/TS 20224-9:2022(E)
Molecular biomarker analysis — Detection of animal-
derived materials in foodstuffs and feedstuffs by real-time
PCR —
Part 9:
Goose DNA detection method
1 Scope
This document specifies a real-time polymerase chain reaction (real-time PCR) method for the
qualitative detection of goose-specific DNA derived from food and feed. It requires the extraction of an
adequate amount of PCR amplifiable DNA from the relevant matrix and can be applied to the detection
of goose material derived from domestic breeds of swan goose (Anser cygnoides domesticus) and
domestic goose (Anser anser domesticus). Cross detection of Anser brachyrhynchus, Anser indicus, Branta
canadensis, Cygnus atratus, Cygnus buccinator, Cygnus cygnus, Cygnus olor, Nettapus auritus, Oxyura
jamaicensis and Stictonetta naevosa of Anseriformes is expected.
The method can be applied to distinguish domestic breeds of swan goose (Anser cygnoides domesticus)
and domestic goose (Anser anser domesticus) from domestic chicken, duck and turkey which are the
[1]
most common adulterants of foie gras. It is also able to differentiate the domestic goose from other
high-end domestic poultry meats (quail, pigeon, pheasant).
The target sequence is a partial fragment of the Anser cygnoides isolate SCWG-2014 breed Sichuan
white goose unplaced genomic scaffold, GooseV1.0 scaffold320 (i.e. GenBank accession number
[2]
NW_025927981.1) , which is present as a single copy per haploid genome. The provided PCR assay for
this target has an absolute limit of detection of five copies per reaction, with ≥ 95 % confidence at this
concentration (LOD ).
95 %
2 Normative references
The following documents are referred to in the text in such a way that some or all of their content
constitutes requirements of this document. For dated references, only the edition cited applies. For
undated references, the latest edition of the referenced document (including any amendments) applies.
ISO 16577, Molecular biomarker analysis —Vocabulary for molecular biomarker analytical methods in
agriculture and food production
ISO 20813, Molecular biomarker analysis — Methods of analysis for the detection and identification
of animal species in foods and food products (nucleic acid-based methods) — General requirements and
definitions
ISO 21571, Foodstuffs — Methods of analysis for the detection of genetically modified organisms and
derived products — Nucleic acid extraction
ISO 24276, Foodstuffs — Methods of analysis for the detection of genetically modified organisms and
derived products — General requirements and definitions
3 Terms and definitions
For the purposes of this document, the terms and definitions given in ISO 16577 apply.
1
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ISO/TS 20224-9:2022(E)
ISO and IEC maintain terminology databases for use in standardization at the following addresses:
— ISO Online browsing platform: available at https:// www .iso .org/ obp
— IEC Electropedia: available at https:// www .electropedia .org/
4 Scientific basis
DNA is extracted from the test portion by applying a suitable method (see ISO 21571:2005, A.1). The
DNA analysis consists of two parts:
— verification of the quality and amplifiability of the extracted DNA using a PCR assay specific for
eukaryotes (i.e. 18S rRNA gene) or mammals and poultry (i.e. myostatin gene);
— detection of the goose species-specific DNA sequence of the single-copy Anser cygnoides isolate
SCWG-2014 breed Sichuan white goose unplaced genomic scaffold, GooseV1.0 scaffold320 (i.e.
GenBank accession number NW_025927981.1) in a real-time PCR.
NOTE The copy number of the eukaryotic ribosomal 18S RNA (18S rRNA) gene in a cell varies from several
hundred to several thousand, while the specific target sequence in the goose genome and myostatin gene in
mammals and poultry genome are single copy. The copy number of the specific target sequence in Anser cygnoides
genome was confirmed by bioinformatics analysis at the whole genome scale (see Annex A) and digital PCR for
absolute quantification.
5 Reagents and materials
5.1 General
For this document, only reagents and water of recognized analytical grade, appropriate for molecular
biology, shall be used. Unless stated otherwise, solutions should be prepared by dissolving the
corresponding reagents in water followed by autoclave sterilization. For all operations in which gloves
are used, gloves shall be powder free. The use of aerosol protected pipette tips (protection against
cross-contamination) is recommended.
5.2 PCR reagents
5.2.1 PCR master mix.
In general, real-time PCR master mix contains thermostable DNA polymerase, dNTPs, MgCl , KCl and
2
buffer as a dilutable concentration, which is ready to use.
Commercial real-time PCR master mix may be used.
5.2.2 Oligonucleotides.
The quality of the oligonucleotides shall be sufficient for their use as primers and probes. See Table 1.
2
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ISO/TS 20224-9:2022(E)
Table 1 — Oligonucleotides
Final concentration
Name DNA sequence of the oligonucleotide
in PCR
Specific sequence in Anser cygnoides isolate SCWG-2014 breed Sichuan white goose unplaced genomic scaffold
a
(GenBank accession number NW_025927981.1)
Goose-121bp-F 5′-ACGAGGATAGGTTGTGACAGC-3′ 400 nmol/l
Goose-121bp-R 5′-GAATCTCTGTGTCGTCTTCTCTATATG-3′ 400 nmol/l
5′-[FAM]-ACTCTGTTCAGCCTTGCGAAGACCTTATGC-[TAMRA]
Goose-121bp-P 200 nmol/l
b
-3′
a
PCR product = 113884 - ACGAGGATAG GTTGTGACAG CTGACTCTGT TCAGCCTTGC GAAGACCTTA TGCTGTCTAC
AATTACCTAA TTGGAGGATA TAGAATTATA GAATCATATA GAGAAGACGA CACAGAGATT C - 114004 - NW_025927981.1.
b
FAM: 6-carboxyfluorescein, TAMRA: 6-carboxytetramethylrhodamine.
Goose-121bp-F is base pairs 113 884 – 113 904, Goose-121bp-R is base pairs 113 978 – 114 404 and
Goose-121bp-P is 113 907 – 113 936 of NW_025927981.1, Anser cygnoides domesticus unplaced genomic
scaffold. Equivalent reporter dyes and/or quencher dyes can be used if they yield the same or better
results.
6 Apparatus
Requirements concerning apparatus and materials shall follow ISO 20813. In addition to the usual
laboratory equipment, the following equipment is required.
6.1 Real-time thermocycler instrument.
A device that amplifies DNA in vitro and performs the temperature-time cycles is needed for PCR.
Additionally, the device shall be capable of exciting fluorescence molecules at specific wavelengths and
detecting sufficient emitted fluorescent light of the fluorophore used to perform TaqMan format assays.
7 Procedure
7.1 Preparation of the test portion/sample
The test sample used for DNA extraction shall be representative of the laboratory sample and
homogeneous, e.g. by grinding or homogenizing the laboratory sample to a fine mixture. Test portion/
sample preparation shall follow the general requirements and specific methods described in ISO 21571
and ISO 20813.
7.2 Preparation of DNA extracts
The extraction/purification and quantification of DNA from the test portion shall follow the
general requirements and methods provided in ISO 21571. DNA extraction methods described in
ISO 21571:2005, Annex A, are recommended.
7.3 PCR setup
7.3.1 Reaction mixes
The method is for a total volume of 25 μl per PCR. The reaction setup is given in Table 2. Reagents
shall be completely thawed at room temperature. Each reagent shall be carefully mixed and briefly
centrifuged immediately before pipetting. A PCR reagent mixture is prepared to contain all components
except for the sample DNA. The required total amount of the PCR reagent mixture prepared depends
on the number of reactions to be performed, including at least one additional reaction as a pipetting
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ISO/TS 20224-9:2022(E)
reserve. The number of sample and control replicates shall follow ISO 20813. Set up the PCR tests as
follows:
a) mix the PCR reagent mixture, centrifuge briefly and pipette 20 µl into each reaction vial;
b) add 5 µl of each sample DNA (20 ng/µl to 200 ng/µl) or positive DNA target control or extraction
blank control or water to the respective reaction vials;
c) mix and centrifuge briefly.
Table 2 — Reaction setup for the amplification
Total reaction volume 25 µl
Sample DNA (20 ng/µl to 200 ng/µl) or controls 5 µl
a
2 × PCR master mix 12,5 µl
Primer Goose-121bp-F, c = 10 μmol/l and Goose-121bp-R, c = 10 μmol/l 1,0 µl for each
Probe Goose-121bp-P, c = 10 μmol/l 0,5 µl
Water to 25 µl
a
In the collaborative trial, a ready-to-use optimized 2 × PCR master mix containing all of the components, excluding
the template and primers, was used. The 2 × PCR master mix contains thermostable DNA polymerase, a blend of dNTPs
with dUTP and uracil-UDG to minimize carry-over PCR contamination, and a passive internal reference based on ROX dye.
Equivalent products can be used if they yield the same or better results. If necessary, the amounts of the reagents and the
temperature-time programme can be adapted.
7.3.2 PCR controls
7.3.2.1 General
PCR controls shall be as described in ISO 24276 and ISO 20813.
7.3.2.2 Inhibition control (reference gene assay)
A reference control gene (i.e. 18S rRNA gene for eukaryotes, myostatin gene for mammals and poultry)
PCR assay using sample DNAs shall be performed to test nucleic acid amplifiability and provide control
to exclude false-negative results.
7.3.3 Real-time PCR thermocycler plate set-up
Transfer the setup reaction vials to the thermocycler. The vials should be arranged to avoid any possible
edge temperature variations associated with a particular real-time thermocycler instrument. Start the
temperature-time programme.
7.4 Temperature-time programme
The temperature-time programme as outlined in Table 3 was used in the validation study. The use of
different reaction conditions and real-time PCR cycles shall be verified. The time for initial denaturation
depends on the master mix used.
Table 3 — Temperature-time programme
Fluorescence
Step Parameter Temperature Time Cycles
measurement
1 Initial denaturation 95 °C 10 min no 1
Denaturation 95 °C 15 s no
2 Amplification 45
Annealing and
60 °C 60 s yes
elongation
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ISO/TS 20224-9:2022(E)
8 Accept/reject criteria
8.1 General
A corresponding real-time PCR-instrument-specific data analysis programme shall be used for the
identification of PCR products. The amplification results can be expressed differently, depending on
the instrument used. In the absence of detectable PCR products (e.g. negative controls), the result
shall be expressed as “undetermined”, “no amplification” or the maximum number of reaction cycles
performed. If amplification of the DNA target sequence in a sample (e.g. positive controls) occurred, a
sigmoid-shaped amplification curve shall be observed. The cycle number at the crossing point of the
amplification curve and the fluorescence threshold shall be calculated [cycle threshold (C ) or cycle
t
quantification (C )].
q
If, due to atypical fluorescence measurement data, the automatic interpretation does not provide
a meaningful result, it may be necessary to set the baseline and the threshold manually prior to
interpreting the data. In such a case, the device-specific instructions provided with the interpretation
software shall be followed.
8.2 Identification
The target sequence is considered as detected if:
— goose-specific primers Goose-121bp-F and Goose-121bp-R and the probe Goose-121bp-P, produce a
sigmoid-shaped amplification curve and a C value or C value can be calculated;
t q
— PCR control reactions with no added DNA (PCR reagent control, extraction blank control) produce
no amplification;
— the amplification controls (positive DNA target control, PCR inhibition control) produce the expected
amplification and C values (or C values).
t q
Trace detections are defined as PCRs with C values later than that defined at the target LOD . In
t 95 %
the event of a trace detection or contradictory positive/negative results from different extracts of the
same sample, then the sample shall be retested. At least two new extracts shall be prepared from the
homogenized laboratory sample. A minimum of 20 PCR replicates shall be conducted across the new
extracts (e.g. ten PCR repeats for two extracted DNA, seven PCR repeats for three extracted DNA).
The target sequence shall be considered as “detected” if ≥ 95 % of the new extract PCR results show
a positive detection. The target sequence shall be considered as “not detected” if < 95 % of the new
extract PCR results show a positive detection.
9 Validation status and performance criteria
9.1 General
Validation followed a two-part process:
a) in-house validation;
b) collaborative trial validation.
9.2 Robustness
The robustness of the method was confirmed for the collaborative trial by changing the reaction
conditions for the following factors:
1)
a) real-time PCR instruments (e.g. ABI 7500, BioRad CFX96, ABI 7900 HT Fast, Eppendorf Realplex 4 );
1) These are examples of a suitable products available commercially. This information is given for the convenience
of users of this document and does not constitute an endorsement by ISO of these products.
5
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ISO/TS 20224-9:2022(E)
b) reaction volume: 19 µl or 21 µl PCR reagent mixture plus 5 µl sample DNA (20 ng/µl to 200 ng/µl);
c) annealing temperature: 59 °C and 61 °C;
d) primer or probe concentration: both reduced by 30 %.
For each factor tested, the PCRs were analysed in triplicate, each with 20 copies of the target sequence
and with 100 copies of the non-target sequence as negative controls. Method performance remained
satisfactory for both samples and negative controls under the changed conditions for each changed
factor.
9.3 Reproducibility
The reproducibility of the method was verified in a collaborative trial with 12 participants, organized
by the Technical Center for Animal, Plant and Food Inspection and Quarantine, Shanghai Customs in
[3] [4]
accordance with the IUPAC protocol and the BVL guidelines . Participants received 12 DNA samples
for the evaluation of false-positive and false-negative rates. All samples were labelled with randomized
coding numbers and consisted of six replicate samples. The 12 DNA samples were:
— six vials of goose DNA solution, 10 copies/µl;
— six vials of bovine DNA solution, 20 copies/µl.
The copy numbers were determined using the real-time PCR of this method and serial dilutions of
plasmid DNA containing the target sequence. The concentration of the plasmid-DNA (copies/µl) was
measured by digital PCR.
Participants received a PCR master mix and the oligonucleotides (primers and probes) from the
collaborative test organizer to conduct the PCR experiments.
Goose and bovine genomic DNA were extracted from goose meat and bovine meat, respectively, and
then adjusted with 0,2 × TE buffer to a nominal concentration of 10 copies/µl for goose DNA and
20 copies/µl for bovine DNA, respectively.
The collaborative trial was designed to determine false-positive and false-negative rates. Each DNA
sample was tested by the participants in a single PCR test with 5 µl of the respective DNA solution,
using the procedure and the conditions given in Tables 2 and 3. The results of the collaborative trial are
listed in Table 4.
Table 4 — Results of the collaborative trial
Number of laboratories 12
Number of laboratories submitting results 12
Number of samples per laboratory 12
Number of accepted results 144
Number of accepted samples containing goose material 72
Number of accepted samples not containing goose material 72
False-positive results 0
False-positive results (in %) 0
False-negative results 1
False-negative results (in %) 1,4
9.4 Sensitivity
The absolute limit of detection (LOD ) for the method is five DNA copies. The collaborative trial of
95 %
the goose detection method was carried out at the same time as collaborative trials for the duck, turkey
and pigeon detection methods. Goose, duck, turkey and pigeon target DNA sequences were synthesized
and cloned into the pUC57 vector (2 710 bp in length, GenBank/EMBL accession number Y14837). This
6
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ISO/TS 20224-9:2022(E)
constructed plasmid pUC57-gdtp (3 167 bp in length) was sequenced to ensure that only one copy
of the goose, duck, turkey and pigeon target DNA sequence was inserted (see Figure 1). No deletion
or insertion mutations were found in the inserted sequences (see Figure 2). The target sequences of
corresponding PCR methods are indicated.
Key
1 nt 1-121 = goose amplicon (121 bp)
2 nt nt 122~226 = duck amplicon (105 bp)
3 nt 227~344 = turkey amplicon (118 bp)
4 nt 345~457 = pigeon amplicon (113 bp)
5 M13 reverse promoter
6 ColE1 origin of replication
7 β-lactamase gene (ampicillin resistance gene)
8 ampicillin resistance gene promoter
9 M13 forward promoter
Figure 1 — Map of the multi-target DNA plasmid
7
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ISO/TS 20224-9:2022(E)
Key
single bold underline nt 1~121 = goose amplicon (121 bp)
double underline nt 122~226 = duck amplicon (105 bp)
dashed underline nt 227~344 = turkey amplicon (118 bp)
dotted underline nt 345~457 = pigeon amplicon (113 bp)
Figure 2 — Complete sequence of nucleotides (nt) and annotation of the insertion in plasmid
pUC57
Each participant in the collaborative trial received a solution containing plasmid pUC57 DNA adjusted
to 1 000 copies/µl of the target sequence (see Figures 1 and 2) in 20 ng/µl sonicated salmon sperm
DNA. The concentration was measured before distribution by digital PCR (QX100 Droplet Digital PCR
2)
System ). Serial dilutions were produced by the 12 laboratories in the range of 0,02 copies/µ
...
© ISO 2022 – All rights reserved
ISO/PRF TS 20224-9:2022(E)
Date: 2022-06-21
ISO TC 03434/SC 16/WG 8
Secretariat: ANSI
Molecular biomarker analysis — Detection of animal-derived
materials in foodstuffs and feedstuffs by real-time PCR —
Part 9: Goose DNA detection method
Analyse de biomarqueurs moléculaires — Détection de matériaux d'origine animale dans les
denrées alimentaires et les aliments pour animaux par PCR en temps réel — Partie 9: Méthode de
détection de l'ADN d'oie
---------------------- Page: 1 ----------------------
ISO/PRF TS 20224-9:2022(E)
© ISO 2022
All rights reserved. Unless otherwise specified, or required in the context of its implementation, no part of
this publication may be reproduced or utilized otherwise in any form or by any means, electronic or
mechanical, including photocopying, or posting on the internet or an intranet, without prior written
permission. Permission can be requested from either ISO at the address below or ISO’s member body in the
country of the requester.
ISO Copyright Office
CP 401 • CH-1214 Vernier, Geneva
Phone: + 41 22 749 01 11
Email: copyright@iso.org
Website: www.iso.org
Published in Switzerland.
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ISO/PRF TS 20224-9:2022(E)
Contents
Foreword . v
Introduction . vi
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 2
4 Scientific basis . 2
5 Reagents and materials . 2
5.1 General . 2
5.2 PCR reagents . 2
6 Apparatus . 3
7 Procedure. 3
7.1 Preparation of the test portion/sample . 3
7.2 Preparation of DNA extracts . 3
7.3 PCR setup . 4
7.3.1 Reaction mixes . 4
7.3.2 PCR controls . 4
7.3.3 Real-time PCR thermocycler plate set-up . 4
7.4 Temperature-time programme . 5
8 Accept/reject criteria . 5
8.1 General . 5
8.2 Identification . 5
9 Validation status and performance criteria . 6
9.1 General . 6
9.2 Robustness . 6
9.3 Reproducibility . 6
9.4 Sensitivity . 7
9.5 Specificity .10
10 Test report .13
Annex A (informative) BlastN +2.12.0 results for query of GenBank RefSeq Genome
(refseq_genomes) and Whole-genome Shotgun Contigs (wgs) .14
Bibliography .22
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ISO/PRF TS 20224-9:2022(E)
Foreword
ISO (the International Organization for Standardization) is a worldwide federation of national standards
bodies (ISO member bodies). The work of preparing International Standards is normally carried out
through ISO technical committees. Each member body interested in a subject for which a technical
committee has been established has the right to be represented on that committee. International
organizations, governmental and non-governmental, in liaison with ISO, also take part in the work. ISO
collaborates closely with the International Electrotechnical Commission (IEC) on all matters of
electrotechnical standardization.
The procedures used to develop this document and those intended for its further maintenance are
described in the ISO/IEC Directives, Part 1. In particular, the different approval criteria needed for the
different types of ISO documents should be noted. This document was drafted in accordance with the
editorial rules of the ISO/IEC Directives, Part 2 (see www.iso.org/directives).
Attention is drawn to the possibility that some of the elements of this document may be the subject of
patent rights. ISO shall not be held responsible for identifying any or all such patent rights. Details of any
patent rights identified during the development of the document will be in the Introduction and/or on
the ISO list of patent declarations received (see www.iso.org/patents).
Any trade name used in this document is information given for the convenience of users and does not
constitute an endorsement.
For an explanation of the voluntary nature of standards, the meaning of ISO specific terms and
expressions related to conformity assessment, as well as information about ISO’s adherence to the World
Trade Organization (WTO) principles in the Technical Barriers to Trade (TBT), see
www.iso.org/iso/foreword.html.
This document was prepared by Technical Committee ISO/TC 34, Food products, Subcommittee SC 16,
Horizontal methods for molecular biomarker analysis.
A list of all parts in the ISO 20224 series can be found on the ISO website.
Any feedback or questions on this document should be directed to the user’s national standards body. A
complete listing of these bodies can be found at www.iso.org/members.html.
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ISO/PRF TS 20224-9:2022(E)
Introduction
Fraudulent adulteration of meat in food and feed threatens both public safety and commerce.
Adulteration can affect those adhering to ethnological dietary rules, economic development and social
stability. This document provides a real-time polymerase chain reaction (real-time PCR) analytical
method for the identification of meat animal species from nucleic acid present in the ingredients of food
and feed.
Animal-derived biological materials in food and feed are detected and identified in the laboratory with
the following successive (or simultaneous) steps: preparation of the test portion/sample, nucleic acid
extraction and purification, PCR amplification and interpretation of results. This document provides
guidance for PCR amplification to detect domestic commercial breeds of swan goose (Anser cygnoides
domesticus) and domestic goose (Anser anser domesticus) and interpretation of results. Cross detection
of Anser brachyrhynchus, Anser indicus, Branta canadensis, Cygnus atratus, Cygnus buccinator, Cygnus
cygnus, Cygnus olor, Nettapus auritus, Oxyura jamaicensis and Stictonetta naevosa of Anseriformes is
expected. The method can be applied to distinguish domestic goose from domestic chicken, duck and
[1]
turkey which are most common adulterants of foie gras. The method is also able to differentiate
domestic goose from other high-end domestic poultry meats (quail, pigeon, pheasant).
The ISO 20224 series consists of technical specifications that describe specific applications. New species
DNA detection methods established in the future will be added as independent parts.
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TECHNICAL SPECIFICATION ISO/PRF TS 20224-9:2022(E)
Molecular biomarker analysis — Detection of animal-derived
materials in foodstuffs and feedstuffs by real-time PCR —
Part 9: Goose DNA detection method
1 Scope
This document specifies a real-time polymerase chain reaction (real-time PCR) method for the qualitative
detection of goose-specific DNA derived from food and feed. It requires the extraction of an adequate
amount of PCR amplifiable DNA from the relevant matrix and can be applied to the detection of goose
material derived from domestic breeds of swan goose (Anser cygnoides domesticus) and domestic goose
(Anser anser domesticus). Cross detection of Anser brachyrhynchus, Anser indicus, Branta canadensis,
Cygnus atratus, Cygnus buccinator, Cygnus cygnus, Cygnus olor, Nettapus auritus, Oxyura jamaicensis and
Stictonetta naevosa of Anseriformes is expected.
The method can be applied to distinguish domestic breeds of swan goose (Anser cygnoides domesticus)
and domestic goose (Anser anser domesticus) from domestic chicken, duck and turkey which are the most
[1]
common adulterants of foie gras. It is also able to differentiate the domestic goose from other high-end
domestic poultry meats (quail, pigeon, pheasant).
The target sequence is a partial fragment of the Anser cygnoides domesticus unplaced genomic scaffold
[2]
(i.e. GenBank accession number NW_013185870.1) , which is present as a single copy per haploid
genome. The provided PCR assay for this target has an absolute limit of detection of five copies per
reaction, with ≥ 95 % confidence at this concentration (LOD ).
95 %
2 Normative references
The following documents are referred to in the text in such a way that some or all of their content
constitutes requirements of this document. For dated references, only the edition cited applies. For
undated references, the latest edition of the referenced document (including any amendments) applies.
ISO 16393, Molecular biomarker analysis — Determination of the performance characteristics of
qualitative measurement methods and validation of methods
ISO 16577, Molecular biomarker analysis —Vocabulary for molecular biomarker analytical methods in
agriculture and food production
ISO 20813, Molecular biomarker analysis — Methods of analysis for the detection and identification of
animal species in foods and food products (nucleic acid-based methods) — General requirements and
definitions
ISO 21571, Foodstuffs — Methods of analysis for the detection of genetically modified organisms and
derived products — Nucleic acid extraction
ISO 24276, Foodstuffs — Methods of analysis for the detection of genetically modified organisms and
derived products — General requirements and definitions
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ISO/PRF TS 20224-9:2022(E)
3 Terms and definitions
For the purposes of this document, the terms and definitions given in ISO 16577 apply.
ISO and IEC maintain terminologicalterminology databases for use in standardization at the following
addresses:
— ISO Online browsing platform: available at https://www.iso.org/obp
— IEC Electropedia: available at https://www.electropedia.org/
4 Scientific basis
DNA is extracted from the test portion by applying a suitable method (see ISO 21571:2005, A.1). The DNA
analysis consists of two parts:
— verification of the quality and amplifiability of the extracted DNA using a PCR assay specific for
eukaryotes (i.e. 18S rRNA gene) or mammals and poultry (i.e. myostatin gene);
— detection of the goose species-specific DNA sequence of the single-copy Anser cygnoides domesticus
unplaced genomic scaffold (i.e. GenBank accession number NW_013185870.1) in a real-time PCR.
NOTE The copy number of the eukaryotic ribosomal 18S RNA (18S rRNA) gene in a cell varies from several
hundred to several thousand, while the specific target sequence in the goose genome and myostatin gene in
mammals and poultry genome are single copy. The copy number of the specific target sequence in Anser cygnoides
genome was confirmed by bioinformatics analysis at the whole genome scale (see Annex A) and digital PCR for
absolute quantification.
5 Reagents and materials
5.1 General
For this document, only reagents and water of recognized analytical grade, appropriate for molecular
biology, shall be used. Unless stated otherwise, solutions should be prepared by dissolving the
corresponding reagents in water followed by autoclave sterilization. For all operations in which gloves
are used, gloves shall be powder free. The use of aerosol protected pipette tips (protection against cross-
contamination) is recommended.
5.2 PCR reagents
5.2.1 PCR master mix.
In general, real-time PCR master mix contains thermostable DNA polymerase, dNTPs, MgCl , KCl, and
2
buffer as a dilutable concentration, which is ready to use.
NOTE: Commercial real-time PCR master mix may be used.
5.2.2 Oligonucleotides.
The quality of the oligonucleotides shall be sufficient for their use as primers and probes. See Table 1.
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ISO/PRF TS 20224-9:2022(E)
Table 1 — Oligonucleotides
Final concentration
Name DNA sequence of the oligonucleotide
in PCR
Specific sequence in Anser cygnoides domesticus unplaced genomic scaffold as the target sequence (GenBank
a
accession number: NW_013185870.1)
Goose-121bp-F 5′-ACGAGGATAGGTTGTGACAGC-3′ 400 nmol/l
Goose-121bp-R 5′-GAATCTCTGTGTCGTCTTCTCTATATG-3′ 400 nmol/l
b
Goose-121bp-P 5′- [FAM]-ACTCTGTTCAGCCTTGCGAAGACCTTATGC-[TAMRA] -3′ 200 nmol/l
a
PCR product = 869408 - acgaggatag gttgtgacag ctgactctgt tcagccttgc gaagacctta tgctgtctac aattacctaa ttggaggata tagaattata
gaatcatata gagaagacga cacagagatt c - 869528 - NW_013185870.1.
b
FAM: 6-carboxyfluorescein, TAMRA: 6-carboxytetramethylrhodamine.
Goose-121bp-F is base pairs 869 408 – 869 428, Goose-121bp-R is base pairs 869 502 – 869 528 and
Goose-121bp-P is 869 431 – 869 460 of NW_013185870.1, Anser cygnoides domesticus unplaced genomic
scaffold. Equivalent reporter dyes and/or quencher dyes can be used if they yield the same or better
results.
6 Apparatus
Requirements concerning apparatus and materials shall follow ISO 20813. In addition to the usual
laboratory equipment, the following equipment is required.
6.1 Real-time thermocycler instrument.
A device that amplifies DNA in vitro and performs the temperature-time cycles is needed for PCR.
Additionally, the device shall be capable of exciting fluorescence molecules at specific wavelengths and
detecting sufficient emitted fluorescent light of the fluorophore used to perform TaqMan format assays.
7 Procedure
7.1 Preparation of the test portion/sample
The test sample used for DNA extraction shall be representative of the laboratory sample and
homogeneous, e.g. by grinding or homogenizing the laboratory sample to a fine mixture. Test
portion/sample preparation shall follow the general requirements and specific methods described in
ISO 21571 and ISO 20813.
7.2 Preparation of DNA extracts
The extraction/purification and quantification of DNA from the test portion shall follow the general
requirements and methods provided in ISO 21571. DNA extraction methods described in
ISO 21571:2005, Annex A, are recommended.
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ISO/PRF TS 20224-9:2022(E)
7.3 PCR setup
7.3.1 Reaction mixes
The method is for a total volume of 25 μl per PCR. The reaction setup is given in Table 2. Reagents shall
be completely thawed at room temperature. Each reagent shall be carefully mixed and briefly centrifuged
immediately before pipetting. A PCR reagent mixture is prepared to contain all components except for
the sample DNA. The required total amount of the PCR reagent mixture prepared depends on the number
of reactions to be performed, including at least one additional reaction as a pipetting reserve. The number
of sample and control replicates shall follow ISO 20813. Set up the PCR tests as follows:
a) mix the PCR reagent mixture, centrifuge briefly and pipette 20 µl into each reaction vial;
b) add 5 µl of each sample DNA (20 ng/µl to 200 ng/µl) or positive DNA target control or extraction
blank control or water to the respective reaction vials;
c) mix and centrifuge briefly.
Table 2 — Reaction setup for the amplification
Total reaction volume 25 µl
Sample DNA (20 ng/µl to 200 ng/µl) or controls 5 µl
a
2 × PCR master mix 12,5 µl
Primer Goose-121bp-F, c = 10 μmol/l and Goose-121bp-R, c = 10 μmol/l 1,0 µl for each
Probe Goose-121bp-P, c = 10 μmol/l 0,5 µl
Water to 25 µl
a
In the collaborative trial, a ready-to-use optimized 2 × PCR master mix containing all of the components, excluding the template
and primers, was used. The 2 × PCR master mix contains thermostable DNA polymerase, a blend of dNTPs with dUTP and uracil-
UDG to minimize carry-over PCR contamination, and a passive internal reference based on ROX dye. Equivalent products can be
used if they yield the same or better results. If necessary, the amounts of the reagents and the temperature-time programme can
be adapted.
7.3.2 PCR controls
7.3.2.1 General
PCR controls shall be as described in ISO 24276 and ISO 20813.
7.3.2.2 Inhibition control (reference gene assay)
A reference control gene (i.e. 18S rRNA gene for eukaryotes, myostatin gene for mammals and poultry)
PCR assay using sample DNAs shall be performed to test nucleic acid amplifiability and provide control
to exclude false-negative results.
7.3.3 Real-time PCR thermocycler plate set-up
Transfer the setup reaction vials to the thermocycler. The vials should be arranged to avoid any possible
edge temperature variations associated with a particular real-time thermocycler instrument. Start the
temperature-time programme.
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ISO/PRF TS 20224-9:2022(E)
7.4 Temperature-time programme
The temperature-time programme as outlined in Table 3 was used in the validation study. The use of
different reaction conditions and real-time PCR cycles shall be verified. The time for initial denaturation
depends on the master mix used.
Table 3 — Temperature-time programme
Fluorescence
Step Parameter Temperature Time Cycles
measurement
1 Initial denaturation 95 °C 10 min no 1
Denaturation 95 °C 15 s no
2 Amplification 45
Annealing and
60 °C 60 s yes
elongation
8 Accept/reject criteria
8.1 General
A corresponding real-time PCR-instrument-specific data analysis programme shall be used for the
identification of PCR products. The amplification results can be expressed differently, depending on the
instrument used. In the absence of detectable PCR products (e.g. negative controls), the result shall be
expressed as “undetermined”, “no amplification” or the maximum number of reaction cycles performed.
If amplification of the DNA target sequence in a sample (e.g. positive controls) occurred, a sigmoid-shaped
amplification curve shall be observed. The cycle number at the crossing point of the amplification curve
and the fluorescence threshold shall be calculated [cycle threshold (C ) or cycle quantification (C )].
t q
If, due to atypical fluorescence measurement data, the automatic interpretation does not provide a
meaningful result, it may be necessary to set the baseline and the threshold manually prior to interpreting
the data. In such a case, the device-specific instructions provided with the interpretation software shall
be followed.
8.2 Identification
The target sequence is considered as detected if:
— goose-specific primers Goose-121bp-F and Goose-121bp-R and the probe Goose-121bp-P, produce a
sigmoid-shaped amplification curve and a C value or C value can be calculated;
t q
— PCR control reactions with no added DNA (PCR reagent control, extraction blank control) produce
no amplification;
— the amplification controls (positive DNA target control, PCR inhibition control) produce the expected
amplification and C values (or C values).
t q
Trace detections are defined as PCRs with C values later than that defined at the target LOD . In the
t 95 %
event of a trace detection or contradictory positive/negative results from different extracts of the same
sample, then the sample shall be retested. At least two new extracts shall be prepared from the
homogenized laboratory sample. A minimum of 20 PCR replicates shall be conducted across the new
extracts (e.g. ten PCR repeats for two extracted DNA, seven PCR repeats for three extracted DNA). The
target sequence shall be considered as “detected” if ≥ 95 % of the new extract PCR results show a positive
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ISO/PRF TS 20224-9:2022(E)
detection. The target sequence shall be considered as “not detected” if < 95 % of the new extract PCR
results show a positive detection.
9 Validation status and performance criteria
9.1 General
Validation followed a two-part process:
a) in-house validation;
b) collaborative trial validation.
9.2 Robustness
The robustness of the method was confirmed for the collaborative trial by changing the reaction
conditions for the following factors:
1
a) real-time PCR instruments (e.g. ABI 7500, BioRad CFX96, ABI 7900 HT Fast, Eppendorf Realplex 4 );
b) reaction volume: 19 µl or 21 µl PCR reagent mixture plus 5 µl sample DNA (20 ng/µl to 200 ng/µl);
c) annealing temperature: 59 °C and 61 °C;
d) primer or probe concentration: both reduced by 30 %.
For each factor tested, the PCRs were analysed in triplicate, each with 20 copies of the target sequence
and with 100 copies of the non-target sequence as negative controls. Method performance remained
satisfactory for both samples and negative controls under the changed conditions for each changed factor.
9.3 Reproducibility
The reproducibility of the method was verified in a collaborative trial with 12 participants, organized by
the Technical Center for Animal, Plant and Food Inspection and Quarantine, Shanghai Customs in
[3] [4]
accordance with the IUPAC protocol and the BVL guidelines . Participants received 12 DNA samples
for the evaluation of false-positive and false-negative rates. All samples were labelled with randomized
coding numbers and consisted of six replicate samples. The 12 DNA samples were:
— six vials of goose DNA solution, 10 copies/µl;
— six vials of bovine DNA solution, 20 copies/µl.
The copy numbers were determined using the real-time PCR of this method and serial dilutions of
plasmid DNA containing the target sequence. The concentration of the plasmid-DNA (copies/µl) was
measured by digital PCR.
Participants received a PCR master mix and the oligonucleotides (primers and probes) from the
collaborative test organizer to conduct the PCR experiments.
Goose and bovine genomic DNA were extracted from goose meat and bovine meat, respectively, and then
adjusted with 0,2 × TE buffer to a nominal concentration of 10 copies/µl for goose DNA and 20 copies/µl
for bovine DNA, respectively.
1
These are examples of a suitable products available commercially. This information is given for the convenience
of users of this document and does not constitute an endorsement by ISO of these products.
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ISO/PRF TS 20224-9:2022(E)
The collaborative trial was designed to determine false-positive and false-negative rates. Each DNA
sample was tested by the participants in a single PCR test with 5 µl of the respective DNA solution, using
the procedure and the conditions given in Tables 2 and 3. The results of the collaborative trial are listed
in Table 4.
Table 4 — Results of the collaborative trial
Number of laboratories 12
Number of laboratories submitting results 12
Number of samples per laboratory 12
Number of accepted results 144
Number of accepted samples containing goose material 72
Number of accepted samples not containing goose material 72
False-positive results 0
False-positive results (in %) 0
False-negative results 1
False-negative results (in %) 1.,4
9.4 Sensitivity
The absolute limit of detection (LOD ) for the method is five DNA copies. The collaborative trial of the
95 %
goose detection method was carried out at the same time as collaborative trials for the duck, turkey, and
pigeon detection methods. Target DNA sequences for separate identification of detection of goose, duck,
turkey and pigeon were synthesized and cloned into the pUC57 vector (2 710 bp in length,
GenBank/EMBL accession number Y14837). This constructed plasmid pUC57-gdtp (3 167 bp in length)
was sequenced to ensure that only one copy of the goose, duck, turkey and pigeon target DNA sequence
was inserted (see Figure 1). No deletion or insertion mutations were found in the inserted sequences (see
Figure 2). The target sequences of corresponding PCR methods are indicated.
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ISO/PRF TS 20224-9:2022(E)
Key
1 nt 1-121 = goose amplicon (121 bp)
2 nt nt 122~226 = duck amplicon (105 bp)
3 nt 227~344 = turkey amplicon (118 bp)
4 nt 345~457 = pigeon amplicon (113 bp)
5 M13 reverse promoter
6 ColE1 origin of replication
7 β-lactamase gene (ampicillin resistance gene)
8 ampicillin resistance gene promoter
9 M13 forward promoter
Figure 1 — Map of the multi-target DNA plasmid
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ISO/PRF TS 20224-9:2022(E)
Key
single bold underline nt 1~121 = goose amplicon (121 bp)
double underline nt 122~226 = duck amplicon (105 bp)
dashed underline nt 227~344 = turkey amplicon (118 bp)
dotted underline nt 345~457 = pigeon amplicon (113 bp)
Figure 2 — Complete sequence of nucleotides (nt) and annotation of the insertion in plasmid
pUC57
Each participant in the collaborative trial received a solution containing plasmid pUC57 DNA adjusted to
1 000 copies/µl of the target sequence (see Figures 1 and 2) in 20 ng/µl sonicated salmon sperm DNA.
2
The concentration was measured before distribution by digital PCR (QX100 Droplet Digital PCR System ).
Serial dilutions were produced by the 12 laboratories in the range of 0,02 copies/µl to 4 copies/µl using
0,2 × TE buffer containing 20 ng/µl sonicated salmon sperm DNA. Each participant measured six
replicates per concentration level. A positive result was achieved for five copies per PCR in 72 out of 72
tests (see Table 5).
Probability of detection (POD) describes the probability that PCR amplification will take place at a given
number of copies of the target sequences (see ISO/TS 16393). Qualitative data generated across all
laboratories and dilution levels (see Table 5) was used to determine the POD = 0,95 of the detection
method (see Table 6) as described in Reference [3]. Standard deviation was determined to be 0,29 and
the LOD was 3,1 copies; both parameters well below the required maximum of 1 and 20 copies,
95 %
[5]
respectively.
2
This is a product supplied by Bio-Rad GmbH. This information is given for the convenience of users of this
document and does not constitute an endorsement by ISO of the product named. Equivalent products may be used
if they can be shown to lead to the sam
...
FINAL
TECHNICAL ISO/DTS
DRAFT
SPECIFICATION 20224-9
ISO/TC 34/SC 16
Molecular biomarker analysis —
Secretariat: ANSI
Detection of animal-derived materials
Voting begins on:
2022-07-20 in foodstuffs and feedstuffs by real-
time PCR —
Voting terminates on:
2022-09-14
Part 9:
Goose DNA detection method
Analyse de biomarqueurs moléculaires — Détection de matériaux
d'origine animale dans les denrées alimentaires et les aliments pour
animaux par PCR en temps réel —
Partie 9: Méthode de détection de l'ADN d'oie
RECIPIENTS OF THIS DRAFT ARE INVITED TO
SUBMIT, WITH THEIR COMMENTS, NOTIFICATION
OF ANY RELEVANT PATENT RIGHTS OF WHICH
THEY ARE AWARE AND TO PROVIDE SUPPOR TING
DOCUMENTATION.
IN ADDITION TO THEIR EVALUATION AS
Reference number
BEING ACCEPTABLE FOR INDUSTRIAL, TECHNO-
ISO/DTS 20224-9:2022(E)
LOGICAL, COMMERCIAL AND USER PURPOSES,
DRAFT INTERNATIONAL STANDARDS MAY ON
OCCASION HAVE TO BE CONSIDERED IN THE
LIGHT OF THEIR POTENTIAL TO BECOME STAN-
DARDS TO WHICH REFERENCE MAY BE MADE IN
NATIONAL REGULATIONS. © ISO 2022
---------------------- Page: 1 ----------------------
ISO/DTS 20224-9:2022(E)
FINAL
TECHNICAL ISO/DTS
DRAFT
SPECIFICATION 20224-9
ISO/TC 34/SC 16
Molecular biomarker analysis —
Secretariat: ANSI
Detection of animal-derived materials
Voting begins on:
in foodstuffs and feedstuffs by real-
time PCR —
Voting terminates on:
Part 9:
Goose DNA detection method
Analyse de biomarqueurs moléculaires — Détection de matériaux
d'origine animale dans les denrées alimentaires et les aliments pour
animaux par PCR en temps réel —
Partie 9: Méthode de détection de l'ADN d'oie
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BEING ACCEPTABLE FOR INDUSTRIAL, TECHNO-
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DARDS TO WHICH REFERENCE MAY BE MADE IN
ii
© ISO 2022 – All rights reserved
NATIONAL REGULATIONS. © ISO 2022
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ISO/DTS 20224-9:2022(E)
Contents Page
Foreword .iv
Introduction .v
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 1
4 Scientific basis . 2
5 Reagents and materials . 2
5.1 General . 2
5.2 PCR reagents . 2
6 Apparatus . 3
7 Procedure .3
7.1 Preparation of the test portion/sample . 3
7.2 Preparation of DNA extracts . 3
7.3 PCR setup. 3
7.3.1 Reaction mixes . 3
7.3.2 PCR controls . 4
7.3.3 Real-time PCR thermocycler plate set-up. 4
7.4 Temperature-time programme. 4
8 Accept/reject criteria . 5
8.1 General . 5
8.2 Identification . 5
9 Validation status and performance criteria . 5
9.1 General . 5
9.2 Robustness . 5
9.3 Reproducibility . 6
9.4 Sensitivity . 6
9.5 Specificity . 9
10 Test report .11
Annex A (informative) BlastN +2.12.0 results for query of GenBank RefSeq Genome (refseq_
genomes) and Whole-genome Shotgun Contigs (wgs) .12
Bibliography .19
iii
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ISO/DTS 20224-9:2022(E)
Foreword
ISO (the International Organization for Standardization) is a worldwide federation of national standards
bodies (ISO member bodies). The work of preparing International Standards is normally carried out
through ISO technical committees. Each member body interested in a subject for which a technical
committee has been established has the right to be represented on that committee. International
organizations, governmental and non-governmental, in liaison with ISO, also take part in the work.
ISO collaborates closely with the International Electrotechnical Commission (IEC) on all matters of
electrotechnical standardization.
The procedures used to develop this document and those intended for its further maintenance are
described in the ISO/IEC Directives, Part 1. In particular, the different approval criteria needed for the
different types of ISO documents should be noted. This document was drafted in accordance with the
editorial rules of the ISO/IEC Directives, Part 2 (see www.iso.org/directives).
Attention is drawn to the possibility that some of the elements of this document may be the subject of
patent rights. ISO shall not be held responsible for identifying any or all such patent rights. Details of
any patent rights identified during the development of the document will be in the Introduction and/or
on the ISO list of patent declarations received (see www.iso.org/patents).
Any trade name used in this document is information given for the convenience of users and does not
constitute an endorsement.
For an explanation of the voluntary nature of standards, the meaning of ISO specific terms and
expressions related to conformity assessment, as well as information about ISO’s adherence to
the World Trade Organization (WTO) principles in the Technical Barriers to Trade (TBT), see
www.iso.org/iso/foreword.html.
This document was prepared by Technical Committee ISO/TC 34, Food products, Subcommittee SC 16,
Horizontal methods for molecular biomarker analysis.
A list of all parts in the ISO 20224 series can be found on the ISO website.
Any feedback or questions on this document should be directed to the user’s national standards body. A
complete listing of these bodies can be found at www.iso.org/members.html.
iv
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ISO/DTS 20224-9:2022(E)
Introduction
Fraudulent adulteration of meat in food and feed threatens both public safety and commerce.
Adulteration can affect those adhering to ethnological dietary rules, economic development and social
stability. This document provides a real-time polymerase chain reaction (real-time PCR) analytical
method for the identification of meat animal species from nucleic acid present in the ingredients of food
and feed.
Animal-derived biological materials in food and feed are detected and identified in the laboratory with
the following successive (or simultaneous) steps: preparation of the test portion/sample, nucleic acid
extraction and purification, PCR amplification and interpretation of results. This document provides
guidance for PCR amplification to detect domestic commercial breeds of swan goose (Anser cygnoides
domesticus) and domestic goose (Anser anser domesticus) and interpretation of results. Cross detection
of Anser brachyrhynchus, Anser indicus, Branta canadensis, Cygnus atratus, Cygnus buccinator, Cygnus
cygnus, Cygnus olor, Nettapus auritus, Oxyura jamaicensis and Stictonetta naevosa of Anseriformes
is expected. The method can be applied to distinguish domestic goose from domestic chicken, duck
[1]
and turkey which are most common adulterants of foie gras. The method is also able to differentiate
domestic goose from other high-end domestic poultry meats (quail, pigeon, pheasant).
The ISO 20224 series consists of technical specifications that describe specific applications. New
species DNA detection methods established in the future will be added as independent parts.
v
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TECHNICAL SPECIFICATION ISO/DTS 20224-9:2022(E)
Molecular biomarker analysis — Detection of animal-
derived materials in foodstuffs and feedstuffs by real-time
PCR —
Part 9:
Goose DNA detection method
1 Scope
This document specifies a real-time polymerase chain reaction (real-time PCR) method for the
qualitative detection of goose-specific DNA derived from food and feed. It requires the extraction of an
adequate amount of PCR amplifiable DNA from the relevant matrix and can be applied to the detection
of goose material derived from domestic breeds of swan goose (Anser cygnoides domesticus) and
domestic goose (Anser anser domesticus). Cross detection of Anser brachyrhynchus, Anser indicus, Branta
canadensis, Cygnus atratus, Cygnus buccinator, Cygnus cygnus, Cygnus olor, Nettapus auritus, Oxyura
jamaicensis and Stictonetta naevosa of Anseriformes is expected.
The method can be applied to distinguish domestic breeds of swan goose (Anser cygnoides domesticus)
and domestic goose (Anser anser domesticus) from domestic chicken, duck and turkey which are the
[1]
most common adulterants of foie gras. It is also able to differentiate the domestic goose from other
high-end domestic poultry meats (quail, pigeon, pheasant).
The target sequence is a partial fragment of the Anser cygnoides domesticus unplaced genomic scaffold
[2]
(i.e. GenBank accession number NW_013185870.1) , which is present as a single copy per haploid
genome. The provided PCR assay for this target has an absolute limit of detection of five copies per
reaction, with ≥ 95 % confidence at this concentration (LOD ).
95 %
2 Normative references
The following documents are referred to in the text in such a way that some or all of their content
constitutes requirements of this document. For dated references, only the edition cited applies. For
undated references, the latest edition of the referenced document (including any amendments) applies.
ISO 16577, Molecular biomarker analysis —Vocabulary for molecular biomarker analytical methods in
agriculture and food production
ISO 20813, Molecular biomarker analysis — Methods of analysis for the detection and identification
of animal species in foods and food products (nucleic acid-based methods) — General requirements and
definitions
ISO 21571, Foodstuffs — Methods of analysis for the detection of genetically modified organisms and
derived products — Nucleic acid extraction
ISO 24276, Foodstuffs — Methods of analysis for the detection of genetically modified organisms and
derived products — General requirements and definitions
3 Terms and definitions
For the purposes of this document, the terms and definitions given in ISO 16577 apply.
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ISO and IEC maintain terminology databases for use in standardization at the following addresses:
— ISO Online browsing platform: available at https:// www .iso .org/ obp
— IEC Electropedia: available at https:// www .electropedia .org/
4 Scientific basis
DNA is extracted from the test portion by applying a suitable method (see ISO 21571:2005, A.1). The
DNA analysis consists of two parts:
— verification of the quality and amplifiability of the extracted DNA using a PCR assay specific for
eukaryotes (i.e. 18S rRNA gene) or mammals and poultry (i.e. myostatin gene);
— detection of the goose species-specific DNA sequence of the single-copy Anser cygnoides domesticus
unplaced genomic scaffold (i.e. GenBank accession number NW_013185870.1) in a real-time PCR.
NOTE The copy number of the eukaryotic ribosomal 18S RNA (18S rRNA) gene in a cell varies from several
hundred to several thousand, while the specific target sequence in the goose genome and myostatin gene in
mammals and poultry genome are single copy. The copy number of the specific target sequence in Anser cygnoides
genome was confirmed by bioinformatics analysis at the whole genome scale (see Annex A) and digital PCR for
absolute quantification.
5 Reagents and materials
5.1 General
For this document, only reagents and water of recognized analytical grade, appropriate for molecular
biology, shall be used. Unless stated otherwise, solutions should be prepared by dissolving the
corresponding reagents in water followed by autoclave sterilization. For all operations in which gloves
are used, gloves shall be powder free. The use of aerosol protected pipette tips (protection against
cross-contamination) is recommended.
5.2 PCR reagents
5.2.1 PCR master mix.
In general, real-time PCR master mix contains thermostable DNA polymerase, dNTPs, MgCl , KCl and
2
buffer as a dilutable concentration, which is ready to use.
Commercial real-time PCR master mix may be used.
5.2.2 Oligonucleotides.
The quality of the oligonucleotides shall be sufficient for their use as primers and probes. See Table 1.
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Table 1 — Oligonucleotides
Final concentration
Name DNA sequence of the oligonucleotide
in PCR
Specific sequence in Anser cygnoides domesticus unplaced genomic scaffold as the target sequence (GenBank
a
accession number NW_013185870.1)
Goose-121bp-F 5′-ACGAGGATAGGTTGTGACAGC-3′ 400 nmol/l
Goose-121bp-R 5′-GAATCTCTGTGTCGTCTTCTCTATATG-3′ 400 nmol/l
5′-[FAM]-ACTCTGTTCAGCCTTGCGAAGACCTTATGC-[TAMRA]
Goose-121bp-P 200 nmol/l
b
-3′
a
PCR product = 869408 - acgaggatag gttgtgacag ctgactctgt tcagccttgc gaagacctta tgctgtctac aattacctaa ttggaggata
tagaattata gaatcatata gagaagacga cacagagatt c - 869528 - NW_013185870.1.
b
FAM: 6-carboxyfluorescein, TAMRA: 6-carboxytetramethylrhodamine.
Goose-121bp-F is base pairs 869 408 – 869 428, Goose-121bp-R is base pairs 869 502 – 869 528 and
Goose-121bp-P is 869 431 – 869 460 of NW_013185870.1, Anser cygnoides domesticus unplaced genomic
scaffold. Equivalent reporter dyes and/or quencher dyes can be used if they yield the same or better
results.
6 Apparatus
Requirements concerning apparatus and materials shall follow ISO 20813. In addition to the usual
laboratory equipment, the following equipment is required.
6.1 Real-time thermocycler instrument.
A device that amplifies DNA in vitro and performs the temperature-time cycles is needed for PCR.
Additionally, the device shall be capable of exciting fluorescence molecules at specific wavelengths and
detecting sufficient emitted fluorescent light of the fluorophore used to perform TaqMan format assays.
7 Procedure
7.1 Preparation of the test portion/sample
The test sample used for DNA extraction shall be representative of the laboratory sample and
homogeneous, e.g. by grinding or homogenizing the laboratory sample to a fine mixture. Test portion/
sample preparation shall follow the general requirements and specific methods described in ISO 21571
and ISO 20813.
7.2 Preparation of DNA extracts
The extraction/purification and quantification of DNA from the test portion shall follow the
general requirements and methods provided in ISO 21571. DNA extraction methods described in
ISO 21571:2005, Annex A, are recommended.
7.3 PCR setup
7.3.1 Reaction mixes
The method is for a total volume of 25 μl per PCR. The reaction setup is given in Table 2. Reagents
shall be completely thawed at room temperature. Each reagent shall be carefully mixed and briefly
centrifuged immediately before pipetting. A PCR reagent mixture is prepared to contain all components
except for the sample DNA. The required total amount of the PCR reagent mixture prepared depends
on the number of reactions to be performed, including at least one additional reaction as a pipetting
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reserve. The number of sample and control replicates shall follow ISO 20813. Set up the PCR tests as
follows:
a) mix the PCR reagent mixture, centrifuge briefly and pipette 20 µl into each reaction vial;
b) add 5 µl of each sample DNA (20 ng/µl to 200 ng/µl) or positive DNA target control or extraction
blank control or water to the respective reaction vials;
c) mix and centrifuge briefly.
Table 2 — Reaction setup for the amplification
Total reaction volume 25 µl
Sample DNA (20 ng/µl to 200 ng/µl) or controls 5 µl
a
2 × PCR master mix 12,5 µl
Primer Goose-121bp-F, c = 10 μmol/l and Goose-121bp-R, c = 10 μmol/l 1,0 µl for each
Probe Goose-121bp-P, c = 10 μmol/l 0,5 µl
Water to 25 µl
a
In the collaborative trial, a ready-to-use optimized 2 × PCR master mix containing all of the components, excluding
the template and primers, was used. The 2 × PCR master mix contains thermostable DNA polymerase, a blend of dNTPs
with dUTP and uracil-UDG to minimize carry-over PCR contamination, and a passive internal reference based on ROX dye.
Equivalent products can be used if they yield the same or better results. If necessary, the amounts of the reagents and the
temperature-time programme can be adapted.
7.3.2 PCR controls
7.3.2.1 General
PCR controls shall be as described in ISO 24276 and ISO 20813.
7.3.2.2 Inhibition control (reference gene assay)
A reference control gene (i.e. 18S rRNA gene for eukaryotes, myostatin gene for mammals and poultry)
PCR assay using sample DNAs shall be performed to test nucleic acid amplifiability and provide control
to exclude false-negative results.
7.3.3 Real-time PCR thermocycler plate set-up
Transfer the setup reaction vials to the thermocycler. The vials should be arranged to avoid any possible
edge temperature variations associated with a particular real-time thermocycler instrument. Start the
temperature-time programme.
7.4 Temperature-time programme
The temperature-time programme as outlined in Table 3 was used in the validation study. The use of
different reaction conditions and real-time PCR cycles shall be verified. The time for initial denaturation
depends on the master mix used.
Table 3 — Temperature-time programme
Fluorescence
Step Parameter Temperature Time Cycles
measurement
1 Initial denaturation 95 °C 10 min no 1
Denaturation 95 °C 15 s no
2 Amplification 45
Annealing and
60 °C 60 s yes
elongation
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8 Accept/reject criteria
8.1 General
A corresponding real-time PCR-instrument-specific data analysis programme shall be used for the
identification of PCR products. The amplification results can be expressed differently, depending on
the instrument used. In the absence of detectable PCR products (e.g. negative controls), the result
shall be expressed as “undetermined”, “no amplification” or the maximum number of reaction cycles
performed. If amplification of the DNA target sequence in a sample (e.g. positive controls) occurred, a
sigmoid-shaped amplification curve shall be observed. The cycle number at the crossing point of the
amplification curve and the fluorescence threshold shall be calculated [cycle threshold (C ) or cycle
t
quantification (C )].
q
If, due to atypical fluorescence measurement data, the automatic interpretation does not provide
a meaningful result, it may be necessary to set the baseline and the threshold manually prior to
interpreting the data. In such a case, the device-specific instructions provided with the interpretation
software shall be followed.
8.2 Identification
The target sequence is considered as detected if:
— goose-specific primers Goose-121bp-F and Goose-121bp-R and the probe Goose-121bp-P, produce a
sigmoid-shaped amplification curve and a C value or C value can be calculated;
t q
— PCR control reactions with no added DNA (PCR reagent control, extraction blank control) produce
no amplification;
— the amplification controls (positive DNA target control, PCR inhibition control) produce the expected
amplification and C values (or C values).
t q
Trace detections are defined as PCRs with C values later than that defined at the target LOD . In
t 95 %
the event of a trace detection or contradictory positive/negative results from different extracts of the
same sample, then the sample shall be retested. At least two new extracts shall be prepared from the
homogenized laboratory sample. A minimum of 20 PCR replicates shall be conducted across the new
extracts (e.g. ten PCR repeats for two extracted DNA, seven PCR repeats for three extracted DNA).
The target sequence shall be considered as “detected” if ≥ 95 % of the new extract PCR results show
a positive detection. The target sequence shall be considered as “not detected” if < 95 % of the new
extract PCR results show a positive detection.
9 Validation status and performance criteria
9.1 General
Validation followed a two-part process:
a) in-house validation;
b) collaborative trial validation.
9.2 Robustness
The robustness of the method was confirmed for the collaborative trial by changing the reaction
conditions for the following factors:
1)
a) real-time PCR instruments (e.g. ABI 7500, BioRad CFX96, ABI 7900 HT Fast, Eppendorf Realplex 4 );
1) These are examples of a suitable products available commercially. This information is given for the convenience
of users of this document and does not constitute an endorsement by ISO of these products.
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b) reaction volume: 19 µl or 21 µl PCR reagent mixture plus 5 µl sample DNA (20 ng/µl to 200 ng/µl);
c) annealing temperature: 59 °C and 61 °C;
d) primer or probe concentration: both reduced by 30 %.
For each factor tested, the PCRs were analysed in triplicate, each with 20 copies of the target sequence
and with 100 copies of the non-target sequence as negative controls. Method performance remained
satisfactory for both samples and negative controls under the changed conditions for each changed
factor.
9.3 Reproducibility
The reproducibility of the method was verified in a collaborative trial with 12 participants, organized
by the Technical Center for Animal, Plant and Food Inspection and Quarantine, Shanghai Customs in
[3] [4]
accordance with the IUPAC protocol and the BVL guidelines . Participants received 12 DNA samples
for the evaluation of false-positive and false-negative rates. All samples were labelled with randomized
coding numbers and consisted of six replicate samples. The 12 DNA samples were:
— six vials of goose DNA solution, 10 copies/µl;
— six vials of bovine DNA solution, 20 copies/µl.
The copy numbers were determined using the real-time PCR of this method and serial dilutions of
plasmid DNA containing the target sequence. The concentration of the plasmid-DNA (copies/µl) was
measured by digital PCR.
Participants received a PCR master mix and the oligonucleotides (primers and probes) from the
collaborative test organizer to conduct the PCR experiments.
Goose and bovine genomic DNA were extracted from goose meat and bovine meat, respectively, and
then adjusted with 0,2 × TE buffer to a nominal concentration of 10 copies/µl for goose DNA and
20 copies/µl for bovine DNA, respectively.
The collaborative trial was designed to determine false-positive and false-negative rates. Each DNA
sample was tested by the participants in a single PCR test with 5 µl of the respective DNA solution,
using the procedure and the conditions given in Tables 2 and 3. The results of the collaborative trial are
listed in Table 4.
Table 4 — Results of the collaborative trial
Number of laboratories 12
Number of laboratories submitting results 12
Number of samples per laboratory 12
Number of accepted results 144
Number of accepted samples containing goose material 72
Number of accepted samples not containing goose material 72
False-positive results 0
False-positive results (in %) 0
False-negative results 1
False-negative results (in %) 1,4
9.4 Sensitivity
The absolute limit of detection (LOD ) for the method is five DNA copies. The collaborative trial
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of the goose detection method was carried out at the same time as collaborative trials for the duck,
turkey and pigeon detection methods. Target DNA sequences for separate identification of detection of
goose, duck, turkey and pigeon were synthesized and cloned into the pUC57 vector (2 710 bp in length,
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GenBank/EMBL accession number Y14837). This constructe
...
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