1、BSI Standards PublicationBS ISO 16578:2013Molecular biomarker analysis General definitions andrequirements for microarraydetection of specific nucleicacid sequencesBS ISO 16578:2013 BRITISH STANDARDNational forewordThis British Standard is the UK implementation of ISO 16578:2013.The UK participation
2、 in its preparation was entrusted to TechnicalCommittee AW/275, Food analysis - Horizontal methods.A list of organizations represented on this committee can beobtained on request to its secretary.This publication does not purport to include all the necessaryprovisions of a contract. Users are respon
3、sible for its correctapplication. The British Standards Institution 2013. Published by BSI StandardsLimited 2013ISBN 978 0 580 75167 7ICS 67.050Compliance with a British Standard cannot confer immunity fromlegal obligations.This British Standard was published under the authority of theStandards Poli
4、cy and Strategy Committee on 30 November 2013.Amendments issued since publicationDate Text affectedBS ISO 16578:2013 ISO 2013Molecular biomarker analysis General definitions and requirements for microarray detection of specific nucleic acid sequencesAnalyse molculaire des biomarqueurs Dfinitions gnr
5、ales et exigences relatives la dtection sur microrseaux de squences dacides nucliques spcifiquesINTERNATIONAL STANDARDISO16578First edition2013-11-15Reference numberISO 16578:2013(E)BS ISO 16578:2013ISO 16578:2013(E)ii ISO 2013 All rights reservedCOPYRIGHT PROTECTED DOCUMENT ISO 2013All rights reser
6、ved. Unless otherwise specified, 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
7、 at the address below or ISOs member body in the country of the requester.ISO copyright officeCase postale 56 CH-1211 Geneva 20Tel. + 41 22 749 01 11Fax + 41 22 749 09 47E-mail copyrightiso.orgWeb www.iso.orgPublished in SwitzerlandBS ISO 16578:2013ISO 16578:2013(E)ForewordISO (the International Org
8、anization 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 establi
9、shed 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 standardizatio
10、n.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 t
11、he editorial rules of the ISO/IEC Directives, Part 2. www.iso.org/directivesAttention 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 rig
12、hts identified during the development of the document will be in the Introduction and/or on the ISO list of patent declarations received. www.iso.org/patentsAny trade name used in this document is information given for the convenience of users and does not constitute an endorsement.The committee res
13、ponsible for this document is ISO/TC 34, Food products, Subcommittee SC 16, Horizontal methods for molecular biomarker analysis. ISO 2013 All rights reserved iiiBS ISO 16578:2013ISO 16578:2013(E)IntroductionThe main focus of this International Standard is DNA microarray-based methodologies.DNA micro
14、array is a molecular biological technique capable of simultaneous detection of multiple nucleic acid sequences and is particularly suitable for identifying nucleic acid sequences of interest and for measuring gene expression levels. Microarray and its derived technology have been developed for use i
15、n the field of food analysis genetically modified organism (GMO) analysis, biomarker identification, etc. Although the standardized parameters required for DNA microarray-based methods have been under consideration (such as MAQC and MIAME), it is necessary to generate minimum requirements for the in
16、terpretation of the results.Therefore, the aim of this International Standard is to provide guidance and requirements for the detection of nucleic acid sequences of interest by microarrays. This information concerns the establishment of validation approaches for methods based on DNA microarray, and
17、the definition of general principles employed in carrying out these laboratory analyses.Microarray technology is evolved from Southern blotting; the core principle is hybridization between two DNA strands, by the property of complementarities of nucleic acid sequences. A DNA microarray is a collecti
18、on of microscopic DNA spots attached to a solid substrate or coded beads. The development of a microarray assay generally needs to design the probe DNAs, to arrange the probe DNAs onto a solid substrate, to label the target nucleic acid sequences, to hybridize the targets with the probe DNAs, and to
19、 elaborate an appropriate detection system. Many types of arrays exist and there are many ways to fabricate microarrays. According to the target labelling techniques used, the hybridization can be detected by electrical, colorimetric, and/or fluorescence signals.At the time of publication of the Int
20、ernational Standard, best practices and standards for data representation and minimum information have been developed for comparability and reproducibility of microarray data. However, only few published work have yet focused on the reliability and comparability of any given microarray platforms, an
21、d a single-laboratory validation would most likely not suffice in this case. Rather, an interlaboratory method validation should be adopted, according to specific international guidelines.NOTE 1 The Microarray Quality Control (MAQC) consortium provides an excellent resource to determine best microar
22、ray practices, including the use of reference material, data assembly, and formats.See http:/www.fda.gov/ScienceResearch/BioinformaticsTools/MicroarrayQualityControlProject/default.htmNOTE 2 The Minimum Information About a Microarray Experiment (MIAME), by establishing common standards for describin
23、g microarray data, systems for data management and transfer, and public repositories for data storage and mining, aids in describing the detailed information that researchers should provide to explain the procedures and biological purposes of their microarray data.See http:/www.mged.org/Workgroups/M
24、IAME/miame.htmlGeneral requirements for the detection of DNA are also laid down in the following International Standards: ISO 21569, ISO 21570, ISO 21571, ISO 22174 and ISO 24276.iv ISO 2013 All rights reservedBS ISO 16578:2013Molecular biomarker analysis General definitions and requirements for mic
25、roarray detection of specific nucleic acid sequences1 ScopeThis International Standard defines terms for the detection of nucleic acid sequence of interest using DNA microarrays for detection of nucleic acid.This International Standard is applicable to all methods that use microarrays for detection
26、of nucleic acids.This International Standard specifies the verification processes and parameters for molecular biology analysis, including the detection and identification of specific nucleic acid sequences.This International Standard has been developed to provide recommendations and protocol for mi
27、croarray design and manufacture, validation of hybridization specificity, interlaboratory validation of qualitative methods, determination of limits of detection for a microarray, determination of range of reliable signals, and criteria to assessing technical performance of the microarray platform.I
28、t does not cover the following protocols: the process of quantitative measurement; the requirements for sample preparation prior to DNA microarray experiments.2 Normative referencesThe following documents, in whole or in part, are normatively referenced in this document and are indispensable for its
29、 application. For dated references, only the edition cited applies. For undated references, the latest edition of the referenced document (including any amendments) applies.ISO 5725-1, Accuracy (trueness and precision) of measurement methods and results Part 1: General principles and definitionsISO
30、5725-2, Accuracy (trueness and precision) of measurement methods and results Part 2: Basic method for the determination of repeatability and reproducibility of a standard measurement methodISO 22174, Microbiology of food and animal feeding stuffs Polymerase chain reaction (PCR) for the detection of
31、food-borne pathogens General requirements and definitionsISO 24276, Foodstuffs Methods of analysis for the detection of genetically modified organisms and derived products General requirements and definitionsISO/IEC 17025:2005, General requirements for the competence of testing and calibration labor
32、atoriesISO/IEC Guide 99, International vocabulary of metrology Basic and general concepts and associated terms (VIM)INTERNATIONAL STANDARD ISO 16578:2013(E) ISO 2013 All rights reserved 1BS ISO 16578:2013ISO 16578:2013(E)3 Terms and definitionsFor the purposes of this document, the terms and definit
33、ions in ISO 5725-1, ISO 5725-2, ISO/IEC 17025, ISO/IEC Guide 99, ISO 22174 and ISO 24276 and the following apply.3.1limit of detection for microarray platformLODPlowest relative quantity of the external measurement standard (or reference material) that can be detected experimentally at a 95 % confid
34、ence level, given a known (determined/estimated) number of copies and/or concentration of the external measurement standard (or reference material)3.2range of reliable signalability (within a given range) to provide results that are directly proportional to the concentration and/or copy number of th
35、e external measurement standard (or reference material)3.3DNA microarrayDNA chipsolid substrate where a collection of probe DNA arranged in a specific design is attached in a high-density fashion, directly or indirectly, that assays large amounts of biological material using high-throughput screenin
36、g methods3.4probe DNAsingle-strand nucleic acid defined by its property to target specific nucleic acid sequence by base complementarities, where the stringency of the binding is linked with the length and nucleic acid composition of the probes, along with reaction parameters3.5platformdevice that s
37、upports a microarray (or DNA chip) technology3.6fluorescence detectionmethod of detecting hybridization using immobilized probe DNA by measuring a fluorescence signal3.7colorimetric detectionmethod of detecting hybridization using immobilized probe DNA by measuring a colorimetric signal3.8electroche
38、mical detectionmethod of detecting hybridization by measuring electric currents of an electrode onto which probe DNA are immobilized3.9external measurement standardmaterial or substrate prepared for testing the compatibility of the microarray-based methods of analysis, whose property value is derive
39、d as a consensus value based on collaborative experimental work under the auspices of a scientific or engineering group3.10cross-hybridizationnon-specificity binding of probe DNA to non-targeted nucleic acid2 ISO 2013 All rights reservedBS ISO 16578:2013ISO 16578:2013(E)4 Principle4.1 Microarray pla
40、tform assayA microarray platform assay, for instance, consists of denaturation of the double- or single-stranded DNA or RNA analyte, hybridization of the target(s) to probe DNAs bound to a solid substrate, detection of hybridization by electrical, colorimetric, and/or fluorescence signals, and data
41、analysis.The laboratory shall implement external measurement standards (or reference material) and suitable controls for the microarray measurement step in the verification process. These requirements governing verification of DNA microarray-based methods also aid in clarifying the interpretations o
42、f results.4.2 Microarray design and manufactureMicroarray analysis should employ the following kinds of probe DNAs, and should be designed to be verifiable.The design contains probe DNAs for detecting external measurement standards (or reference material), a positive control, a negative control, and
43、 the nucleic acid sequence of interest.The immobilized probe DNA shall be replicated at least in duplicate locations. Probe DNAs shall be designed taking into consideration the Tm value, GC ratio, and sequence specificity. The sequence should be described. In order to avoid confusion between nucleot
44、ide bases, a lower-case g shall be used to clearly differentiate between G and C in the description (i.e. C, g, A, and T shall be used to indicate bases). The quality of probe DNA shall be ensured by an appropriate method (spectroscopic analysis, mass-spectral analysis, etc.).4.3 Validation of hybri
45、dization specificity4.3.1 Theoretical assessment of specificityTheoretical assessment of probe DNA consists of screening one or more of the major nucleic acid sequence databases (such as Refseq: http:/www.ncbi.nlm.nih.gov/RefSeq/) with a sequence homology search algorithm (BLAST: http:/blast.ncbi.nl
46、m.nih.gov/Blast.cgi, SSEARCH program in FASTA package, etc.). Specific sequences should be selected that are not likely to generate cross-hybridization. These sequences should be tested experimentally.4.3.2 Experimental assessment of specificityThe specificity of the probe DNAs should be validated e
47、xperimentally on samples having nucleic acid sequences similar to the target sequence, as well as on organisms identified through the theoretical assessment of specificity as presenting sequence homologies likely to cause cross-hybridizations. The experimental conditions should be the same as those
48、employed routinely by the laboratory.4.3.3 Experimental assessment of cross-hybridizationThe validation process should demonstrate that no cross-hybridizations occur on a probe DNA that is capable of experimentally detecting an external measurement standard (or reference material) in the ISO 2013 Al
49、l rights reserved 3BS ISO 16578:2013ISO 16578:2013(E)matrix. The results are accepted if the probe DNAs for detecting the external measurement standards (or reference material) are all positive and the probe DNAs for detecting negative controls are negative.4.4 Interlaboratory validation of qualitative methods4.4.1 GeneralBy their very nature, qualitative tests result only in yes/no answers. However, the determination of the range of use of the method is always necessary in the validation study. The me
