Application of Sampling and Detection Methods in Agricultural Plant Biotechnology

Application of Sampling and Detection Methods in Agricultural Plant Biotechnology
Copyright
Foreword
List of contributors
1. Introduction: genetically modified crops and their detection
References
Further reading
2. Seed purity testing and low-level presence
2.1 Background
2.2 Sampling
2.3 Detection methods and techniques
2.4 Protein-based detection methods
2.5 DNA-based detection methods
2.6 Managing costs in a detection laboratory
2.7 Bioassays
2.8 Low-level presence and purity
2.9 Data analysis and reporting
2.10 Conclusion
References
3. Grain supply chain stewardship and testing—import and export
3.1 Introduction
3.2 Testing for import and export
3.2.1 Biotechnology traits in the movement of grain globally
3.2.2 Available methods and suitability for each testing application
3.2.2.1 Protein-based detection methods
3.2.2.2 DNA-based methods
3.2.3 Grain supply chain critical testing points and associated methods
3.2.4 Managing challenges in global grain movement
3.2.5 Emerging challenges and future testing technologies
3.2.5.1 Low-level presence of genetically engineered material
3.3 Regulation and official controls
3.4 Analytical strategy
3.4.1 GMO detection using real-time PCR method
3.4.2 GMO screening
3.4.3 Gene-specific detection
3.4.4 Construct-specific detection
3.4.5 Event-specific detection
3.4.6 Source of reference material
3.5 Stewardship
References
Further reading
4. Principles of nucleic acid-based detection methods
4.1 Introduction
4.2 DNA preparation and requirements
4.2.1 DNA extraction methods
4.2.2 Requirements of DNA quality
4.3 Nucleic acid hybridization
4.3.1 Southern blot analysis
4.3.2 Probes
4.3.3 Choice of target nucleic acids
4.4 Amplification methods
4.4.1 Polymerase chain reaction
4.4.1.1 Targets for GMO detection
4.4.1.2 Qualitative and quantitative PCRs
4.4.2 Ligase amplification reaction
4.4.3 Transcription-based amplification system
4.4.4 Strand displacement amplification
4.5 Detection platforms
4.6 Next-generation sequencing
4.7 Closing remarks
References
5. Method validation: DNA-based detection methods
5.1 Introduction
5.1.1 Method validation standards and guidelines
5.1.1.1 Codex alimentarius guidelines
5.1.1.2 European Union guidelines
5.1.1.3 ISO standards
5.2 PCR validation
5.2.1 Qualitative and quantitative PCR method validation requirements
5.2.1.1 Specificity
Definition
Acceptance criteria
5.2.1.2 The limit of detection
Definition
Acceptance criteria
5.2.1.3 Limit of quantification
Definition
Acceptance criteria
5.2.1.4 Dynamic range
Definition
Acceptance criteria
Quantitative method
5.2.1.5 Trueness (accuracy)
Definition
Acceptance criteria
5.2.1.6 Precision-relative repeatability standard deviation (RSDr)
Definition
Acceptance criteria
5.2.1.7 Precision-relative reproducibility standard deviation (RSDR)
Definition
Acceptance criteria
5.2.1.8 Robustness
Definition
Acceptance criteria
5.2.1.9 Amplification efficiency
Definition
Acceptance criteria
5.2.1.10 R2 coefficient
Definition
Acceptance criteria
5.3 Data interpretation and sources of error
5.3.1 Data interpretation
5.3.2 Source of error
5.3.2.1 General considerations
Biological sources of errors
Analytical/instrumental sources of errors
5.3.2.2 False positive and false negative
False positives
False negatives
5.4 Reference materials
5.5 Assay transfer and proficiency testing
5.5.1 Interlab verification
5.5.2 Proficiency testing
5.5.2.1 Technical guidance for PT
5.5.2.2 Programs for PT
5.6 Summary
References
6. Protein-based detection methods
6.1 Introduction
6.2 History
6.3 Principle
6.4 Application of immunoassays to GE crops
6.4.1 Why use immunoassays
6.4.2 Immunoassay formats
6.4.3 Sandwich ELISA
6.4.4 Lateral flow strip assay
6.4.5 Other formats
6.5 Production of antibodies
6.5.1 Choice of immunogen
6.5.2 Polyclonal antibodies
6.5.3 Monoclonal antibodies
6.5.4 Recombinant antibodies
6.6 Assay design and operation
6.6.1 Microtiter plate ELISAs
6.6.1.1 ELISA creation and quality control
6.6.1.2 Grinding/tissue disruption
6.6.1.3 Choice of buffer
6.6.1.4 Protein extraction
6.6.1.5 Standard curves
6.6.1.6 Cross-reactivity
6.6.1.7 Determination of the useful range of the assay
6.6.1.8 Other factors
6.6.2 Lateral flow strips
6.6.2.1 LFS creation and quality control
6.6.2.2 LFS for testing single seed or single leaf
6.6.2.3 LFS for testing bulk grain or bulk leaf samples
6.6.2.4 Evolution of the LFS design
6.6.2.5 Validation of a lateral flow assay
6.7 Conclusions
Acknowledgments
References
7. Protein methods: antibody-based protein method validation and assay verification
7.1 Introduction
7.1.1 Standards and validation parameters
7.2 Quantitative ELISA method validation
7.2.1 Sensitivity
7.2.2 Specificity
7.2.2.1 Cross-reactivity with purified proteins
7.2.2.2 Matrix effects/interferences
7.2.3 Extraction efficiency
7.2.4 Accuracy
7.2.5 Precision
7.2.5.1 Fortified sample approach
7.2.5.2 Dilution linearity
7.3 Independent laboratory validations
7.4 Qualitative method validation
7.4.1 Specificity/selectivity
7.4.1.1 Specificity
7.4.1.2 Selectivity
7.4.2 Sensitivity, establishing the cut-off value (fixed vs. floating)
7.4.2.1 Sensitivity
7.4.2.2 Defining the threshold value
7.4.3 Hook effect
7.4.4 Accuracy
7.4.5 Precision
7.4.6 Ruggedness
7.5 Assay verification
7.5.1 Kit verification
7.5.1.1 Verification of plate-based ELISA kits
7.5.1.2 Verification of lateral flow test strips
7.5.1.3 Critical consumable and reagent verification
a) Lot verification of ELISA kits
b) Lot verification of lateral flow strips
References
8. Reference materials and working standards
8.1 Background
8.2 Uses of reference materials
8.3 What constitutes a reference material?
8.4 Reference materials in agricultural biotechnology
8.5 Practical limitations on reference material
8.6 Sources of reference materials
8.7 Reference material types
8.7.1 Seed
8.7.2 Nonviable seed
8.7.3 Grain/seed powder
8.7.4 Powder produced from nonseed/grain plant parts
8.7.5 Plant DNA
8.7.6 Plasmid DNA
8.7.7 Proteins and plant extracts
8.7.8 Intellectual property issues
8.8 Specific considerations for using reference materials for quantification
8.8.1 True negative or 100% positive reference materials
8.8.2 Zygosity of reference materials
8.8.3 Application of reference materials to stacked events
8.8.4 Uncertainty considerations for quantitative analysis when constructing standard curves
8.9 International coordination and standardization
8.10 Future of reference material and the drivers
Acknowledgments
References
Further reading
9. Seed and grain sampling
9.1 Introduction
9.2 Sampling procedures
9.3 Probabilities of sampling
9.4 Testing of the laboratory sample
9.5 Acceptance sampling with qualitative testing
9.6 Acceptance sampling with quantitative testing
9.7 Acceptance sampling with qualitative testing on multiple subsamples
9.8 Conclusion
References
10. Plant and field sampling
10.1 Introduction
10.2 Plant breeding
10.3 Seed and commercial crop testing
10.4 Direct testing in the field
10.5 Sampling for laboratory testing
10.6 Marking and labeling
10.7 Collecting the sample
10.8 Safety considerations
10.9 Specific procedures
10.9.1 Tube sampling
10.9.2 Hand sampling
10.9.3 Disposable test-tube cap method
10.9.4 Core samplers
10.9.5 Tissue punch
10.10 Shipping samples
10.11 Summary
11. Testing laboratory design and management
11.1 Introduction
11.2 Laboratory design
11.3 Laboratory workflow
11.4 Physical laboratory processes
11.5 Equipment management
11.6 Reagents
11.7 Assay quality control
11.8 Personnel management
11.9 Summary
References
12. International standards and guidelines
12.1 Background and purpose of standards
12.2 Standards setting process
12.3 Standards organizations
12.3.1 Scientific association SDOs
12.3.2 ISO
12.3.3 Government-led organizations
12.3.3.1 Codex Alimentarius
12.3.3.2 ISTA
12.3.4 National and regional organizations
12.3.4.1 National organizations
12.3.4.2 Regional organizations
12.4 Development of a standard
12.5 Standards relevant to GM detection
12.5.1 Sampling
12.5.2 Guidelines and standards regarding analytical methods
12.5.3 General analytical methods standards
12.5.4 Sources of methods
12.5.5 Laboratory accreditation standards
12.6 Conclusions
Acknowledgment
References
Further reading
13. Analytical strategy and interpretation of results
13.1 Introduction
13.2 Confirming the presence of intended trait
13.2.1 Herbicide bioassay
13.2.1.1 Introduction
13.2.1.2 Methodologies
13.2.1.3 Seedling morphology of susceptible seedlings
13.2.1.4 Training resources
13.2.2 Immunoassay
13.2.2.1 Enzyme-linked immunosorbent assay
13.2.2.2 Lateral flow strips
13.2.2.3 Other immunoassay formats
Meso scale discovery
Microbead-based array-Luminex
13.3 Confirming the absence of unintended traits
13.3.1 Immunoassay
13.3.1.1 Enzyme-linked immunosorbent assay
13.3.1.2 Lateral flow strips
13.3.1.3 Other formats
Antibody-based homogeneous proximity assays
Spatial proximity analyte reagent capture luminescence
Antibody-free detection methods
13.4 Interpreting results
13.4.1 Introduction
13.4.2 Qualitative test
13.4.3 Quantitative test
References
14. Detection methods for genome-edited crops
14.1 Introduction
14.2 What is genome editing—the key technologies
14.3 The drivers for detection methods
14.4 Detection method approaches
14.4.1 PCR
14.4.1.1 Challenges
14.4.2 Digital PCR
14.4.2.1 Challenges
14.4.3 Sequencing
14.4.3.1 Challenges
14.5 Differentiation of genome edits and spontaneous or induced untargeted mutations
14.6 Conclusions
References
15. Future perspectives and challenges
15.1 Introduction
15.1.1 Issues and challenges
15.2 New GMO detection technologies
15.2.1 DNA-based technologies
15.2.1.1 qPCR-based multiplex strategies
15.2.1.2 Digital PCR technology
15.2.1.3 Isothermal amplification
15.2.1.4 Next-generation sequence
15.2.2 Protein-based technologies
15.2.2.1 LC-MS multiplexing technology
15.2.2.2 Immunoassays
MSD multiplexing array (electrochemical luminescence)
Biacore biosensor system (piezo-electric)
High throughput AlphaLISA (optical through FRET)
Bead-based multiplex technology (optical—fluorescence with flow cytometry)
15.3 Closing remarks
References
Further reading
Index
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
Z