GENEWATCH
 
WHAT'S THE HOLDUP?
By Peter Christey
 

from GeneWatch 26-5
Nov-Dec 2013

DNA barcoding is an immensely powerful technology. It offers the ability to take any biological sample and with a relatively fast, cost-effective and accurate test, answer the simple question: What species is this? 

The capability to answer the species ID question in a simple manner is valuable in many arenas.

  • Customs and quarantine inspectors are interested in identifying biological materials they intercept at borders: Is this piece of meat from an endangered species? Is this larva from an insect that will devastate our national citrus harvest? Is this wood illegally logged?
  • Authorities responsible for monitoring water quality are interested in identifying species present in rivers, streams and lakes: Does the species profile indicate that the water is polluted or pure?
  • Companies and regulators involved in the medicinal plant business are interested in identifying plants used as raw materials: Is this dried plant I received from my supplier what he says it is? Is this plant material I am testing for a new product formulation what I think it is? Is this company labeling its product accurately?
  • Authorities responsible for monitoring the integrity of the food supply need to have robust species identification methods: Is the fish being sold what the vendor says it is? Is this minced beef really all beef? Is this meat from an endangered species or illegally imported?

These are all critical questions that need to be answered on a daily basis by regulatory, commercial and enforcement entities around the world.  DNA barcoding uniquely offers a single, standardized approach to this problem, yet it is not utilized broadly. Instead a variety of manual, time-consuming and expensive approaches are used.

The obvious question: Why is DNA barcoding not used broadly outside the academic community if it offers such benefits in speed, accuracy and cost in so many arenas?

The answer is two parts: One factor is that many of the non-academic (applied) applications are governed by a legal umbrella that must be satisfied. The second important factor is that in these applied areas there are stakeholders, often with conflicting interests, that must be accounted for. The net result is that for barcoding approaches to be accepted and utilized broadly they must be implemented in a manner that is credible and satisfies the various stakeholders involved.

One example is water quality testing. Currently, a commonly used measure of water quality is to take samples from a water reservoir, such as a river, and measure the frequency of different species that are typically found in that habitat. As different species have different tolerances for low water quality, the species profile is an excellent indicator of the quality of the water and possible pollution. There are well-established indices, based on extensive historical data, that were created using manual collection and taxonomic classification of species. Replacing those manual methods with DNA barcoding would greatly streamline the process, and making the switch seems like an easy decision.

 However there are several stakeholders in this process who need to be satisfied. The regulators who use this data to monitor water quality need to be assured that the new methodology is sound. The entities subject to the regulators oversight (local authorities, companies that discharge into the reservoir) need to accept the new methodology as fair and robust, and need to be assured that it does not represent a change in standard against which they are measured. There may also be legal requirements written into local law that need to be satisfied. To implement a change in methodology from traditional approaches requires multiple development activities: standardized techniques for sample collection, storage and transport need to be developed and tested to ensure the integrity of the DNA is reliably maintained; standardized primer sets and DNA barcoding protocols need to be developed and tested; a DNA barcode database that reflects the local species profile needs to be developed with controls and rigor that satisfies both the regulator and the regulated entities; studies demonstrating equivalence of results obtained from DNA barcoding vs. traditional approaches need to be performed. Funding this work, performing the various studies, demonstrating the benefit of change and gaining acceptance of the new methodology can take several years.

A second example is the use of DNA barcoding for monitoring labeling of seafood in the U.S. The FDA facilitates programs related to the integrity of the U.S. seafood supply and have validated DNA barcoding for seafood identification. The FDA developed their own protocols and performed comprehensive validations of the methodology. They also have developed their own DNA barcode reference database under rigorous controls that satisfy the requirements of the environment in which they work.1

It's easy to assume that the FDA methods are easily portable to another country. However, while the FDA has established an excellent example of forward-thinking with a new technology, another country establishing this technology for fish surveillance would need to do its own validations and testing to satisfy its own legal/regulatory environment and stakeholders. It would also need to develop its own DNA barcode database to reflect the idiosyncrasies of the local fish supply.

From these two examples we start to see why there are multiple steps that must be implemented before DNA barcoding can be used in regulatory or legal contexts:

1. Standardization: Standardized protocols for key parts of the process, including sample collection, sample transport, sample tracking, chain of custody and barcoding, may need to be established and validated. Standardization is often facilitated by the availability of commercial products manufactured to rigorous standards under modern quality control systems.

2. Comparison to current methods: In regulated environments, a full understanding of how barcoding methodologies compare to current methodologies needs to be established.

3. Demonstration of benefits: The benefit of moving to barcode-based methodologies needs to be accepted.

4. Availability of a reliable reference database: A robustly developed and managed reference database for DNA barcodes needs to be developed. The publicly available databases represent an extraordinarily valuable resource for the scientific community. As content is derived from many sources with differing degrees of reliability, these databases are unfortunately not acceptable for use in more regulated or legalistic contexts.

5. Certification: A means to determine that a laboratory is qualified to perform such tests.

6. Optimization to meet local conditions: One size does not fit all! A robust and acceptable barcoding system for use in one country, city or jurisdiction cannot simply be cloned across the globe - modification and development to address local needs will be required.

The conditions outlined above are not unique to DNA barcoding. Two other examples offer models for what may be required for new technologies to expand to widespread use outside academia. The first is the use of DNA-based technologies for human identification in the forensic/law enforcement arena.  The environment for use of DNA technology for forensics has evolved over 20 years. Now in the U.S. there is a sophisticated system of controls to ensure the integrity of the system. Before a new DNA-based product can be used in this environment, the manufacturer must perform comprehensive validations to establish the performance parameters of the product. Guidelines for these validations are provided by an independent expert group. The product must be approved by the appropriate agencies before it can be used in conjunction with the national DNA profile database. Only certified labs may upload profiles into the database or search against the database. The database itself is subject to strict controls and regulations to ensure its integrity.

A second model is the in vitro diagnostic model. Again we see similar themes. Before a new diagnostic test can be used, its protocol must be standardized and validated. The test must go through clinical trials to prove its utility and performance. A governing body must approve the test. The test can only be utilized in appropriately qualified laboratories.  Again, similar systems governing in vitro diagnostics exist in different countries, but each has evolved differently to meet local conditions.

So, does this mean that it will be a long time before we see the widespread use of DNA barcoding technology? Fortunately the answer is no.  The requirements above apply to highly regulated and/or legalistic environments. Barcoding is a powerful tool that will be applied in many areas where the requirements are not so high such as in educational programs, national park management, biodiversity monitoring and environmental impact assessment. Even in more stringent environments, barcoding may be used as a tool to guide investigations (but not used as evidence) and as a means of performing research.

Now that the scientific foundation of barcoding has been firmly established in the academic community, we are seeing many creative uses of this technology. Use will grow as more people become familiar with the technology and DNA barcoding becomes more accessible through the development of commercial products and services and less complex instrumentation. The formal processes and structures required for regulated/legalistic environments will evolve in tandem - as for the biological ecosystems that DNA barcoding helps us understand, the DNA barcoding ecosystem itself will evolve and grow over time.

 

Peter Christey, PhD, is Vice President and General Manager for the capillary electrophoresis and 5500 DNA sequencing businesses at Life Technologies, Inc.


 
ENDNOTES

1. Further detail can be found on the FDA website at: http://www.fda.gov/Food/FoodScienceResearch/DNASeafoodIdentification/

 
 
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