Substantial equivalence

One important concept that is used in most countries to regulate products of genetic engineering is substantial equivalence. The way to determine substantial equivalence is comparative assessment. What do substantial equivalence and comparative assessment mean? Depending on the source we use, we might find different definitions and different opinions of how useful they are in determining the safety of products of genetic engineering. The USDA provides information on Food Safety Assessment and Considerations as part of their Focus on Food Biotechnologypage at the Food Safety Research Information Office.
What substantial equivalence can do is give us a starting point.
We know that there is variation in amounts and types of proteins and metabolites, gene expression, and other parameters from variety to variety, from environment to environment, and from plant to plant. For example, if I use a microarray to find similarly and differently expressed genes in two genetically identical plants grown in slightly different environments, such as different temperatures, I will find some genes that have significantly different expression. Similarly, plants of different varieties grown in the same environment will have different gene expression profiles and even two identical plants in the same environment will have some differences.
The first step in a comparative assessment is to test and compare the genetically engineered variety to a genetically similar variety that doesn’t have the trans- or cis-gene. Tests can include gene expression, metabolic profiles, feeding studies, and more. If differences aren’t found in a reasonably wide panel of tests, then the genetically engineered variety can be called substantially equivalent to the genetically similar variety.
If differences are found, two questions need to be asked. First, does the change fall within the natural variation found among different varieties of the same species? For example, some varieties of corn with the Bt gene have been found to contain more lignin than genetically similar varieties without the Bt gene, but the amount of lignin falls within the normal range of lignin content for corn plants. Second, is there a scientific explanation for each change? For example, a transgene that causes higher calcium uptake from the soil is expected to result in higher amounts of calcium.
If there is a change that doesn’t fall within the natural variation for that species, especially if there isn’t an obvious scientific explanation for the change, then more testing needs to be done to determine safety with regard to environment and human health.
What substantial equivalence does not do is give license to make assumptions. The process of genetic engineering does have the potential to cause unintended changes in the resulting organism. That’s why a comparative assessment needs to be conducted before a plant, animal or microbe that has been genetically engineered can be deemed substantially equivalent to a non-genetically engineered but genetically similar organism.
One major problem with determining substantial equivalence is that it is hard to know which tests are appropriate. This problem has improved greatly as “omics” type tests have become more widely used. Tests for macronutrient content could be expected to miss small but significant changes but wide screens for changes in the transcriptome, proteome, or metabolome could be expected to find those small changes.
The metabolome seems to hold the most promise because it effectively tests the end product of gene expression and enzyme activity. Owen Hoekenga presented metabolomics in an excellent 2008 paper as a method that could be used to help determine substantial equivalence.

ResearchBlogging.orgHoekenga OA (2008). Using metabolomics to estimate unintended effects in transgenic crop plants: problems, promises, and opportunities. Journal of biomolecular techniques : JBT, 19 (3), 159-66 PMID: 19137102.
Abstract:  Transgenic crops are widespread in some countries and sectors of the agro-economy, but are also highly contentious. Proponents of transgenic crop improvement often cite the “substantial equivalence” of transgenic crops to the their nontransgenic parents and sibling varieties. Opponents of transgenic crop improvement dismiss the substantial equivalence standard as being without statistical basis and emphasize the possible unintended effects to food quality and composition due to genetic transformation. Systems biology approaches should help consumers, regulators, and other stakeholders make better decisions regarding transgenic crop improvement by characterizing the composition of conventional and transgenically improved crop species and products. In particular, metabolomic profiling via mass spectrometry and nuclear magnetic resonance can make broad and deep assessments of food quality and content. The metabolome observed in a transgenic variety can then be assessed relative to the consumer and regulator accepted phenotypic range observed among conventional varieties. I briefly discuss both targeted (closed architecture) and nontargeted (open architecture) metabolomics with respect to the transgenic crop debate and highlight several challenges to the field. While most experimental examples come from tomato (Solanum lycoperiscum), analytical methods from all of systems biology are discussed.

“Omics” studies that have been conducted on the substantial equivalence of genetically engineered plants to their non-genetically engineered counterparts have found that there are differences but those differences fall within the range of differences found within different varieties of the same species. Below are some such studies.

Kogel KH, Voll LM, Schäfer P, Jansen C, Wu Y, Langen G, Imani J, Hofmann J, Schmiedl A, Sonnewald S, von Wettstein D, Cook RJ, & Sonnewald U (2010). Transcriptome and metabolome profiling of field-grown transgenic barley lack induced differences but show cultivar-specific variances. PNAS, 107 (14), 6198-203 PMID: 20308540
Baker JM, Hawkins ND, Ward JL, Lovegrove A, Napier JA, Shewry PR, & Beale MH (2006). A metabolomic study of substantial equivalence of field-grown genetically modified wheat. Plant biotechnology journal, 4 (4), 381-92 PMID: 17177804
Coll A, Nadal A, Collado R, Capellades G, Messeguer J, Melé E, Palaudelmàs M, & Pla M (2009). Gene expression profiles of MON810 and comparable non-GM maize varieties cultured in the field are more similar than are those of conventional lines. Transgenic research, 18 (5), 801-8 PMID: 19396622
Lehesranta SJ, Davies HV, Shepherd LV, Nunan N, McNicol JW, Auriola S, Koistinen KM, Suomalainen S, Kokko HI, & Kärenlampi SO (2005). Comparison of tuber proteomes of potato varieties, landraces, and genetically modified lines. Plant physiology, 138 (3), 1690-9 PMID: 15951487
Gregersen PL, Brinch-Pedersen H, & Holm PB (2005). A microarray-based comparative analysis of gene expression profiles during grain development in transgenic and wild type wheat. Transgenic research, 14 (6), 887-905 PMID: 16315094

Another problem with comparative assessments is that each genetically engineered trait may require different types of testing, depending on what the trait is. For example, a drought tolerant crop may need to be tested under wet and dry conditions while a nutritional trait may not need to be tested under different environmental conditions.
An alternative view to substantial equivalence and comparative assessment is the precautionary principle. Instead of starting  by looking for differences between a genetically engineered organism and a non-genetically engineered but genetically similar organism as we find in a comparative assessment, the precautionary principle requires us to start with the assumption that there are differences and enough studies must be conducted to determine that something is completely safe before release. The precautionary principle is an important enough idea that it deserves its own post, but I will say here that it has some problems, the biggest of which is that the amount of testing that is deemed to be “enough” is rarely defined, so the amount of tests that “need” to be conducted can always be made larger, which may actually be the point.

Written by Anastasia Bodnar

Anastasia Bodnar is a science communicator and science policy expert with a PhD in plant genetics and sustainable agriculture from Iowa State University. Anastasia has had various risk analysis roles in US government and military service. She serves as BFI's Director of Policy and as Co-Executive Editor of the Biofortified Blog.


  1. One of the biggest misunderstandings about substantial equivalence that I have found is that early misunderstandings about it have fueled the idea that it equals an assumption that there is no difference, to preclude any need to test. But Substantial Equivalence is what is determined after a trait has been examined and compared to genetically similar plants that lack the new gene.
    You make a very good point about the precautionary principle, in that it starts from the premise that whatever differences that exist, however minor, must be determined to be completely safe before release. Naturally, everyone wants it to be safe before release. But no conventionally bred trait must demonstrate that it is completely safe, and conventional breeding causes enormous changes in plant composition, physiology, and environmental impact. So why does one change invite no precaution, and the other has the potential to never be satisfied? “Newness” is a relative term – are seedless watermelons ‘new’ enough to require the precautionary principle?

    1. Naturally, everyone wants it to be safe before release. But no conventionally bred trait must demonstrate that it is completely safe, and conventional breeding causes enormous changes in plant composition, physiology, and environmental

      My quibble on this particular point would be that the market itself does require that conventionally bred traits perform in a manner that satisfies a sufficient number of market participants to justify their existence. Safety is seldom an issue for conventionally bred crops in terms of excluding them – but it is very important in terms of gaining market access by safening them – here I’m primarily thinking of Canola as a new and different form of rape seed. By removing uricic acid the grain is now safe for human consumption (or “safer”).
      The market will provide push back to conventionally bred products whose new traits are in a ‘package’ that is not competitive. Here I’m thinking in terms of modified oil soybean genetics. There are both conventional and GMO modified oil soybean varieties. Current soybean varieties with these traits are struggling to gain wide market acceptance. There are successes, and I expect there will be more progress in time, but my point here is that the marketplace does have a moderating impact on even conventionally bred materials (both positively and negatively).

      So why does one change invite no precaution, and the other has the potential to never be satisfied?

      So I’m not entirely agreeing with the premise of your question (there is the precaution of the marketplace)- I would also suggest that as conventional it is familiar (it is conventional after all)whereas the GMO is still new enough in many communities of thought to require a precautionary approach to satisfy. A question I’d like to pose instead is how long will it take before transgenic approaches to plant breeding are more widely considered to be “conventional”?

    2. Nice spin on substantial equivalence as a more reasonable approach, but your facts about the Precautionary Principle have been modified to support your lame legal measure.
      What the Precautionary Principle requires is that a novel food or drug demonstrate safety and efficacy before entering the market. One only needs to look at the numbers of drug recalls to know that a claim of absolute safety is laughable.
      The loophole of substantial equivalence has narrowed the meaningful measures to similar nutrients and ignored any novel proteins or any human health and safety tests or post market followup. It is a don’t look – don’t find policy of no scientific value but priceless when profits are the measure that counts most.

      1. I am not sure I have fully understood this comment.
        There are several definitions for the precautionary principle. The introductory part of the Wikipedia article (quite skewed…) on the subject says:

        The precautionary principle states that if an action or policy has a suspected risk of causing harm to the public or to the environment, in the absence of scientific consensus that the action or policy is harmful, the burden of proof that it is not harmful falls on those taking the action.
        This principle allows policy makers to make discretionary decisions in situations where there is the possibility of harm from taking a particular course or making a certain decision when extensive scientific knowledge on the matter is lacking. The principle implies that there is a social responsibility to protect the public from exposure to harm, when scientific investigation has found a plausible risk. These protections can be relaxed only if further scientific findings emerge that provide sound evidence that no harm will result.

        The first formulation of the principle appears in the the Rio Declaration:

        “In order to protect the environment, the precautionary approach shall be widely applied by States according to their capabilities. Where there are threats of serious or irreversible damage, lack of full scientific certainty shall not be used as a reason for postponing cost-effective measures to prevent environmental degradation.”

        A reasonable implementation of the principle would require that the risks, or threats, are (1) plausible and (2) serious or irreversible.
        Many proponents of precaution would like the applicant for a market authorisation for a GMO (or, given their belief that those applicants cannot be trusted, the public authorities – and in that case, public officials who would never have had a connection with industry…) to prove beyond doubt that it presents no risks or threats whatsoever, i.e. is absolutely safe. They would also like that each and every scientific investigation, even if highly unscientific (Séralini’s, for instance), concluding to a possible risk or threat be enough to withhold the authorisation until the objection is cleared (by which time, of course, a new one will have been found or an old one recycled). This, unfortunately, is the situation in Europe.
        Note that, for the precautionary principle fundamentalists and the coward policy-makers, it is irrelevant that the GMO would eliminate or reduce a proven risk or threat of much greater concern. Bt brinjal (aubergine) for instance must be proven absolutely safe in India, even though we know that Bt corresponds to a protein that has already been proven safe (it is even widely used in organic farming); one must not consider that brinjal growers apply on average two insecticide treatments per week, presumably with little protective measures for their own health, and that the aubergines currently sold to consumers are likely to contain insecticide residues.
        The amalgamation of novel food with drugs is also a major problem, yet not without interest. We want a drug to have an effect on health, and actually expect it to have (1) undesirable side effects and (2) possibly severe side effects that will only be revealed if the drug is widely used. We decide to live with (1) and take the risk of (2) until they are proven and lead to a recall. In the case of a GMO, we want it to have no effect on health, or possibly a nutritional one. Unless circumstances warrant otherwise, a reasonable assumption is that they are safe and can be tested according to the substantial equivalence principle.
        The precautionary principle hardliners want GMOs to be tested for health and environment safety on the basis of rules that would be much more stringent than for drugs. As a matter of fact, drugs are not tested for environmental safety even though you may eventually find them, even massively, in sewage water.

        1. You state that GMO opponents want a standard for human health and safety testing to exceed the testing standards for drugs but to date the Biotech Industry has done NO human health and safety testing for all the products fed to Americans.
          Show us where even basic human health and safety testing has been done. It’s tiring to hear the same argument for limiting excessive testing when basic testing isn’t required or done.

  2. If differences are found, two questions need to be asked. First, does the change fall within the natural variation found among different varieties of the same species? … Second, is there a scientific explanation for each change?

    Well, the very first question is whether the difference is relevant or an artefact. For instance, in the testing of Bt brinjal, in India, it was found that the GM-fed cows had produced much more milk (14.3%). The great Séralini opined that it “was almost if they were treated by a light hormone” (see ); this is obviously a by-product of cattle raising (was effective for scaremongering, though).

    But no conventionally bred trait must demonstrate that it is completely safe… So why does one change invite no precaution, and the other has the potential to never be satisfied?

    I have considerable difficulties with this argument because it may be turned on its head and force plant breeders to also test each new conventionally bred variety for safety. The fact is, moreover, that we (particularly public opinion) assume conventional food to be safe. Save for special cases, we do not know with the kind of precision that would be required if we were to make safety comparisons within the range of ‘natural’ variation.
    Clem Weidenbenner has referred to oil seed rape and canola. Interesting point: whilst it is now generally assumed that canola is safe, and that its predecessor was not, you can find quite convincing literature to support the view that erucic acid did not have the detrimental health effects which triggered the conversion.

    1. That report by Seralini isn’t very good. Even if we assume the information he’s presenting is factual, the presentation is extremely biased. How could anyone be expected to take that report seriously?

      1. “That report by Seralini isn’t very good”? Séralini is GOD to the anti-GMOs, including Governments which position themselves on the basis of opinion polls. And since the (mainstream) scientific community has been so critical of him, he is also a MARTYR.
        “How could anyone be expected to take that report seriously?” Ramesh did!
        And so you are back to your question…

      2. One reason why it is being taken seriously is because the headline confirmed predispositions, but the likelihood of someone with such predispositions finding out it didn’t really support their view is very low because it was hardly readable to those who tried. Marion Nestle, a knowledgeable person said it was “confusing.” A scientist in the field who is familiar with the topic called it “convoluted.” But Tom Philpott called it “Fascinating.”

      3. So does anyone here have (or can point to) counter arguments to what he is saying? For example, on page 7 he states:

        “All the risks above considered are true even if the company says that « the antibiotic resistance has little chance to spread out from this agriculture, and that this will have if any very little effect on human and animal health ». This belief is not supported by well-designed experiments to prove it.”

        where “all the risks above” refers to development of antibiotic resistance.

          1. Thanks Anastasia. So are we saying Seralini is being intentionally deceptive (aka lying) when he says “This belief is not supported by well-designed experiments to prove it”?
            I had to stop reading the article as it was too frustrating being full of strong statements like this with no references to back them up. What well-designed experiments? Conducted by whom?

  3. Seralini goes on about single blips that show up in a single sex and a single dose, saying that these could be mysterious effects that should be investigated, instead of statistical blips as they would seem to be. He even questions the use of other varieties of Brinjal as a reference group at all. How else are we to evaluate the relevance of any unintended side effects? He repeats the same kinds of criticisms that he did in his feeding trial re-evaluation. A very troublesome read. But I did catch something very interesting at the very bottom:
    “This critical review of Mahyco’s data on Bt brinjal is commissioned by Greenpeace”
    Seralini has a good business going for him, I don’t suspect he would change that pattern anytime soon.

    1. Yes, I did see the GP quip at the end too. These people complain, on one hand, that industry and government studies and positions are biased, but then turn around and do the equivalent kind of “studies” from the opposite side. Would they seriously say that GP is unbiased!?
      — That was rhetorical 🙂

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