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Dangers of Gene-Edited Foods

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Scientific studies highlight safety concerns
Industry lobbyists and their allies in research institutes wrongly claim that gene editing of food is a safe new technology. However, a growing body of gold standard (peer reviewed) scientific research highlights unintended and potentially dangerous effects. The studies support the need for gene-edited plants, crops and farm animals to undergo as much strict safety assessment, regulation and labelling as other genetically modified (GM) food. See:
GM advocates falsely claim that the products of gene editing from techniques such as CRISPR should not be classified as genetically modified organisms; do not require rigorous testing, because they are evolutionary, natural and carry no more risk than conventional plant breeding. The truth is that there is no evidence of safety because no feeding studies have been carried out in humans or animals.

Warnings from Leading Scientists about New Toxins & Allergens

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Dr Michael Antoniou, London-based molecular geneticist, warns that
“In the medical research community, it is not disputed that gene-editing techniques are GM techniques that give rise to Genetically Modified Organisms (GMOs) and that these procedures and their products carry risks that require strict regulation.”
In the case of gene-edited foods and crops, the risks include the possibility of the presence of new toxins and or allergens.
61 leading international scientists have expressed grave concerns about unexpectedly high levels of toxins in gene-edited plant foods:“Even non-GMO plants are efficient at producing their own toxins – for example, to defend themselves against pests. The radical nature of the changes that can be introduced by NGMTs [new genetic modification techniques] could result in unexpectedly high levels of such toxins or in the production of novel toxins.”  See the full statement and signatories of the European Scientists for Social and Environmental Responsibility (ENSSER)
Two prominent UK scientists warn about health risks from new toxins:
Experts in gene editing and toxicology have recently written to George Eustice, Secretary of State for Environment, Food and Rural Affairs saying, “the likelihood of altered biochemistry in gene-edited food plants, with consequent health risks (toxicity, allergenicity) is very real”.
Statement from group of scientists
A group of scientists who published a study showing that a wide range of unintended effects were found in gene-edited rice warned, “understanding of uncertainties and risks regarding genome editing is necessary and critical before a new global policy for the new biotechnology is established."
Bayer scientist comments 
Dr Larry Gilbertson of Bayer has admitted that gene-editing techniques, which the industry calls "New Breeding Techniques", are GM techniques and are "the same", in terms of the fact that they make changes in DNA. He adds that "there’s no intrinsic difference in the risk" between older-style GM and newer techniques. He also says, contrary to frequent claims, that organisms obtained by gene-editing techniques are
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Proven risks & unintended outcomes from gene editing include:

Explanation of terms used below

CRISPR = the most popular gene-editing tool
GENOME = the complete set of genetic material (DNA or RNA) of an organism
GENE =  a basic unit of inheritance within the genome of an organism
OFF-TARGET EFFECT = unintended genetic mutations that occur in gene editing and take place at a location other than the intended gene-editing site (hence “off-target”), including deletions, insertions, inversions, and rearrangements.
INDEL = insertion or deletion of DNA base units into the genome of an organism
BASE UNIT = the basic molecular unit from which DNA is constituted. There are 4 base units: adenine (A), guanine (G), thymine (T), and cytosine (C). In regions of the genome that encode for proteins, a sequence of base unit triplets (for example, CAG) makes up the genetic code.

MUTATION = Damage to a gene, resulting in a change to the genetic message carried by that gene, usually with harmful consequences to the organism.
The sequence is:

SDN-1 = knocks-out a gene
SDN-2 = gene modification
SDN-3 = gene insertion
The summary below is based on the list of studies compiled by GMWatch:
New GM plants do not have a history of safe use and should not be exempted from biosafety assessments
Eckerstorfer MF et al (2019). An EU perspective on biosafety considerations for plants developed by genome editing and other new genetic modification techniques (nGMs). Front. Bioeng. Biotechnol.
Gene editing makes the whole genome accessible for changes – unlike naturally occurring genetic changes
In conventional breeding and spontaneous mutations, some regions in the genome undergo changes less frequently than others because these regions are especially protected by repair mechanisms in the cell. CRISPR/Cas applications can bypass these naturally occurring processes and make the whole genome accessible for changes.
Kawall K (2019). New possibilities on the horizon: Genome editing makes the whole genome accessible for changes. Frontiers in Plant Science, 10:525. doi:
CRISPR/Cas9 gene editing can cause greater genetic damage than was previously thought
Potential consequences in gene therapy include triggering cancer.
Kosicki M et al (2018). Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements. Nature Biotechnology 36:765–771.
COMMENT: The CRISPR/Cas9 technique as used in plants is the same. In the case of food plants, the cancer finding is not relevant, but the types of changes seen in this study could result in unexpected toxicity or allergenicity.
CRISPR-Cas9 gene editing produced unexpected new types of mRNAs (messenger RNA molecules) or proteins
When CRISPR was used to knock-out a gene function in human cells, instead of the intended outcome of destroying the function of a CRISPR-targeted gene, unintended insertions and deletions of DNA (“indels”) occurred. The indels resulted in an alteration of the gene’s DNA base unit sequence, so that it now produced new types of mRNAs (messenger RNA molecules) or proteins.
Tuladhar R et al (2019). CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation. Nature Communications vol 10, Article number: 4056, 6 Sept.
COMMENT: This study focused on an “SDN-1” (gene deletion) application of CRISPR, which is intended to knock-out the function of a gene. If gene editing is de-regulated, products developed using this type of CRISPR application would not be subjected to safety checks or GMO labelling. Yet alterations, such as those found in this study, in gene-edited food crops could result in unexpected toxicity or allergenicity.
A new tool for analysing CRISPR edits revealed the frequent production of unintended edits around the site of the intended cut in the DNA
Sansbury BM et al (2019). Understanding the diversity of genetic outcomes from CRISPR-Cas generated homology-directed repair. Commun Biol 2, 1–10.
COMMENT: No matter to what extent scientists succeed in the future in improving the targeting of the initial CRISPR edit, their efforts cannot solve this problem, as the unwanted effects are seen around the intended editing site.
A CRISPR editing tool turned out not to be as clean or specific as previously thought
The tool, known as Cpf1, was prone to making unintended off-target single-strand cuts, or "nicks", in the double-stranded DNA molecules. Off-target double-strand DNA cuts were also found.
Murugan K et al (2020). CRISPR-Cas12a has widespread off-target and dsDNA-nicking effects. Journal of Biological Chemistry March 11, 2020 doi: 10.1074/jbc.RA120.012933.
Various types of off-target effects (genetic damage) occur in gene-edited plants
The authors of this study noted, “development of plant genome editing has not yet fully considered potential off-target mismatches that may lead to unintended changes within the genome”.
Wolt JD et al (2016). Achieving plant CRISPR targeting that limits off-target effects. The Plant Genome 9: doi: 10.3835/plantgenome2016.05.0047.
Gene editing outcomes varied in efficiency, accuracy, and mutation structure, depending on the editing tool used and the genome targeted
The authors of this study noted that of the editing tools examined, “CRISPR… is more susceptible to off-target effects and great care is required during target selection to minimize the likelihood of unwanted mutations”.    
Zhu C et al (2017). Characteristics of genome editing mutations in cereal crops. Trends in Plant Science 22:38–52.
The CRISPR editing process, taken as a whole, resulted in many off-target mutations in rice plants
In this study, the CRISPR tools in themselves did not introduce many off-target mutations, but many such mutations did arise from other aspects of the CRISPR genetic manipulation process taken as a whole – namely tissue culture and Agrobacterium infection.  
Tang X et al (2018). A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice. Genome Biology 19:84. 
CRISPR gene editing in rice varieties caused a wide range of undesirable and unintended on-target and off-target mutations
This was an SDN-1 application of CRISPR that was only intended to knock-out a gene. In order to disrupt or knock-out the targeted gene, the researchers designed the CRISPR gene-editing tool to produce small indels (insertions and deletions of bases in the genome). However, what they got was quite different – large insertions, deletions, and rearrangements of DNA, raising the possibility that the function of genes other than the one targeted could have been altered. In addition, and surprisingly, the range of on-target mutations (unintended mutations at the intended editing site) varied, depending on the rice variety. The authors warned that "early and accurate molecular characterization and screening must be carried out for generations before transitioning of CRISPR/Cas9 system from lab to field" (something that is not normally done by gene-edited plant developers and would only be done if enforced by regulation). They added, “Understanding of uncertainties and risks regarding genome editing is necessary and critical before a new global policy for the new biotechnology is established". 
Biswas S et al (2020). Investigation of CRISPR/Cas9-induced SD1 rice mutants highlights the importance of molecular characterization in plant molecular breeding. Journal of Genetics and Genomics. May 21. doi:10.1016/j.jgg.2020.04.004  
COMMENT: The study confirmed that the types of mutations seen in gene-edited animal and human cells also occur in plants.
Unintended integration of foreign, contaminating DNA into the edited genome
This study found that DNA from the E. coli genome can integrate into the target organism's genome, as well as the vector plasmid, the 'delivery vehicle' that was designed to carry the CRISPR editing tool into the cells. The source of the E. coli DNA was traced back to the E. coli cells that were used to produce the vector plasmid. The study also found that plasmid and tissue culture DNA contaminants can be inserted by one of the cell’s DNA repair mechanisms into the genome targeted for editing, following a CRISPR cut. In this case, edited mouse genomes were found to acquire bovine DNA or goat DNA. This was traced to the use, in standard culture medium for mouse cells, of foetal calf serum and goat serum; that is, body fluids extracted from cows and goats. Even more worrisome, amongst the DNA sequences inserted into the mouse genome were bovine and goat retrotransposons (jumping genes) and mouse retrovirus DNA (HIV is a retrovirus). Thus gene editing is a potential mechanism for horizontal gene transfer of unwanted pathogens, including, but not limited to, viruses.    Ono R et al (2019). Exosome-mediated horizontal gene transfer occurs in double-strand break repair during genome editing. Communications Biology 2: 57
COMMENT: Jonathan Latham, PhD, director of the Bioscience Resource Project, wrote      “These findings… imply, at the very least, the need for strong measures to prevent contamination by stray DNA, along with thorough scrutiny of gene-edited cells and gene-edited organisms... these are needs that developers themselves may not meet.”
Unexpected types of insertions or deletions of DNA (indels)
This study looked at the molecular consequences of 17 CRISPR gene-editing events in four different gene regions of the mouse genome. The researchers found that CRISPR editing resulted in unexpected types of indels at all 17 sites in the mouse genome. Depending on the site being targeted, the size of the deletion was unexpectedly large. 
Shin HY et al. (2017). CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome. Nature Communications 8, Article number: 15464. doi:10.1038/ncomms15464.
Insertions of multiple copies of the DNA molecules used as a template for bringing about the desired gene modifications
When the CRISPR/Cas system was used in an SDN-2 ("gene modification") gene editing procedure aimed at engineering insertion of genetic material in mice, a high frequency was found of insertions of multiple copies of the DNA molecules used as a template for bringing about the desired gene modifications. The researchers were concerned by the fact that the insertions could not be detected using standard PCR analysis. This in turn led to what they called "a high rate of falsely claimed precisely edited alleles" (gene variants). In other words, scientists have been unduly claiming precision for CRISPR when in reality it is not precise.    
Skryabin BV et al. (2020). Pervasive head-to-tail insertions of DNA templates mask desired CRISPR-Cas9–mediated genome editing events. Science Advances 12 Feb 2020: Vol. 6, no. 7, eaax2941. DOI: 10.1126/sciadv.aax2941.
Antibiotic resistance genes in gene-edited cattle
In spite of the developer’s claim that gene-edited cattle were “free” of unintended effects, US food regulator FDA scientists found bacterial DNA in their genomes, including genes conferring resistance to antibiotics.   
Norris AL et al (2020). Template plasmid integration in germline genome-edited cattle. Nat Biotech 38(2): 163-164.
COMMENT: The antibiotic resistance genes in the gene-edited cattle could potentially transfer to disease-causing bacteria, adding to the huge public health problem of antibiotic resistance.  The US FDA cited this finding to illustrate the fact that gene editing in animals can lead to unintended consequences and must be subjected to stringent regulation:   
This SDN-3 (gene insertion) application in the cattle was being used by the developer to argue for deregulation of all gene editing in the US (including SDN-3)—something that the FDA is now resisting after their discovery. SDN-3 gene-edited organisms are not being currently targeted for de-regulation in the UK. However, if amendment 275 to the UK Agriculture Bill goes through, we will be subjected to unlabelled imports of gene-edited organisms from the US. If SDN-3 types of gene-edited animal do become de-regulated in the US, such animals and their products (meat and dairy) could be present in our food chain without GMO labelling.
Unintended large deletions of DNA, in some cases in excess of 500 base units, resulting from single CRISPR-induced cuts
In this study in human cells, in some cases, subregions of genes (“exons”), which carry information for the protein(s) for which they encode, were deleted. This resulted in the formation of novel gene structures encoding truncated forms of proteins.
Mou H et al. (2017). CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion. Genome Biology 18:108. DOI: 10.1186/s13059-017-1237-8.
COMMENT: On the level of a whole living organism, such novel proteins could either be benign or harmful.

CRISPR edits intended to knock-out the function of a gene failed to do so – instead, proteins were still produced from the damaged genes
This study in human cells revealed a major unintended effect from the CRISPR-Cas9 gene-editing tool. Many of the proteins that were produced were still functional, but they were also mutant, which means they could gain a novel function, with unknown consequences.
Smits AH et al (2019). Biological plasticity rescues target activity in CRISPR knock outs. Nat Methods 16, 1087–1093.
COMMENT: The study has major implications for the food safety of gene-edited plants, as they could turn out to be unexpectedly toxic or allergenic. CRISPR-edited plants with gene knockouts should be subjected to stringent safety checks, as they could contain new proteins or compounds that pose a food safety risk. These include the non-browning mushroom that has been de-regulated in the US. The developer of the mushroom stated that it did not need to be regulated since it was free from transgenes (genes inserted from another organism) and only contained “small deletions in a specific gene”. However, these findings, as well as those of Tuladhar and colleagues (above) suggest that the developer and the US regulators should revisit their assessment. The “small deletion” in a single gene in the CRISPR-edited mushroom may have led to the production of new proteins and altered biochemistry that put consumer health at risk.

The above summary is based on the list of studies compiled by GMWatch: