The technology of genetic engineering is currently very crude. It is not possible to insert a new gene with any accuracy, and the gene transfer may disrupt the tightly controlled network of DNA in an organism.
Current understanding of the way in which genes are regulated is extremely limited, and any change to the DNA of an organism at any point can have side effects that are impossible to predict or control. The new gene could, for example, alter chemical reactions within the cell or disturb cell functions. This could lead to instability, the creation of new toxins or allergens, and changes in nutritional value. As Richard Lewontin, Professor of Genetics at Harvard University, has said, "we have such a miserably poor understanding of how an organism develops from its DNA that I would be surprised if we don’t get one rude shock after another."
Example: When genetically engineered coho salmon were compared to a control group of normal coho salmon, it was found that the genetic engineering had affected the activity of a number of non-target genes in the transgenic fish. These changes included an increased amount of the protein parvalbumin-b in the genetically engineered salmon, a protein that has been identified as a major food allergen in fish.