Here's the nut of it:
In order to understand the allergy tests, a bit of backstory on how AquAdvantage salmon are made is necessary. First, genetic engineers create a "diploid" fish, meaning like people, it has two sets of chromosomes. Then, to make the final market product, they add genetic material from other fish and breed a new salmon with three sets of chromosomes—a "triploid" female that can't reproduce. AquaBounty researchers compared the allergenicity—or potential to cause an allergic reaction—of a control group of salmon to both the genetically engineered diploids and triploids. They found (PDF, see page 102) that the diploid salmon were 40 percent more allergenic than the control, while the triploid group was 19 percent more allergenic.
AquaBounty says that the triploids' allergenicity level wasn't statistically significant, and although the diploids' level is significant, it doesn't matter because only triploids will be sold. But Hansen of the Consumers Union finds a few problems with this argument. For starters, the test wasn't double blind, meaning the researchers knew which fish were part of which test group. Second, the sample size of triploid fish was tiny—only six fish in all. Third, although AquaBounty is going to try to turn all its market-bound fish into triploid sterile females, the process isn't perfect, and some 5 percent could end up as the more allergenic diploid. Especially scary when you consider that unlike the triploids, the diploids aren't sterile. So if they escaped, they could breed with wild salmon.