This response by Cami Ryan, research associate at the College of Agriculture and Bioresources at the University of Saskatchewan, addresses the study referenced in your question. An excerpt from the response is included below:
“From ‘I smell a rat‘ to ‘when pigs fly,’ bad science has been making the rounds of late. The multi-authored article 'A long-term toxicology study on pigs fed a combined genetically modified (GM) soy and GM maize diet' [referenced in the question] reports that pigs fed a diet of only genetically modified grain show a markedly higher incidence of stomach inflammation than pigs that ate conventional feed.
"However, it seems that—post-publication—the paper and its evidence fail the independent peer-review process on many fronts:
"David Tribe reviews the paper here: He says, ‘It’s what some call a fishing expedition in search of a finding, and a known pitfall of animal feeding trials on whole foods…’ Tribe points out (among other things) that some of the study’s observations might be attributed to compositional differences in the variety of soybeans or corn fed to the pigs: ‘[T]here is relatively little information in the paper about nutritional formulation, methods used for producing the pig diets, storage time for the grain and which particular varieties of grain were used in the diets.’
"Anastasia Bodnar expands upon this further in her Biofortified post 'Lack of care when choosing grains invalidates pig feeding study': ‘The authors aimed to do a real world study, with pig feed that can be found in real life. It intuitively seems right to just go get some grain from some farms. After all, that is what pigs eat, right? Unfortunately, it’s just not that simple…To hone in on any differences that may be caused by the GM traits, they would have to use feed with one or more GM traits and feed that doesn’t have the GM traits but that is otherwise as similar as possible. If the feeds aren’t very similar, then we can’t know if any differences in the animals is due to the GM traits or due to something else.’
"Dr. Robert Friendship (via Terry Daynard)—swine expert from the University of Guelph—points to methodological problems with ‘visual scoring’ and assessment of ‘inflammation’: '[I]t was incorrect for the researchers to conclude that one group had more stomach inflammation than the other group because the researchers did not examine stomach inflammation. They did a visual scoring of the color of the lining of the stomach of pigs at the abattoir and misinterpreted redness to indicate evidence of inflammation. It does not. They would have had to take a tissue sample and prepare histological slides and examine these samples for evidence of inflammatory response such as white blood cell infiltration and other changes to determine if there was inflammation.’
"Andrew Kniss clearly demonstrates the failings of the statistical analysis, poking holes in the study’s evidence. He states, ‘If I were to have analyzed these data, using the statistical techniques that I was taught were appropriate for the type of data, I would have concluded there was no statistical difference in stomach inflammation between the pigs fed the two different diets. To analyze these data the way the authors did makes it seem like they’re trying to find a difference, where none really exist.’”
If you have additional questions after reading this response, please ask.