The study referred to looked at the question of whether fragments of DNA, consumed in our food, could pass into the blood stream. The main finding was that this could happen and that fragments of DNA large enough to contain whole genes could enter the human circulation system. Previous to this study, it was thought than DNA would be completely degraded during the digestion process. We consume large amounts DNA from plants in our everyday diet. If the diet contained some GM products then some of the DNA consumed could come from this source. DNA from a GM plant source would be no different to DNA from any other source. If DNA from our food can pass into the blood stream then this has always happened and has caused us no problems. The study does not in any way claim that GM foods can alter human DNA and there is no evidence at all for this.
For more information on this topic, please review this recent response from David Tribe, Senior Lecturer, Agriculture and Food Systems/Microbiology and Immunology at the University of Melbourne: http://gmoanswers.com/ask/i-recently-looked-article-states-new-genetically-modified-wheat-can-silence-wheat-genes-and-can.