The only way your body would know or care if it was consuming a genetically modified food was if that modification produced something toxic (poisonous). Barring than that, to your body, it's all proteins, carbohydrates, fats, etc... If you are concerned about genetically modified foods, you should probably also be concerned with domesticated foods, since those have been selected by their farmers for many generations to produce specific things - bigger fruits, better tasting meats. We've been doing genetic modification since we started farming. It's only been the past generation or so that we started hacking the DNA directly.