Yes, there are some published examples of GMO products that, during development, had data collected that stopped further development. One early example was the identification of a Brazil nut protein that, when expressed in soybeans, improved their nutritional quality (increased methionine, an essential amino acid for mammals). This product was never commercialized when it was learned that this protein is associated with Brazil nut food allergic reactions (Nordlee, et al, 1996).
Another example started as a very promising lead to protect corn from corn rootworm damage. Farmers were experiencing over $1 billion in annual yield losses and expenses to control corn rootworm (CRW) infestations in the early 2000s (Marra et al, 2012). Expression in corn of a protein from potato, called patatin, inhibited growth of CRW larvae and represented a new class of insect-control proteins to prevent CRW damage to corn (Strickland et al, 1995). However, in 1999, patatin was identified as a food allergen in potatoes (Seppala, et al, 1999). Potatoes are not commonly allergenic foods, but patatin was found to be the major allergen for individuals allergic to potatoes. Monsanto conducted further research to identify the regions within the patatin protein structure that bind IgE antibodies (the immune response proteins common to allergenic reactions) from potato-allergic individuals (Astwood et al, 2000), A modified form of patatin was developed that had reduced IgE binding, thereby reducing the likelihood that this modified protein would be allergenic (Alibhai et al, 2000). However, even with these safety improvements, patatin was never advanced to a commercial product and several more years of research were required before the first CRW-resistant GMO corn product (MON 863) was commercialized in 2003. This CRW-resistant corn used a different protein (Cry3Bb1 from Bacillus thuringiensis) to protect corn from pest damage (Vaughn, et al, 2005).
As is required prior to commercialization of all GMO crops, regulatory agencies around the world reviewed extensive data on MON 863, concluding in each case that this GMO was safe for the environment and for human and animal consumption. The data that these regulatory agencies reviewed included assessments showing that Cry3Bb1 has no characteristic of a food allergen and, therefore, is safe for consumption. The improved nutrition soybean with Brazil nut protein, and the early promise to control CRW damage with patatin are two examples of the comprehensive safety assessment process that stopped GMO products from commercialization.
Astwood, J., Alibhai, M., Lee, T., Fuchs, R., Sampson, H. 2000. Identification and Characterization of IgE Binding Epitopes of Patatin, A Major Food Allergen of Potato. Journal of Allergy and Clinical Immunology. Vol. 105, Issue 1, Part 2, page S184 http://www.jacionline.org/article/S0091-6749(00)90983-7/abstract
Alibhai, M., Astwood, J., Joyce, E., Pershing, J., Sampson, H., Purcell, J. 2000. Re-engineering Patatin (Sol t 1) Protein to Eliminate IgE Binding. Journal of Allergy and Clinical Immunology. Vol. 105, Issue 1, Part 2, page S79. http://www.jacionline.org/article/S0091-6749(00)90669-9/abstract
Marra, MC, Piggott, NE and Goodwin, BK. 2012. The impact of corn rootworm protected biotechnology traits in the United States. AgBioForum 15(2): 217-230. http://www.agbioforum.org/v15n2/v15n2a09-marra.htm
Nordlee JA, Taylor SL, Townsend JA, Thomas LA, Bush RK. 1996. Identification of a Brazil-nut allergen in transgenic soybeans. New England Journal of Medicine 334, 688-692. http://www.nejm.org/doi/full/10.1056/NEJM199603143341103
Seppala U, Alenius H, Turjanmaa K, Reunala T, Palosuo T and Kalkkinen N. 1999. Identification of patatin as a novel allergen for children with positive skin prick test responses to raw potato. J Allergy Clin Immunol. 103(1 Pt 1):165-71. http://www.sciencedirect.com/science/article/pii/S0091674999705415
Strickland, JA, Orr, GL and Walsh, TA 1995. Inhibition of Diabrotica larval growth by patatin, the lipid acly hydrolase from potato tubers. Plant Physiol., 109, 667-674. http://www.plantphysiol.org/content/109/2/667.abstract
Vaughn T, Cavato T, Brar G, Coombe T, DeGooyer T et al 2005. A method of controlling corn rootworm feeding using a Bacillus thuringiensis protein expressed in transgenic maize. Crop Sci 45:931–938.