Yes, there could be unexpected side effects from any new crop variety, GM or non-GM, as well as with any new agricultural practices. Risk assessment and appropriate testing of all new crops, along with on-going monitoring should mitigate the risks.
GM crops are more extensively tested than non-GM varieties before release (see Q14) both for their environmental effects and as foods. They also tend to have fewer genetic differences from their predecessor than new non-GM varieties.
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