Fraiture Marie-Alice, D'aes Jolien, Guiderdoni Emmanuel, Meunier Anne-Cécile, Delcourt Thomas, Hoffman Stefan, Vandermassen Els, De Keersmaecker Sigrid C J, Vanneste Kevin, Roosens Nancy H C
Sciensano, Transversal Activities in Applied Genomics (TAG), rue Juliette Wytsman 14, 1050 Brussels, Belgium.
CIRAD, UMR AGAP Institut, F-34398 Montpellier, France.
Foods. 2023 Jan 18;12(3):455. doi: 10.3390/foods12030455.
Similar to genetically modified organisms (GMOs) produced by classical genetic engineering, gene-edited (GE) organisms and their derived food/feed products commercialized on the European Union market fall within the scope of European Union Directive 2001/18/EC. Consequently, their control in the food/feed chain by GMO enforcement laboratories is required by the competent authorities to guarantee food/feed safety and traceability (2003/1829/EC; 2003/1830/EC). However, their detection is potentially challenging at both the analytical and interpretation levels since this requires methodological approaches that can target and detect a specific single nucleotide variation (SNV) introduced into a GE organism. In this study, we propose a targeted high-throughput sequencing approach, including (i) a prior PCR-based enrichment step to amplify regions of interest, (ii) a sequencing step, and (iii) a data analysis methodology to identify SNVs of interest. To investigate if the performance of this targeted high-throughput sequencing approach is compatible with the performance criteria used in the GMO detection field, several samples containing different percentages of a GE rice line carrying a single adenosine insertion in were prepared and analyzed. The SNV of interest in samples containing the GE rice line could successfully be detected, both at high and low percentages. No impact related to food processing or to the presence of other crop species was observed. The present proof-of-concept study has allowed us to deliver the first experimental-based evidence indicating that the proposed targeted high-throughput sequencing approach may constitute, in the future, a specific and sensitive tool to support the safety and traceability of the food/feed chain regarding GE plants carrying SNVs.
与通过经典基因工程生产的转基因生物（GMO）类似，在欧盟市场上商业化的基因编辑（GE）生物及其衍生的食品/饲料产品属于欧盟指令2001/18/EC的范围。因此，主管当局要求转基因生物执法实验室在食品/饲料链中对其进行管控，以确保食品/饲料安全和可追溯性（2003/1829/EC；2003/1830/EC）。然而，由于这需要能够靶向和检测引入基因编辑生物中的特定单核苷酸变异（SNV）的方法，因此在分析和解释层面上对它们的检测都具有潜在挑战性。在本研究中，我们提出了一种靶向高通量测序方法，包括（i）基于PCR的富集步骤，以扩增感兴趣的区域；（ii）测序步骤；以及（iii）数据分析方法，以识别感兴趣的SNV。为了研究这种靶向高通量测序方法的性能是否与转基因生物检测领域中使用的性能标准兼容，制备并分析了几个含有不同百分比携带单个腺苷插入的基因编辑水稻品系的样品。含有基因编辑水稻品系的样品中感兴趣的SNV在高比例和低比例下都能成功检测到。未观察到与食品加工或其他作物品种存在相关的影响。目前的概念验证研究使我们能够提供首个基于实验的证据，表明所提出的靶向高通量测序方法未来可能构成一种特定且灵敏的工具，以支持关于携带SNV的基因编辑植物的食品/饲料链的安全和可追溯性。
