Table 1.
Datasets used for the five case studies as possible scenario occurring in routine GMO analysis.
| Sample name | Sample content | Sample type | Study case | NGS Platform |
|---|---|---|---|---|
| Bt rice 100% | Bt rice*,# 100% (200000 HGE) | DNA walking (p35S, tNOS, t35S pCAMBIA) | 1,2 | PacBio |
| Bt rice 1% | Bt rice*,# 1% (2000 HGE) | DNA walking (p35S, tNOS, t35S pCAMBIA) | 3 | PacBio |
| Bt rice 0.1% | Bt rice*,# 0.1% (200 HGE) | DNA walking (p35S, tNOS, t35S pCAMBIA) | 3 | PacBio |
| Bt rice 0.01% | Bt rice*,# 0.01% (20 HGE) | DNA walking (p35S, tNOS, t35S pCAMBIA) | 3 | PacBio |
| Bt noodles 100% | Noodles made from Bt rice*,# 100% | DNA walking (p35S, tNOS, t35S pCAMBIA) | 3 | PacBio |
| Bt noodles 1% | Noodles made from Bt rice*,# 1% | DNA walking (p35S, tNOS, t35S pCAMBIA) | 3 | PacBio |
| Bt rice MinION 100% | Bt rice*,# 100% (200000 HGE) | DNA walking (p35S, tNOS, t35S pCAMBIA) | 3 | MinION |
| Kuwaiti matrix | Food matrix from Kuwaiti market: NK603 and DAS1507 at quantifiable levels, MON810 and Bt11 at trace levels£ | DNA walking (p35S, tNOS, t35S pCAMBIA) | 4 | PacBio |
| Mixture 1 | Bt rice* (2000 HGE) + MON863 (2000 HGE) | DNA walking (p35S, tNOS, t35S pCAMBIA) | 5 | PacBio |
| Mixture 2 | Bt rice* (2000 HGE) + MON863 (2000 HGE) + GTS-40–3-2 (2000 HGE) | DNA walking (p35S, tNOS, t35S pCAMBIA) | 5 | PacBio |
| Mixture 3 | Bt rice* (20 HGE) + MON863 (20 HGE) + GTS-40–3-2 (20 HGE) | DNA walking (p35S, tNOS, t35S pCAMBIA) | 5 | PacBio |
HGE: haploid genome equivalents. Detailed description on the creation of the datasets can be found in (Fraiture et al., 2017). Bt rice may act as a known (#) or unknown (*) GMO depending on the version of the Nexplorer database that is used for the data analysis. All other events represent known GMOs, £according to qPCR analysis described in (Fraiture et al., 2017).