Characterization of unknown genetic modifications using high throughput sequencing and computational subtraction.
BACKGROUND
When generating a genetically modified organism (GMO), the primary goal is to give a target organism one or several novel traits by using biotechnology techniques. A GMO will differ from its parental strain in that its pool of transcripts will be altered. Currently, there are no methods that are reliably able to determine if an organism has been genetically altered if the nature of the modification is unknown.


RESULTS
We show that the concept of computational subtraction can be used to identify transgenic cDNA sequences from genetically modified plants. Our datasets include 454-type sequences from a transgenic line of Arabidopsis thaliana and published EST datasets from commercially relevant species (rice and papaya).


CONCLUSIONS
We believe that computational subtraction represents a powerful new strategy for determining if an organism has been genetically modified as well as to define the nature of the modification. Fewer assumptions have to be made compared to methods currently in use and this is an advantage particularly when working with unknown GMOs.
Tengs
Torstein
T
National Veterinary Institute, Oslo, Norway. Torstein.tengs@vetinst.no
Zhang
Haibo
H
Holst-Jensen
Arne
A
Bohlin
Jon
J
Butenko
Melinka A
MA
Kristoffersen
Anja Bråthen
AB
Sorteberg
Hilde-Gunn Opsahl
HG
Berdal
Knut G
KG
D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D018076:DNA, Complementary / Q000235:genetics; D020224:Expressed Sequence Tags; D015723:Gene Library; D005818:Genetic Engineering / Q000379:methods*; D030821:Plants, Genetically Modified / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*
D018076:DNA, Complementary; D018749:RNA, Plant