Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products

Abstract

The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.

The use of targeted genomic capture and massively parallel sequencing in diagnosis of Chinese Leukoencephalopathies

“…Whole exome sequencing (WES) represents a significant breakthrough in clinical genetic as a powerful tool for etiological discovery in many kinds of disorders10. Benefited from the WES technology, a lot more pathogenic genes have been found and many types of diseases have been identified111213. Innovative application of new technologies is one of the major factors driving advances in medical science, most clinical applications of next-generation sequencing (NGS) concentrate on known and potential candidate genes to generate clear reports and finally promote clinical diagnosis1415161718.…”

Decision Support for the Comparative Evaluation and Selection of Analytical Methods: Detection of Genetically Modified Organisms as an Example

“…Two additional qPCR applications (SIMQUANT; Berdal et al 2008) use qPCR chemistry together with the limiting dilutions principle, which is near to the idea of the ddPCR-based methods, of which two were included Dobnik et al 2015). Other selected methods include LAMP with end-point fluorescent (Chen et al 2011;Wang et al 2015) or bioluminescence real-time detection (Kiddle et al 2012), multiplex PCR with hybridization on microarrays (Leimanis et al 2008;Hamels et al 2009) or detection with capillary gel electrophoresis (Nadal et al 2006), a protein-based method (Van Den Bulcke et al 2007), and two NGS methods (unpublished, developed within the EU FP7 Decathlon project), one for enriched samples and another for whole genome sequencing (see, e.g., Arulandhu et al 2016;Holst-Jensen et al 2016). The majority of the selected methods are validated in-house or within international collaborative trials and their fitness for purpose demonstrated elsewhere (see Table 1 for references).…”

Critical assessment of digital PCR for the detection and quantification of genetically modified organisms

“…The two common formats are whole-genome sequencing and sequencing after enrichment. Whole-genome sequencing was shown to be applicable for detection and characterization of GMOs and derived products; however, there are still problems with sensitivity for all targets [33]. To increase sensitivity, DNA enrichment approaches can be coupled with NGS [34], and such a combination can allow reliable identification of authorized and unauthorized GMOs [35].…”