Tag Archives: NGS

Adventitious Virus Testing Via Next Generation Sequencing

Adventitious viruses are a major safety concern in biological products. For a substance to be considered “free” of an adventitious agent, assays must demonstrate that a defined quantity of the biological product is negative for an agent at a defined level of sensitivity. In vivo animal testing, in vitro cell culture testing, transmission electron microscopy and molecular assays like quantitative PCR (qPCR) are the current gold standards for viral safety testing. However, if for example the cell substrate contains potential contaminating agents coming from a tumor derived cell line, then current standard methods need to be supplemented by using novel technologies.

Deep sequencing approaches via the next generation sequencing (NGS) techniques may be the method of choice. They allow the detection not only of known viruses but also of unknown viruses or viral subspecies at the detection limit of qPCR-based methods. On the Pathogen Safety Summit (Munich (Germany), November 27-28, 2012) the application of NGS testing approaches were introduced and intensely discussed. The application of NGS into routine testing of production cell banks is presently evaluated by several biological and vaccine producing companies.

Currently, NGS is used for initial characterisation of cell banks, but it iss expected that this new technology will become a standard method for adventitious agent testing soon. There are still challenges that need to be overcome with regard to bioinformatic analyses as well as to the speed of the technological development. Furthermore, also the biological relevance of the NGS data needs to be confirmed. In this regard the expectation is that with the ability to purify active viral particles and subject them to NGS analysis this problem can be overcome.

Btw: Eurofins Medigenomix offers the detection of adventitious viruses in biologicals and biotechnological products by next generation sequencing on platforms from Illumina and Roche 454.

NGS and Personalised Medicine

With the advent of NGS came the promise of personalised medicine (PM) based on our unique genetic differences. The link below takes you to a seminar series from Harvard University which discusses the current status of NGS and its applications in a clinical setting.

There are many hurdles still to leap before PM is a mainstay of clinical diagnosis and treatment, reduction in cost, clinical grade databases, patient sceptisism and insurance implications to name but a few. However, we are at the begining of a revolution in clinical diagnostics and we cannot turn back now. The benefits of rapid diagnosis are obvious, provided we have the associated therapies to treat them. Otherwise it is just knowledge but without the power. There has been disappointingly slow progress in gene therapies and focus on this must also be maintained if the benefits of personalised medicine are to be realised. Furthermore,  in relation to a previous post – NGS and personalised medicine may also help characterise the complex relationship of disease and health, infection and immunological defense between ourselves and our personalised microbiome.

NGS In The Fight Against Multidrug Resistant Bacteria

A recent study (Lancet Infect Dis. 2011 May;11(5):355-62. Epub 2011 Apr) exploring the transfer of the drug resistance gene NDM1 (New Delhi Metallo-Beta Lactamase-1) highlights the practical advatages of NGS.

In a realtively very short time the researchers in the paper were able to isolate the plasmids carring the the NDM-1 gene and sequence 12 plasmids to confirm that the transfer of the NDM-1 (drug resistance gene) amongst other species of bacteria. The implications are serious. Bacteria do not necessarily need to be challenged with a drug or be susceptable for long periods to develop resistance. The resistance can simply be transformed amongst adiverse microbial population. The use of NGS meant that all plasmids could be sequenced in one run to determine the previously unkown, location and the presence of the NDM-1 gene.

Conventional sequencing of over 160Kb of plasmids to try and locate the resisitance marker would have taken a great deal more effort. Thus, NGS is a key tool to track the spread of resisitance genes and hopefully enable researchers to develop prophelactic solutions. Potentially by sequencingf the genomes of all know phages- the natural viral enemy of bacteria. NGS provides another tool to hasten the end to the resistance wars.