NGS Expert Blog

Do you know the blog of the Wellcome Trust Sanger Institute?

The Wellcome Trust Sanger Institute is one of the leading genomic research centres in Europe and a leader in the Human Genome Project. Within their blog they are talking about the role of genetics in health and disease by using the latest genomic and genetic techniques.

Read more at http://sangerinstitute.wordpress.com/

Scientists estimate that the cells of our bodies are outnumbered 10 to 1 by bacterial cells which live in or on our body.  A previous blog has already pointed out the impact of this fact on sequencing the corresponding host genomes. On the other hand, microbiomes have the potential to play an important role as diagnostic markers, or opening up new ways of treating diseases, such as personalized medicine.

However, we are just beginning to understand the complex relationships of this “social network”, as the Scientific American has called it. The most complex bacterial community within the human body resides inside the gut. In order to obtain a deeper understanding of the bacterial communities of the human gut, there have been several attempts of sequencing the gut microbiomes of larger groups of individuals, such as projects by Arumugam et al., Yatsunenko et al or Schloissnig et al. However, so far, the number of individuals which were analyzed was relatively small (up to several hundreds).

A group of US scientists have now started the “American Gut Project“.  As reported by Genome Web News, this project is planned as a crowd-sourcing study of 10.000 or more individuals in the US. Since this study is part of the “American Food Project”, it will mainly focus on gut microbiome patterns in relation to diet, age and lifestyle. People who would like to participate in this study need to sign up via a website and donate $99. This money will be used to cover a significant part of the cost of the study. In return, participants will receive a taxonomic profile of their gut microbiome.

The analysis itself will be based on 16S sequencing. For part of the samples, additional analyses such as sequencing the complete metagenomes and long term surveys are planned. No doubt, this study will clearly provide us with a huge data set. However, this data set will be highly complex. Also, it still needs to be brought in context with data from other projects.  To my opinion, interpretation of the data still remains the hardest part. Or, as project organizer Jeff Leach has put it in an interview with Genome Web Daily News: “We don’t expect to be able to address some questions, but because of the size of the sample and because of the broad patterns we expect to see in diet and lifestyle, we think some stuff will fall out.”

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.