European Molecular Biology Laboratory

Published: Wednesday, January 1st, 2014
Tags: Corporate News, Customer Stories, Fragment Analyzer

No bottlenecks allowed

Authors: Rajna Hercog, Jelena Pistolic, Paul Collier, Dinko Pavlinic and Dr. Vladimir Benes; European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, Heidelberg, D-69117, Germany

There is no sign that interest in massively parallel sequencing (MPS) will fade away anytime soon. Exactly the contrary is happening: application of this technique is spreading into more and more areas of basic as well as applied research. It is getting increasingly popular among researchers investigating genomes, transcriptomes, methylomes and other nucleic acid derived –omes of many different organisms, large and small. Also the capacity of sequencing instruments is on the rise. Thanks to the possibility of pooling many barcoded libraries in one ‘lane’ it is nowadays feasible to sequence simultaneously large numbers of samples. However, it is important to match the throughput of sequencers with the throughput of instrumentation used in the upstream steps such as, for example, quality check of incoming samples, preparation of sequencing libraries and once they are completed also inspection of their quality and quantity.

EMBL GeneCore facility provides its MPS competence to sizeable community in need of high quality DNA/RNA sequence data for their research projects. We are also experiencing steady increase of samples for preparation of sequencing libraries for various MPS applications. These samples come from various sources and organisms. In order to deal with this demand we have implemented automated library preparation with liquid handling robot with processing capacity of up to 96 libraries per a run. However, for required process streamlining we were missing the piece of equipment with the similar throughput and also providing clear visual information, among other output features, which would enable us to cover preceding and following steps. These include checking distribution of DNA fragments after sample fragmentation or quality and quantity check of completed sequencing libraries before loading them on the sequencer. To fill that gap, after testing several systems available on the market, we decided to acquire a 12-capillary Fragment Analyzer™ manufactured by Advanced Analytical Technologies Inc. (AATI). From our own experience with capillary DNA sequencing we knew that capillary electrophoresis is a proven and robust separation method that has been successfully used in many different applications. We have not been disappointed! The Fragment Analyzer™ is easy to operate, both sample costs and maintenance of the instrument are low while providing a high data quality (we affectionately call it “Frag”). It has met our requirements for affordable and straightforward analysis of DNA as well as RNA samples for next generation sequencing in a truly walk-away fashion.

GeneCore participates in a large study spearheaded by Peer Bork and his group to determine content and composition of human gastro-intestinal microbiome. It has been described that microbiomes generally play critical role in many aspects of our lives and well-being. Contrary to our genome, which remains more or less constant throughout our lives, our microbiome is dynamic and changes with our conditions. In addition, it is speculated that its composition or dysbalance can have a predictive value. Peer Bork has embarked upon the ambitious project aiming at analysis of several thousands of DNA samples and our “Frag” is an important component of our from-sample-to-data workflow also in this project. It has already run well over a thousand samples and does a really good job.

Primary Contact: Dr. Vladimir Benes, benes@embl.de

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