MFPL: Update on Next Generation Benchtop Sequencing

DNA sequencing has become an indispensible tool in biological research, diagnostics as well as forensics. The demand for affordable technologies, allowing sequencing whole genomes, has driven the development of high-throughput sequencing technologies and Next Generation Sequencing machines.

In the study “Updating benchtop sequencing performance comparison”, published in Nature Biotechnology today, scientists including Arndt von Haeseler’s team compare benchtop sequencing machines affordable enough for application in routine epidemiologic surveillance in clinical and public health microbiology.

Challenging three Next Generation Sequencing systems
For about two years, affordable Next Generation Sequencing machines with a fast turnaround time have been available on the market. Now, a team of researchers from the Universities of Münster and Bielefeld, Alfred Wegener Institute Bremerhaven and the Max F. Perutz Laboratories in Vienna compared three different benchtop Next Generation Sequencing platforms and how they evolved in the course of time. They put the GS Junior (Roche), MiSeq (Illumina) and PGM (Ion Torrent) to the test for sequencing a whole bacterial genome. Discrepancies to a high-quality reference genome sequence were furthermore clarified by traditional bidirectional Sanger sequencing.

Useful tools for microbial epidemiologic surveillance in the public health sector
The team found that the MiSeq made a very strong official debut with only very few substitution and no insertion and deletion errors at consensus level. The GSJ had by far the lowest throughput thereby making it more costly to operate than the other two platforms. The PGM evolved rapidly in the past two years and with the newest chemistries this platform showed only one substitution error and a dramatic reduced number of insertion and deletion errors. “However, these errors are systematic by nature and appropriate software tools can compensate for them,” says corresponding author Dr. Dag Harmsen from the Department for Periodontology at the University of Münster.

He adds: “The de novo assembly qualities of the MiSeq and PGM systems are amazingly good. Therefore, I expect that both platforms will be used routinely for microbial epidemiologic surveillance in the public health sector to detect outbreaks faster and more accurately.”

“To conduct a ‘fair’ Next Generation Sequencing platform comparison is pretty hard. However, it is certainly the consensus accuracy, not the raw read accuracy, that is most relevant for normal end users,” explains Dr. Arndt von Haeseler from the Max F. Perutz Laboratories at the University of Vienna and the Medical University of Vienna. Now the focus is on developing user-friendly software solutions that bridge the gap from data to knowledge to open the door for routine application of Next Generation Sequencing in clinical and public health microbiology.

Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D. Updating benchtop sequencing performance comparison.
Nature Biotechnology 31 (4), 5. April 2013.

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