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Oxford Nanopore Expands MinIon Early-Access Program as Users Present, Publish Early Results

NEW YORK (GenomeWeb) – Oxford Nanopore Technologies said last week that it is admitting additional users to its early-access program for the MinIon sequencer, while increasing numbers of program participants are presenting and publishing their results.

At the Advances in Genome Biology and Technology meeting in Marco Island, Fla., this week, for example, researchers from The Genome Analysis Centre in the UK and from Cold Spring Harbor Laboratory are scheduled to talk about real-time surveillance approaches, cDNA sequencing, and de novo genome assembly using MinIon data.

Early-access users have also been publishing new applications and data analysis methods for the technology. Among them, Mark Akeson's group at the University of California Santa Cruz last week published a single nucleotide variant detection tool for nanopore data and showed that they were able to resolve the copy number of a cancer gene in an unresolved region of a human chromosome.

Other research groups have demonstrated the de novo assembly of a bacterial genome from MinIon data alone and the de novo assembly of a yeast genome from MinIon reads after error correction with Illumina short reads, and have presented results on metagenomic sequencing, human gene sequencing, bacterial antibiotic resistance island characterization, and bacterial outbreak analysis.

Oxford Nanopore first opened registration for the MinIon Access Program in late 2013 and has admitted two rounds of participants so far who started to receive MinIon devices last spring.

Until now, the early-access program has focused on DNA sequencing but is "expected to encompass the direct analysis of RNA and proteins" in the future, according to the company.

The technology has improved in several areas during the program, the firm said. Library preparation kits have been updated several times, contributing to improved data accuracy, shorter workflows, and better robustness. The company has also introduced new library prep kits and protocols to enable additional applications, such as cDNA sequencing and barcoding of genomic DNA and amplicons.

Also, Oxford Nano has shipped three versions of flow cells so far, each time increasing the number of working nanopores and, as a result, data yield and quality.

Data quality has improved overall by increasing the proportion of 2D reads, where reads from the forward and reverse strand are combined to increase accuracy.

The instrument control software, MinKnow, has also been updated several times. Changes to the frequency of data sampling, for example, have improved yield and accuracy.

Metrichor, the cloud-based basecalling software, "will evolve for more comprehensive analyses and services," according to the firm, and will include additional applications. It has already updated the analysis algorithms and other aspects of Metrichor to improve data quality and analysis speed, and users have developed various data analysis tools.