Tag Archives: MinIon

First Oxford Nanopore MinIon data available: Is this the end of PacBio?

Nanopore SequencingResearchers from the University of Birmingham in the UK last week publicly released data they generated with Oxford Nanopore Technologies’ MinIon nanopore sequencer, the first group to do so since the company started its early access program this spring (see In Sequence report).

The sequence is derived from a Pseudomonas aeruginosa genome and is a single 8.5 kilobase read. It was posted by Nick Loman from the institute of Microbiology and Infection at the University of Birmingham. It was possible to identify the serotype O6. The sequence can be found here. It is of low quality with 71% identity of the spanned region.

Konrad Paszkiewicz, director of the Wellcome Trust Biomedical Informatics Hub and head of the sequencing service at Exeter, has been writing about the group’s experience on the Exeter Sequencing Service’s blog. “Even at this stage, this platform has the potential to steal large chunks out of the market from the likes of PacBio,” Paszkiewicz said.

We will have to wait for more data until we see how useful the technique will be and how the technique is able to compete against other Nanopore sequencers e.g. the device of Genia that was recently acquired by Roche.

Nanopore MinION to be tested and evaluated in Sweden

There are many researchers and service providers who are talking about the MinION from Nanopore on a regular basis. Great things are expected from this innovative sequencing technology.

As previously mentioned, Oxford Nanopore has shipped some MinIon devices to early access users to receive some more data. As one of the few laboratories in Scandinavia, the Department of Animal Breeding and Genetics at the Swedish University of Agricultural Sciences has been chosen to test one of the latest sequencing technologies from Oxford Nanopore. By the size of the sequencer it is possible to bring the sequencer in the field.

Previously the department has tested leading NGS technologies in research related to the genes involved in the immune system of horses. Now the Nanopore technology will be used, compared and evaluated against the existing well-proven sequencing technologies.

I guess it is just to wait and see what the MinION will bring, if it will come up to expectations or not.

New kids on the show – who will be the winner?

Next Generation Sequencing is still a quite young market. Therefore we face the same situation every year: there is a lot of innovation going on in regard to new technologies, new instruments and other inventions. Amongst all these innovations GenomeWeb picked out the new platforms and asked in a survey about the expectancies in the market.

Instruments that were part of this survey are (at least in one of several questions):

  • Oxford Nanopore’s MinIon
  • Illumina’s X-Ten
  • Illuminas NextSeq 500
  • QIAGEN’s GeneReader
  • Life Technologies’ Ion Torrent PGM
  • Illumina HiSeq

Here are some of the results:

  • 35% of the participants say that the MinIon has the greatest impact on the sequencing community
  • 30% of the participtants will purchase most likely the NextSeq 500
  • Illumina HiSeq / MiSeq outperform the Ion Torrent Proton / PGM in data accuracy and throughput, the Ion Torrent instruments are better in respect of run time and instrument price

Read the complete survey here.

Will Oxford Nanopore´s MinION hold its promises?

When I first heard of the Oxford Nanopore technology, it sounded rather exciting: The company proclaimed a new technology which enabled sequencing with extremely long read lengths of up to 100 kbp at a reasonable accuracy and in a very short time.

The technology is based on so-called “strand sequencing”. This technique involves a protein nanopore, in combination with a specific enzyme. This enzyme is designed to feed a single strand of DNA through the nanopore. The bases of the DNA strand are identified as they pass through the pore.

The sequencing systems are called “GridION” and “MinION”, with the GridION representing a high throughput system, and the MinION being a miniaturised system the size of a USB stick.

NewsFirst data for the GridION system have been presented in February 2012 at the AGBT conference. After that, there had been hardly any news from Oxford Nanopore for a long time. Then in November 2013, Oxford Nanopore announced an early access program for the MinION system on the ASHG meeting. They also gave demonstrations of the system to selected customers in the company´s labs. However, the company did not show any sequencing data yet. In February 2014, Oxford Nanopore has started to issue invitations to the early access program, and the first MinION systems should be shipped soon.

On the AGBT meeting in Feburary, the first MinION sequencing data, generated by Oxford Nanopore and analysed by David Jaffe from Broad Institute, Cambridge, have finally been presented.  However, the first results were rather disappointing: The average read length was way below the expectations. As reported by In Sequence, Jaffe told that the average read lengths were 5.4 kbp and 4.9 kbp for the two bacterial genomes analysed. The raw error rate of the data was not disclosed. However, Jaffe said that there were “long perfect stretches” and “blocks of errors”.  The data was not suitable for de novo assemblies from MinION data alone. In the end, the researchers used the sequences to create better assemblies from Illumina data.

On a Plant Genomics Meeting in Kuala Lumpur in the end of February, Oxford Nanopore Technologies presented more data. They claim that they could “easily obtain” 50 kbp reads. They had generated reads spanning the entire 48 kbp bacteriophage lambda genome. They also show data to underline that the read length distribution obtained by Nanopore sequencing is determined by the size distribution of the input DNA. Slides of the presentation can be viewed here.

Even if the first results are somewhat disappointing, I think this is still an interesting new technique. Like it was with the PacBio system, the technology may need more time to overcome its childhood diseases. The next few months will show if the technology can hold the high expectations that have been raised.

Innovation or Excess?

It seems that Next Generation Sequencing (NGS) is as seasonal or innovative as fashion. Early this year Oxford Nanopore Technologies announced a revolutionising technology where NGS can be performed on very small sequencers in USB-Stick format.  Just recently Complete Genomics reported about a new technology, named Long Fragment Read (LFR). LFR enables to increase the sequencing accuracy by 10-fold and reduces the amount of starting material at the same time. Additonally QIAGEN disclosed the acquisition of Intelligent Bio-Systems Inc. (IBS). A previously undisclosed NGS benchtop sequencing instrument, combining IBS and QIAGEN technology will be launched soon. The main focus of this technology is the processing of multiple samples in parallel. I am looking forward to learn more about this technology, which seems to have some things in common with the Illumina technology, since Illumina just sued QIAGEN for infringement of NGS patents.

So do we have an excess in development for Next Generation Sequencing or do we need more? My personal opinion is that innovation is the source of science and that it is important to develop new technologies. But it remains fascinating if and when any of the new technologies will replace any of the currently used technologies, like Roche GS FLX or Illumina. I’ll keep you updated.

Survey result: What do you think about Nanopore sequencing?

Earlier this year Oxford Nanopore Technologies presented their solution for Next Generation Sequencing: the MinIon & GridIon instruments outranges the current available techniques like Illumina or Roche systems by read length, hands on time and pricing. But since the technology is not launched yet, we don’t know if these specs are realistic.

This is why we asked you about your opinion in our latest poll (Nanopore sequencing from Oxford Nanopore Technologies sounds really fascinating. What is your opinion regarding this technology?). More than 50 voters took part in this survey and 42% share my opinon: “I prefer to wait and check out the real system before judging it”.

“Paper doesn’t blush” is what 15% think of this announcement – like every other company the first presentation needs to be spectacular, but let’s see what happens when the instrument is really on the market.

And still some of you are convinced that this will change a lot in the NGS market – and I agree it would be great if it turns out to be true.

Some of you haven’t heard about this technology – so if you are interested to learn more about it you might start by reading our recent blog post about it.

Thanks again to all you participated in our voting and please have a look at our new poll.

Focus on FLX+ ?

In the last weeks we were continuously following the hostile bid from Roche for Illumina. Now, after the shareholder meeting, Roche didn’t extend the offer and let Illumina from the hook – for the moment?
However, this could also be good news. From my point of view there is a wide range of applications that work best with the FLX technology. In order to be competitive with all other NGS technologies Roche needs to invest more in FLX+. After launching the upgrade last year they faced continuously problems with the performance of the technique as highlighted for example in an article in InSequence last week.

I think, because the NGS future of Roche is again more focussed on FLX+, they will work even harder to get the long reads up an running on every GS FLX site – maybe a FLX+ upgrade for the GS Junior might be possible soon.

Of course it also might be that they are looking for an alternative for Illumina as highlighted by Julia Karow and Monica Heger. However, all possiblities discussed in this article – a cooperation with Life (Ion Torrent), an acquisition of Oxford Nanopore technologies or the development of a brand new technique might not be as scary for the FLX technology as Illumina because all technologies are “very early in the commercialization”.

How Small Can Next Generation Sequencing Devices Get?

Scarcely any biotech blog and bulletin is not reporting about Oxford Nanopore Technologies MinIon & GridIon.

Truly, the specs of the new instruments sound fantastic: read length up to 100 kbp, raw read error rate ~1%, no sample preparation necessary (at least with blood samples), RNA can be sequenced directly, costs per base comparable to competitors, only 900$ for the MinIon device and data production in the range of 20-400 bases / second / pore (GenomeWeb).

And it goes without saying that these new instruments cause a lot of fuss in the Next Generation Community: shares from competitors are down up to 6 percent, and every one discusses fictive scenarios that might now be possible.

I am also really excited about this news and it still sound unbelievable that Next Gen Sequencing devices can be so small. But I also have my doubts  and agree with the following statements:

“… If only 75% of what they claimed is true it would be impressive.” (Pathogenomics)

“…that new DNA sequencers, like everything else in life, often look better when they’re vapourware.”(Forbes)

What is definitely true is that you really have to read also the small prints at the bottom of the page. You cannot, for example, use the USB-Stick-like device “MinIon” to sequence the complete genome in 15 minutes. You would need to run 20 GridIon instruments or “nodes” in parallel to achieve this turnaround time with a coverage of 50x.

So it is definitely fascinating what might be possible with the MinIon – just think about the point-of-care market, where we would need small, disposable devices to work on site. But still you should be able to interpret the data and I look forward to learning how they will solve this issue. And furthermore I am even more curious what kind of instruments we will be using in 5 years: Smaller or faster ones or something completely different? What do you think?


Oxford Nanopore Technologies Ltd.