Tag Archives: Illumina Sequencing

The future of miRNA analysis

We asked you in which technology you see the future of miRNA analysis.
Find here the voting of the 102 participants:

miRNA

 

Why should I buy Illumina stock shares?

What is the impact for a company of winning an award? In case of Illumina you can cleary see it is about brand and market awareness. Only recently we reported about the award for Illumina of beeing the smartest company in 2013. Today we have a short interview for you that answers the question: why to buy stock shares for Illumina.

From my point of view the only risk of being a market leader in a highly dynamic area like next generation sequencing is, that you have a lot to loose. But Illumina is working on this. One example: only this year Illumina launched two new next generation sequencing instruments: the X-Ten for human whole genome sequencing and the Next500 – a mid-size sequencer that fills the gap between the HiSeq and the MiSeq. So let’s see what happens next…

Acquisitions And Rumours

The last time I wrote about acquisitions is a while ago. But that does not mean that nothing happened – yet the opposite is the case: the NGS business is so dynamic that I am not sure which news are already outdated one day later.

But now it might be time to have all news comprised in this blog to at least list the lastest mergers, acquistions and rumours in the field of NGS:

 

1. QIAGEN acquired Ingenuity for $105M

QIAGEN one of the market leaders in Sample & Assay Technologies now builds up a branch in Next Generation Sequencing. The 1st step was the acquisition of Intelligent Bio-Systems in 2012. The expected launch of the upcoming sequencing device is scheduled for mid 2013. The acquisition of Ingenuity now seems to be last piece of the jigsaw for a complete NGS workflow from sample preparation to complete data analysis (see PR QIAGEN). From my point of view I am really confident regarding the sample preparation and the data analysis. But some doubts remain in respect to the NGS device – at least I have never heard about it before….

1. Life Tech – in great demand

Just two days ago an article in GenomeWeb revealed that two other bidders for Life Tech were Roche and Sigma-Aldrich. The rumours I heard so far only said, that Roche was interested in IonTorrent to push their own NGS business. According to the respective GenomeWeb article the Thermo – Life deal is anticipated to be completed in early 2014.

3. Roche – expanding or downsizing?

But although some rumours say that Roche is still interested in IonTorrent it might also be that they will shift their focus. Especially since Roche has downsized their effort in Applied Science business. According to the announcement Roche will integrate these products with other units and they also stopped the collaboration with DNAe to develop a semiconductor sequencing platform. Maybe because a new development might take too long. Maybe because the deal for IonTorrent is under way…

And while writing the summary I remembered again why these updates are so difficult to phrase: I don’t get rid of the feeling that something new, something more interesting is already close to publication.

A Method to Increase Accuracy in Next Generation Sequencing

B) Duplex Sequencing workflow. Sheared, T-tailed double-stranded DNA is ligated to A-tailed adapters. Because every adapter contains<br />a Duplex Tag on each end, every DNA fragment becomes labeled with two distinct tag sequences (arbitrarily designated α and β in the single fragment shown).<br />PCR amplificationwith primers containing Illumina flow-cell–compatible tails is carried out to generate families of PCR duplicates. Two types of PCR products are<br />produced from each DNA fragment. Those derived from one strand will have the α tag sequence adjacent to flow cell sequence 1 and the β tag sequence<br />adjacent to flow cell sequence 2. PCR products originating from the complementary strand are labeled reciprocally.

Next-generation sequencing allows detection of minor variants in a heterogeneous sample. However, errors in PCR and sequencing pose limits on its sensitivity.
A group at University of Washington developed a method, called Duplex Sequencing, to dramatically improve accuracy by sequencing both strands of each DNA duplex. Mutations that are detected in the consensus sequence of one strand but not the other are discounted as technical errors.

The authors adopted the method to Illumina sequencing. It involves the use of modified adaptors that have a tag with random sequence attached. After ligation of these modified adaptors, each duplex DNA fragment is flanked by two different tags and subjected to paired-end sequencing. Sequences of the same duplex from the complementary strands can therefore be uniquely identified by having the same tags on either ends. Comparing sequences of the two strands allows identification of true mutations. The authors estimated that Duplex sequencing has a theoretical background error rate of less than one per 109 nucleotides sequenced.
Full text article can be accessed here: http://www.pnas.org/content/early/2012/07/31/1208715109.full.pdf

 

Appendix: Strategies from two companies

Just after posting my last update about the fight between Roche and Illumina I read two more interesting news which I would like to share with you.

  1. Three important shareholder advisors aid Illumina’s board. Glass Lewis, ISS and Egan-Jones recommend that all shareholders shall support the board by not voting for any of Roche’s candidates to extend the Illumina board. From my point of view this is a clear announcement towards Roche.
  2. The current behaviour of Roche is not new. They acquired already two companies in the same way: Genentech & Ventana. Roche always needed to increase the offer per share once and in both cases it took more than 6 months until the deal was signed. Since the discussion about the takeover is public since January I won’t expect a solution now before autumn this year.

On the annual Illumina shareholder meeting this week we will definitely learn how the shareholders react on the recommendations of all advisors and on the offer from Roche.  Will they adopt a clear position? We will know that soon.

Why Choose LJD Libraries Rather Than Mate-Pair Libraries?

Why should you choose long jumping- distance (LJD) libraries rather than mate-pair libraries, especially for de novo sequencing projects? There is a simple answer to this question: Because the resulting data are much more suitable for de novo assembly and scaffolding.

Why is this so? Mate-pair libraries contain higher percentage of undesired inward-facing read-pairs (if you are not familiar with inward and outward facing reads, just take a look into our FAQs on this subject). These reads are not mate-pair (in other words they are shotgun paired-end). The portion of such reads in the LJD library is greatly reduced.

Furthermore, if using mate pair libraries, it is not clear, if (and if yes, where) there is the changeover within the resulting reads. In other words: A read may contain sequence from one AND the other end without knowing where the changeover is. As a result chimeric reads go into the assembly. This effect is almost completely eliminated if LJD libraries are used, because of the differences in library generation.

Which experiences did you gain with LJD or mate-pair libraries? I’d be happy to hear from you.

NuGen 384 Sample Prep Kit for Illumina

NuGen has launched a new kit > to multiplex 384 samples on Illumina HiSeq 2000, while we by today offer on routine  max 96 samples per channel. I guess this is quite interesting new update.

Has anyone  by today already got experience with this new kit? Have you observed any problems during handling? How would you rate this kit?

Cheers, Axel