NGS Expert Blog

With today’s press release I am happy to announce that AROS Applied Biotechnolgy A/S  is now a member of the Eurofins group.

Here is a short introduction of our new colleagues from AROS:

• AROS was founded in the year 2000
• AROS started as a spin off of from the Aarhus University Hospital and was the first service provider for Affymetrix in Europe
• AROS is based in Denmark and provides a long term experience in sample preparation, microarray analysis and next generation sequencing (NGS)
• Nowadays AROS has a leading position in NGS service for pharmaceutical research
• AROS is an Illumina reference lab for next generation sequencing
• The main focus in NGS is RNA-Seq and exome sequencing that is accomplished with the exome designs of the leading provider in this area (Illumina TruSeq Exome Enrichment, NimbleGen EZ Capture & Agilent SureSelect)

“AROS is an excellent fit […] with our focus on high-quality next-generation sequencing […]” (Dr. Gilles Martin) and therefore I am confident that this new alliance will help us both in further expanding our experience level in NGS and to benefit from our complementary strength.

I am sure you will hear more about the activities from AROS on our blog and hope you join me in welcoming AROS as a member of Eurofins.

Opinions differ as to whether next generation sequencing is already mature enough to be a useful tool in diagnostic routine.

Below you can find an interview of the cardiologists from the university of Heidelberg about their studies to integrate next generation sequencing into a diagnostic tool. Therefore they do collaborate with Siemens to receive best possible results that can be used by the doctors in the same way as current reports from other technologies.

Researchers of the Wellcome Trust Sanger Institute have reported DNA sequencing on the PacBio RS sequencer without prior library preparation. As described in an article in BioTechniques last month, the method has so far been applied for sequencing single- and double-stranded viral genomes, bacterial plasmids, plasmid vector models for DNA modification analysis, as well as linear DNA fragments covering an entire bacterial genome.

The standard library preparation step was skipped and the DNA was directly used in the sequencing reaction. With this approach, the researchers around first author Paul Coupland were able to generate sequencing data with as little as 1 ng of starting material, taking only about 8 hours of time.

“In terms of read length and accuracy, the direct sequencing method is comparable to the standard sequencing protocol on the PacBio”, as Coupland told InSequence. “There are no drawbacks in terms of read length and accuracy because PacBio is already single molecule sequencing, so it’s just skipping the library prep and going straight into the sequencing part.”

Since random hexamers can be applied as sequencing primers, and no growth of organisms is needed during sample preparation, the method can be applied without any a priori information on the organisms in the sample.

Clearly, this technique still needs to be optimised. For example, the sequence yield obtained with this approach is considerably lower than with standard methods (3,000 reads per SMRT cell, in contrast to 35,000 to 50,000 reads for standard methods).

However, the authors think that the technique has great potential for clinical applications, where unknown organisms need to be quickly identified. As Dr. Harold Swerdlow, lead author from the Wellcome Trust Sanger Institute says in their press release: “Our technique can be performed without any prior knowledge of the sequence and with no organism specific reagents, in a short space of time. This makes it a promising alternative for clinical situations such as infection control.”

The analyst and sequencing community is currently divided on whether to believe the rumors of a new bid from Roche to buy Illumina. The source of the controversial discussions is an article from the Swiss Newspaper L’Agefi that reported end of December that Roche and Illumina might have agreed to a deal for Roche to acquire Illumina. Since Illumina turned down Roche’s original bid in January, continuous interest from Roche has been reported several times, but the report from L’Agefi is also mentioning concrete amounts of the bid. According to them, the acquisition might take place for $66 per share, valuing the deal at about $8.14 billion in total.

The offer is $15 per share higher than the previous offer of $51 in April last year. According to the analyst Devia Ferreiro of Oppenheimer the new bid is definitely at a level that might lead to a final deal.

With Roche having only about 9% of the NGS market and next generation sequencing becoming most likely an important clinical diagnostic tool in the next years, the strategy focus of Roche must be to get better access to the NGS market and to take NGS to clinical practice. The acquisition of the NGS market leader Illumina represents an optimal starting point.

We’ll see if the rumors are built on a solid foundation within the next two weeks: The Swiss newspaper L’Agefi reported that the announcement might come during the first half of January.

Illumina is currently in the midst of the MiSeq sequencer updates. The software update, the new flowcells and the new sequencing chemistry enable runs with outputs of around 8 Gbp and 250 bp read length. The first updates have reached Europe just recently and only a few days ago our own MiSeq has received the update.

That’s not the end of the story for Illumina. Just a week ago, they already have announced the next update. In the second half of 2013 Illumina is planning to offer another MiSeq update that will increase the output to 15 Gbp. They achieve this tremendous output for their benchtop device by increasing the read length to 300 bp and resolving about 25 million clusters on the flowcell.

Considering the intense competition with Life Tech’s Proton and Ion Torrent sequencer, Illumina needs to steadily improve the specs of their sequencing devices. In March, Life Tech plans to increase the output of their Proton sequencer to around 36 Gbp. That’s still a bit more than the new MiSeq upgrade can deliver, but one also has to evaluate the differences in the read length. While the MiSeq will be able to produce 300 bp reads soon thereafter, the Ion Proton is generating reads from 100 to 150 bp. And the difference is even more remarkably when the sequencing on the MiSeq is performed with the paired-end module – an approach that is not possible with Life Techs devices. By using library insert sizes of around 450 – 500 bp, the two overlapping reads can generate a single consensus read of about that size.

In my opinion the Illumina MiSeq is at the forefront of the race and if Illumina’s plan works out they will be there in 2013, too. But we all know how short-lived the NGS market is. So let’s see what’s coming!

To me the article “Early Adopters Say NGS-based Forensic Testing Could Lead to More Precise Identification” by GenomeWeb (http://bit.ly/WKKIPC) is a very good sign of the “maturation” of the rather young next generation technology. It may find its way into criminal police offices soon.

Currently, forensic profiling is based on STR analysis with capillary electrophoresis, or analysis of mitochondrial DNA with PCR and Sanger sequencing. But next gen sequencing opens up new possibilities. Researchers are now looking at moving both STR profiling and mitochondrial DNA analysis to next gen sequencing, but are also looking to develop SNP-based targeted sequencing panels for forensics, which would enable researchers to identify a person’s ancestry, hair color, or other defining characteristics based on their DNA.

So, what do you think: Will there still be classical DNA profiling or will NGS have taken over in the next decade?

Six floors for Next Generation Sequencing in the middle of Manhatten – this is going to be exiting. Listen to the interview from Bio-IT World with Nancy Kelly, founding executive director of the New York Genome Center.

BGI announced the acquistion of Complete Genomics this week. According to the press release and the statement from BGI’s CEO Wang Jun, Ph.D.  one of the reasons for the acquistion was that “Complete has developed a proprietary whole genome sequencing technology … (that) fit well with our research and business requirements …”. It is important to note that although the Complete Genomics technology shows a slower performance than the Illumina technology it appears to be more accurate (Georg Church, Advisor of BGI & CG).

But what are the market/industry responses to the new acquisition?

• BGI gets “an immediate infrastructure and service offering that will complement the facilities in China” (Isaac Ro, Goldman Sachs)

• “Now BGI gets their US front… And CG is sparred a slow and painful demise…” (Seqanswers)

I would really like to read an interview in 6 months from employee’s of both parties to learn who is the actual “winner” of this deal? Is it BGI since they now have access to the US market or Complete Genomics whose questionable financial situation gained a significant boost from the acquistion. Will Complete Genomics still be an independent operating company? We will find out.

Just some days ago we discussed the dynamics in NGS and here we are with some news. Life Technologies Corporation announced that the new software v3.0 for the IonTorrent PGM consistently delivers 99.9% consensus accuracy for both short and long homopolymer regions and increases the frequency of correctly called insertions, deletions and homopolymer sequences by two-fold (Press Release LIFE).

In addition to the read accuracy also the read length increased with the launch of the new kit to 400 bp. The aim of the company is to improve their system further for microbial applications (PR LIFE).

But not only improvements in bacterial identification is on the priority list for LIFE’s RnD team but also more innovations in the area of diagnostics. A new AmpliSeq(TM) sample ID panel will increase the confidence during data analysis and a new kit is soon to be launched (PR LIFE).

I think from a customer’s perspective it is a good idea to further improve the technology in several areas since there could be some cross-linking innovations. But it also bears the risk that some competitors, focussing on a specific application, will adapt their system more quickly. But of course these are only speculations. So what is your opinion?

We are happy to extend our next generation sequencing capabilities with the new Illumina HiSeq 2500 and Illumina MiSeq. Thanks to these new machines, we can provide customers with unsurpassable NGS services at high accuracy rates and shorter turnaround time (TAT). Read more at http://bit.ly/OTv9AP