Tag Archives: NGS

WANTED: NGS Expert to support our team in Germany

NewsTo support our team in Ebersberg near Munich we are looking for a Next Generation Sequencing Specialist.

Your tasks:

  • Sell NGS products
  • Be in charge with projects and customers
  • Represent the company and its products and services at meetings, fairs and events
  • Be responsible for the overall sales cycle
  • Support the field sales team in your role as NGS expert
  • Take care of internal processes

Your skills:

  • Experience in the field of NGS
  • Excellent communication skills
  • Focus on customers
  • Positive and entrepreneurial thinking
  • Proactive attitude

Interested? Just visit our website and send your application to application-eu@eurofins.com.

Assessment of NGS Tools for Crime Laboratories

protocolUS Researchers has been awarded with $825,000 to evaluate the use of NGS technology for forensic applications.

Pennsylvania State University will work in conjunction with the Battelle Memorial Institute, the lead institution on the grant, and 6 other laboratories. As the sole university partner, Penn State will be performing evaluations of forensic investigative tools that will expand the capabilities of forensic DNA laboratories.

The grant will test the feasibility of new instruments, laboratory materials and software tools in the field of DNA-based forensics. The study’s aim is to vet tools using next generation sequencing technology and implement them into working crime laboratories.

According to the grant abstract, DNA samples are provided by the National Institute of Standards and Technology. They will be sequenced using Illumina’s MiSeq platform or Life Technologies’ Ion PGM Sequencing System.

The laboratories hope to be able to get tools that use NGS into working crime laboratories to replace current less-informative forensic methods. The new technology will increase efficiency in forensic work and could also help generate investigative leads and identify individuals with only traces of genetic evidence.

Visit forensics.psu.edu/research for more information about the Department of Forensic Science at Pennsylvania State University.

Note: NGS in Diagnostic Testing

Yes, this amazing technology is not just a tool for basic researcher anymore, but has made its way in to the clinical routine testing. It currently all about exome sequencing and targeted gene panel analysis, but whole genome sequencing is expected to come into clinical routine soon. Have a read through this comprehensive article which describes very nicely which applications are suitable for the diagnostic testing and which may come in the future.

Read the article about NGS in diagnostic testing

Are you a NGS expert?

Some months ago we asked you for how long you have been involved with next generation sequencing.

blog

Almost 200 people sent their feedback and gave us a very interesting insight in their experience with NGS. To take this into account, we want to further align our posts with the focus topics of our readers.

Feel free to send me your comments and suggestions to make ngs-expert.com even more valuable for you.

Global Next Generation Sequencing Market in Clinical Applications

A brand new market research by BCC Research was announced yesterday: “Next Generation Sequencing Emerging Clinical Applications & Global Markets”.

The report wants to provide an in-depth analysis of the clinical next generation sequencing (NGS) industry. The approach of analysing the industry is taken in terms of workflow (e.g. sequencers, sequence capture, informatics) and key indications where NGS diagnostics will have market share by 2018.

Key findings of the NGS market research:ngs_survey

  • The global market for sequencing products was nearly $3 billion in 2011. It is forecast to grow at a compound annual growth rate (CAGR) of 17.5% to reach $6.6 billion by 2016.
  • Sequencing instruments and consumables made up the largest market segment in 2011, with revenues of nearly $1.6 billion.  BCC expects this market to grow to $2.2 billion by 2016, a CAGR of 7.3%.
  • The sequencing services market was $838 million in 2010, which reached nearly $988 million in 2011. Sequencing services comprise the fastest-growing market segment with a 29% CAGR estimated to reach $3.5 billion by 2016.

The research examines the markets for NGS diagnostics for the years 2012, 2013 and 2018.
Unfortunately the report costs about $5450. More details on BCC Research.

As soon as there are details and results available, we will share them with you.

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.

The Galaxy of the Genomics Virtual Lab

The Genomics Virtual Lab (GVL) project – using the computing resources from the NeCTAR Research Cloud – is an Australian Government project conducted as part of the “Super Science” initiative. It is developing infrastructure supporting genome informatics research.

Their Galaxy-based NGS and HTS tutorials are really excellent:

You will love the precise explanations, the hands-on demonstration and the additional material like screenshots and in-depth information!

Cardiologists are the next target group

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.

Summary from 4th Next Generation Sequencing Congress 2012 – Part 2

Dear all,

Here is my second summary from 4th NGS Congress at London Heathrow end of 2012. It will bring to you some (hopefully) interesting new facts about sequencing with PacBio RS – the second long read technology present in the actual markets and also the only system delivering reads even longer than 10,000 bp…

Kevin Corcoran, Senior Vice President at Pacific Biosciences held an interesting and very nice talk about the most recent developments for the PacBio RS system. He also showed some nice detailed road maps about future aims and plans. One important thing actual to be mentioned is the launch of the new “XL Chemistry” – while still “C2 Chemistry” may be used as well. The other very interesting story is about “Stage Start” a new feature enabling a parallel start of all sequencing detection similar to the well-known “hot start” technology for PCR. Such detection of sequences better will start from a defined position for most of the libraries than starting from somewhere in the middle. Last but not least, I’m very keen to learn how the future “Photo Protected DNA Polymerases” may further develop – an idea being really very, very next-next-generation…

First of all I can summarize that applying “XL Chemistry” looks really interesting and this being true also in terms of Eurofins MWG Operon de novo sequencing and assembly focus.  This new feature of the PacBio RS machine may also open some new doors to other types of applications, while in general the need for extrem high data coverages may be reduced in parallel.

Currently “C2 Chemistry” is on the machine and running a 90 min video may deliver you about 20-50,000 reads and data outputs of 30-50 Mb – of course higher yields may be possible for “ideal” DNA samples. The average read length is about 3,000 bp (!), while the 95% percentile is about 8,000bp. With the new “XL Chemistry” we got an average yield of about 40,000 reads per SMRT cell with an average read length of about 4,000bp (+30%). Overall, we are very pleased with these first results, especially since we see some good potential to further increase data yields using the new software pipeline started in parallel (Hierarchical Genome Assembly Process and Quiver).

— See picture 1: —

Kevin-Corcoran-Pacific-Biosciences_Seite_16

 

It is also important to mention two different ways of “How-to-deal” with the XL Chemistry. 1) “XL chemistry for Polymerase binding”, but “C2 chemistry for sequencing”. This allows for longer reads at the same quality (currently we still do have a single error rate of 10% to 20 %, average maybe 15%). 2) “XL chemistry for Polymerase binding” AND “XL chemistry for sequencing”. Such one can yield even longer reads, but unfortunately the error rate will also increase by a few %. Therefore this method is being recommended especially for de novo assembly or finishing genomes.

— See picture 2: —

Kevin-Corcoran-Pacific-Biosciences_Seite_52

 

Finally one real “next-next-gen” highlight was the presentation of a development at Pacific Biosciences scoping with the idea to protect the polymerase enzyme from being killed by the energy of the laser. A picture shows how this should work in principle – by setting in place a laser-light protecting sun-blocker – this story was really fascinating for me and I hope to see in future more than the very promising first data results …

— See picture 3: —

Kevin-Corcoran-Pacific-Biosciences_Seite_56

 

So over all Pacific BioSciences keeps also moving very fast in year 2013 and it will be very nice to see and learn how all these additional improvements and new features may  improve the overall data results of this fascinating very long read technology offering today real single reads longer than 10,000 bp.

Cheers now and see you on our next BLOG,
Axel