NGS Expert Blog

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.

Is sequencing your personal genome a curse or a blessing? A recent radio broadcast from NPR news summarises two scientist’s opinions and their practical experiences with genome sequencing  (listen to the radio broadcast below).

World renowned scientist James Watson, from the famous Watson & Crick team that discovered the DNA structure, recently sequenced his own genome. His discovery didn’t earn him the next Nobel prize for science, but he found out that he belongs to the elite few people whose body is more sensitive to ß-blockers. Now James Watson finally realized why it was so difficult for him to balance his blood pressure. It definitely paid off for Watson to sequence his own genome since he could significantly reduce his weekly ß -blocker intake. But despite this “health-changing” experience, he forbid his colleagues to reveal any information about his likelihood to develop Alzheimer. He said, “since you cannot cure it why would you like to know about it?”

The second candidate to share his experience after he personally sequenced his genome is Stanford geneticist Michale Snyder. His genome sequencing revealed that he was at high risk to develop Type 2 diabetes. A few months after his discovery, Synder got the disease that his genome anticipated. Was this a coincidence or fate? For Snyder, knowledge about his genome gave him a head start against the disease.  By completely transforming his diet and participating in various sport activities,  he overcame his Type 2 diabetes.

From my perspective, both examples show that knowledge about our genetic information can be useful in preventing and treating diseases. It boils down to how much experience exist to reliably interpret the data.

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?

While data output and quality of Next Generation Sequencing is continually increasing, the cost per base is steadily dropping. A survey  from the National Human Genome Research Institute (NHGRI) shows that the cost development even exceeds Moore’s law. New doorways  for research are opening, which may not have been regarded as realistic in the past  due to this trend.

For example, over the past years, several approaches have been made to use DNA as a means of storing information. In a study recently published online in Science, scientists developed a strategy to encode and read digital information using DNA Synthesis and  Next Generation Sequencing Systems.

A html document containing more than 50,000 words, 11 JPG images, and a Java Script program was encoded in DNA by synthesizing nearly 55,000 oligonucleotides on high-fidelity microarrays. The information stored in the oligonucleotides library was later “read” by Illumina sequencing.

According to the authors, DNA is a very useful medium for long term storage of information:   DNA is very stable over many years,  allows data storage at very high density and  small volumes. The senior author, Kosuri, told InSequence, they only used some 50 ng of oligonucleotides to store the information of this html document! Kosuri admitted that the study costed several thousand dollars. However, if Next Generation Sequencing continues to develop at the same speed as today, new applications such as using DNA for (long-term) data storage may become a feasible option.

So let us see what is coming next!

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

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

Dr. Georg Weinstock from the Genome Institute at the Washington University presents in a webinar how to create the perfect genome assembly by using the optical mapping system from OpGen Inc.