NGS Expert Blog

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!

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.

Next Generation Sequencing (NGS) is transforming today’s genomic research and is used in numerous applied areas from clinical diagnostics to academic research. In Texas USA, Dr. Steven Phelps and his research team recently used NGS sequencing to discover a gene which allows mice to communicate by singing a song. I have to admit it sounds more like screaming than singing to me. But Phelps and his team found out that a gene called FOXP2 is responsible for this way of communication.

Phelps’ uses next-generation sequencing to decipher how FOXP2 interacts with DNA to regulate the function of other genes. The process involves reading tiny fragments of overlapping DNA so that the entire sequence can be deduced. It is a procedure that generates massive amount of data that only the processing power of a supercomputer can handle, said O’Connell (Source: www.tacc.utexas.edu). So data handling & storage is still one of the biggest challenges when performing Next Generation Sequencing projects. But now take the chance an listen to the song of this little mouse.

Whole Genome Mapping (WGM) using the OpGen Argus technology delivers high resolution, ordered whole genome restriction maps from single DNA molecules. To receive such a restriction map it is crucial to isolate long DNA fragments (200 kb in size and longer) and to capture the DNA on a solid phase. Afterwards the DNA is digested revealing restriction cleavage sites as gaps when using a fluorescence microscope to visualize the DNA. This optical map will then be converted into digital data, the so called “single molecule restriction maps” (see video below). The software MapSolver enables the following analysis options (see details in the analysis video):

• Perform Genome Comparisons
• Identify Motifs, Annotate Features, and view in silico sequence data
• Perform Sequence Placement
• Create Similarity Clusters

 Video about step 3: How to scan and assemble single molecule restriction maps (SMRM)

Recently we gained access to this innovative technology and are able to combine our Next Generation Sequencing Service with the WGM technology. The combination of NGS and WGM can be used to order the contigs from a next generation sequencing project against the optical map scaffold. This method is able to highly improve sequencing assemblies. If you are interested in a combined or stand-alone project for WGM, please do not hesitate to contact us.

We look forward to discuss WGM in detail with you.

Eurofins MWG Operon and Integrated Genomics have announced a cooperation agreement to combine their expertise in sequencing and analysis services for microbial, fungal and algal organisms. The goal of the cooperation is to provide customers “one-stop-shopping” for complete genome projects that delivers analysis results from the raw extracted DNA. Read the press release.