NGS Expert Blog

The upcoming conference in August will showcase expanding applications of NGS shaping the industry.

Agenda topics include:

• RNA-seq
• What’s next in sequencing platforms?
• Nanopore sequencing
• Desktop sequencers
• Structural variation

Attend Cambridge Healthtech Institute’s Applying Next Generation Sequencing to learn from large sequencing centers, core laboratories, and specialized groups as they share their practical knowledge, real-world experiences and solutions.

The conference takes place August 13-15 in Providence, Rhode Island, USA. Visit there our worldwide exclusive cooperation partner Genomatix.

Note: If you register by Friday, July 13 and save up to $200.  Registration includes access to CHI’s Fifth Annual Next-Generation Sequencing Data Analysis conference running concurrently.

Rather than resting on the successes of the MiSeq launch, Illumina is continuously improving the performance of their small Benchtop Next Generation Sequencing System. Geoff Smith is talking about improvements in the read lenght of the MiSeq in the video attached.

This instrument is not only another next gen sequencing device but really has remarkable advantages over other instruments when sequencing for example bacterial genomes. This is why I am really delighted that we now can offer services using the MiSeq instrument. (More info on our MiSeq services can be found here)

16S rRNA sequencing of samples from 54 office-common surfaces in 3 different cities (New York, San Franscisco, Tuscon) revealed that offices of men are dirtier than these of women and the offices in San Francisco are the cleanest among the three cities. This is part of the results from Hewitt et al. published in PLoS ONE just recently. Overall they found “more than 500 bacterial genera from 20 different divisions” (Hewitt et al.) whereas most could be found on chairs and phones (see graph). But interestingly the bacterial population from Tuscon was significant different to the one from San Francisco and NewYork although the distance between Tuscon and San Francisco is smaller. From my point of view this is a great study showing that distribution is not as obvious as we think and that we haven’t revealed every secret on earth yet.

Nacreous luster is held in high industrial value since ancient time. It is a jewelry which is generated in pearl oysters, so it is also called “biomineral”. Nacre consists of two kinds of layer structures: an “inorganic crystal layer by calcium carbonate” and a “protein layer”. The protein layer is made of a laminate structure, which comes up the characteristic luster by multilayer reflective. Recently, pearls are not only used as jewels but take on greater importance like as a new functional material for nano technology, as a CO2 fixation carrier for environmental science, and as a model of bone formation/bio-calcification for medical science.

However, molecular entity of the protein layer is not understood so much. To clarify it, Kinoshita et al. tried transcriptome analysis of the pearl oyster Pinctada fucata with 3’-fragment library and GS FLX sequencing. They could identify 29,682 novel genes, and clustering analysis of gene expression pattern with known nacreous genes revealed 20 candidates that most probably have an association with bio-mineralization. Furthermore, Takeuchi et al.　determined the 1.15 Gb draft genome sequence of P. fukata. They found 23 257 complete gene models that included the candidate genes reported in the study from Kinoshita et al.

The spinning process of nacreous luster will be clarified by harmony of gene expression in near future!

Earlier this year Oxford Nanopore Technologies presented their solution for Next Generation Sequencing: the MinIon & GridIon instruments outranges the current available techniques like Illumina or Roche systems by read length, hands on time and pricing. But since the technology is not launched yet, we don’t know if these specs are realistic.

This is why we asked you about your opinion in our latest poll (Nanopore sequencing from Oxford Nanopore Technologies sounds really fascinating. What is your opinion regarding this technology?). More than 50 voters took part in this survey and 42% share my opinon: “I prefer to wait and check out the real system before judging it”.

“Paper doesn’t blush” is what 15% think of this announcement – like every other company the first presentation needs to be spectacular, but let’s see what happens when the instrument is really on the market.

And still some of you are convinced that this will change a lot in the NGS market – and I agree it would be great if it turns out to be true.

Some of you haven’t heard about this technology – so if you are interested to learn more about it you might start by reading our recent blog post about it.

Thanks again to all you participated in our voting and please have a look at our new poll.