NGS Expert Blog

In the April issue of the journal Spektrum der Wissenschaft I found a very interesting article from Jan Dönges about data storage of information with the help of synthetic DNA (oligonucleotides). He describes the work of Ewan Birney and Nick Goldman from the European Bioinformatics Institute (EBI) in Hinxton, UK who have developed a strategy that allows coding data in strings of A, C, G and T nucleotides (Nature 494, 77-80, February 7 2013). They coded all sonnets of Shakespeare, a photo of the institute, the original paper of Watson and crick about the structure of DNA, an audio recording of the speech of Martin Luther King “I have a dream” and file with coding instructions; all together 739 kilobyte of information. They ordered the oligos and sequenced them on an Illumina HiSeq 2000. They received a text file of the letters A, C, G and T that could be converted into the original data. The complete code and sequence can be found here.

From sequencing experiments like the mammoth or the Neanderthal man we know that DNA is at least 10,000 years stable, longer than any other data storage. In addition it is extremely dense. With 1 gram of DNA it is possible to code more than 2 petabyte (10¹⁵ byte), or 2.3 million gigabyte. The volume of a coffee cup would be sufficient to code 100 million hours of high resolution videos. It is to be expected that the technology could even be improved in the future as long as mankind still is interested in DNA. The cost for the experiment was quite high compared to other storage media like tapes, HDD or DVDs. However, already after 600 years of making consecutive security copies of tapes the cost is compensated. So, if we want to conserve the knowledge of mankind for very long periods and make sure that it survives possible major disasters in the future, this seems to be a reasonable strategy

Recently, a number of groups have attempted to compare the two platforms PGM and MiSeq, including the Sanger Institute a group from the University of Birmingham, and BGI. None of these studies have conclusively named a winner, and each group comes to slightly different conclusions.

In a blog of Genome Web’s “The Daily Scan” the different findings in the three comparison studies are discussed heavily. On the one hand different chemistries or older versions are compared with newer ones, on the other hand different application require different technologies.

According to a report by Jon Groberg at Macquarie Equities Research, Groberg cites several factors leading to Life Tech’s better selling success of the PGM over Illumina’s MiSeq (1300 vs. 700 systems sold): price — the PGM sells for $75,000, while the MiSeq goes for $125,000; Life has a more extensive commercial reach; the trajectory of improvement for the PGM is greater than for the MiSeq; and the PGM excels at certain key applications.

Of note are the differences in sequencing cost, based on list prices (see Sanger Institute study). The MiSeq came out cheapest, at $502 per gigabase, followed by the PGM, at $1,000 per gigabase using the Ion 318 chip, and the PacBio, at $2,000 per gigabase. All three platforms produce data at a greater cost than the Illumina GAIIx, at $148 per gigabase, and the HiSeq 2000, at $41 per gigabase.

What is your experience with the two systems?

Recently the Hollywood filmmaker James Cameron (director of “Titanic”) reached in a custom made submarine the deepest point of the Mariana Trench, breaking a world record for the deepest solo dive. Deep-sea trenches have lured explorers for decades, tantalizing them with glimpses of an ecosystem shrouded in darkness.

Although Cameron’s journey to the abyss yielded little new scientific data, it whetted the public appetite for information about life in the otherworldly environments of deep-sea trenches.

An international group of marine scientists may soon provide a feast of such data, from the first major systematic study of a deep-sea trench. If all goes well the team will start exploring the South sea of New Zealand in a depth between 6.000 and 11.000 meters. A team around Timothy Shank from the Woods Hole Institution (WHI) inMassachusetts will systematically explore this complete unknown biotope with robots. An article about this program is published in the recent issue of Science.

New forms of life and deep insight into evolution are to be expected.

As a scuba diver I am excited to learn more about this fascinating biotope and I am sure that Next Generation sequencing technologies will significantly contribute to new chapters of the book of life.

It is well known that some people are more attractive to mosquitoes than others. In an article of the sueddeutsche zeitung I learned that this has however nothing to do with the taste of the blood, it is the composition of the skin microbiome.

Researchers around the group of the Dutch insect expert Niels Verhulst published that Anopheles gambiae, the main carrier of malaria in Africa is attracted by odours, produced by certain bacteria of the skin microbiome.

Blends produced by some bacterial species were more attractive than those of others. Test persons that had a high amount of Staphylococcus on their skin were attractant, while test persons carrying Pseudomonas aeruginosa produced odours that were repellent for the insects.

As a consequence these volatiles could be synthesized and used as mosquito attractants or repellents.

Recently we discussed already the importance of the gut microbiome. It becomes more and more obvious that we cannot regard our body as a single human being, we are part of a large community living in and on us, with all the consequences it may have.

What will come next?

A social network wants to sequence your gut microbiome. The non-profit programme MyMicrobes, is inviting people to have their gut bacteria sequenced for about €1,500. Acting as both, social network and DNA database, the website offers a place for people to share diet tips, stories and gastrointestinal woes with one another. In exchange, researchers hope to gather a wealth of data about the bacteria living in peoples guts.

The same team of researchers showed earlier this year that people fall into one of three groups, or enterotypes, when it comes to the genetics of their gut bacteria (Gut study divides people into three types).

So far, the team has found links between certain gut-specific genetic markers and obesity and other diseases. And they suspect that gut enterotypes might affect how people react to different drugs and diets.

The group has been careful not to make promises to project participants. The research is still in its infancy, and there is no proven link between enterotypes and disease remedies. But the researchers hope the project will provide a bounty of data while helping volunteers connect with one another. Participants will have access to their own data, but all public results will be anonymous.

What is your opinion? Are you ready to sequence your gut microbiome?

Many large scale exome sequencing projects are funded and underway to analyze rare Mendelian diseases. This technology is often the choice as it is more affordable than whole genome sequencing (WGS) and therefore allows analyzing more patients. In addition it has the advantage that resulting data volumes are much smaller and therefore easier to handle.

But – when looking only on those regions targeted by the exome technology – are the results of an exome sequencing experiment really comparable to a WGS experiment?
 
The study from Clark et al., 2011 focused on this question and found that neither of the technologies managed to cover all sequencing variants. When applying 50 million reads for exome sequencing and 35-fold coverage for WGS, the study came to the following results.

- WGS detected between 660 and 4600 SNPs that were not called from the exome sequencing data and
- Exome Sequencing detected between 2600 and 3200 SNPs that were not called from the WGS data.

What can we conclude from this? First, WGS can not and will not replace exome sequencing as due to genome characteristics there will always be regions that are not covered sufficiently for SNP calling. As oligonucleotide designs of available exomes are balanced regarding regions with low coverage, exome sequencing shows higher sensitivity towards these regions. Second, WGS has its value in detecting variants in regions that are not covered by exome enrichment technologies. These are regions where enrichment fails as well as regions that are not present on the current exome designs.

So for covering really all variants it might be worth thinking about doing both experiments in parallel. Both technologies complement each other.

Recently Illumina reported a drop in preliminary Q3 revenues. They expect 1% less revenue compared to previous Q3, while Wall Street expected 17% growth (genomeweb). Illumina explains this with uncertainty in funding and higher throughput of the V3 sequencing Kit. They also report that the upgrade rate from Genome Analyzer to HiSeq 2000 was lower as expected and that the use of Genome Analyzer reagents dropped significantly.
In an earlier post I have already speculated that many sequencer are only used at a low percentage of their capacity. This might explain the low upgrade rate of older sequencer and the drop in use of reagents. They are simply not in use.
I have currently no information about the upgrade rate of Roche GS FLX/454 sequencer for use of the new FLX+ chemistry.
Did you upgrade your sequencer already?

Recently Investment Bank William Blair lowered top-line and bottom-line estimates for Illumina and Pacific Biosciences, citing government funding worries that could impact sales of both firms’ instruments <genomeweb>.

They lowered the forecast for shipping of 260 Illumina instruments in 2012 and 248 instruments in 2013. They also report a recent decrease of HiSeq consumables and lowered the forecast for consumable sales in 2012 by 3%. They predict also only a slight increase of 5% for consumable sales in 2013 over 2012.

If the shipping of 248 instruments increases the consumable sales only by 5%, than I have to wonder, how many of these instruments are really in use. If 248 instruments in average need 5% of the consumables this would mean, that at that time 4960 instruments are placed, which is far away from reality. The conclusion can only be that in average the instruments are used at less than 20% capacity. 

A huge amount of research money is used for buying instruments, instead of sourcing the service. As a consequence it takes long to fill a flow cell and the operators often have limited experience with sample preparation, data handling and analysis. This produces often pure data quality and is not helpful for high end research.

I am very curious about your opinion.

Some new studies published online in Science Translational Medicine  ( Sirota et al. > and Dudley et al. > ) demonstrate the potential of genomics to find new applications for existing drugs ( GenomeWeb >). They detected 53 significant drug-disease interactions. In one case they could find evidence that the ulcer drug cimetidine might be effective against lung cancer.

This gives new hope for effective treatment of rare diseases, where new potential orphan drugs are not available.

Recently I saw this sign on a house in the China Town of Singapore, advertising for “Genetic Testings for Health and Innate Talents”. Having a look on their homepage > I could find that they have two main objectives:

1. Discovery of genetic variations that contribute to disease risk. (Disease Susceptibility Genetic Test or Genetic Predisposition Test)
2. Discovery of genetic variations that contribute to intelligence, personality characteristics, superior athletic performance, vocal ability, dancing ability, and other areas where humans can excel. (Innate Talents & Traits Genetic Test)

Obviously a lab in the US is testing some SNPs on Affymetrix Arrays > for them. It is not clear what they are testing, especially in terms of “Innate talents”. They have some testimonials > that do not really say much. With or without knowing a genetic disposition it makes sense to take care on ones diet and exercise the body. If an inherited disease is known in the family, it is wise to be careful and observe the body. Many genetic markers are only linked to a disease at a low percentage of penetration, but there is no guarantee that the carrier develops the disease later. Often this is a severe psychological burdon and requires genetic and psychological consulting.

Even more suspicious is the testing for “Innate Talents”. What is really known about it and how far shall we go?